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Comparative genomics of nematodes
Abstract
Recent transcriptome and genome projects have dramatically expanded the biological data available across the phylum Nematoda. Here we summarize analyses of these sequences, which have revealed multiple unexpected results. Despite a uniform body plan, nematodes are more diverse at the molecular level than was previously recognized, with many species- and group-specific novel genes. In the genus Caenorhabditis, changes in chromosome arrangement, particularly local inversions, are also rapid, with breakpoints occurring at 50-fold the rate in vertebrates. Tylenchid plant parasitic nematode genomes contain several genes closely related to genes in bacteria, implicating horizontal gene transfer events in the origins of plant parasitism. Functional genomics techniques are also moving from Caenorhabditis elegans to application throughout the phylum. Soon, eight more draft nematode genome sequences will be available. This unique resource will underpin both molecular understanding of these most abundant metazoan organisms and aid in the examination of the dynamics of genome evolution in animals.
... In contrast to the above studies, Ghedin et al. [56] have sequenced ~90 megabase pairs genome of B. malayi and inferred that the parasite has between 14,500 and 17,800 protein-coding genes [57], have reviewed the comparative genomics of nematodes. The review highlighted that analysis of conserved synteny between B. malayi and C. elegans revealed a preponderance of within-chromosome linkage, but little local synteny [57,58]. ...
... In contrast to the above studies, Ghedin et al. [56] have sequenced ~90 megabase pairs genome of B. malayi and inferred that the parasite has between 14,500 and 17,800 protein-coding genes [57], have reviewed the comparative genomics of nematodes. The review highlighted that analysis of conserved synteny between B. malayi and C. elegans revealed a preponderance of within-chromosome linkage, but little local synteny [57,58]. B. malayi has ive chromosome pairs, and comparisons of genes linked in B. malayi against C. elegans suggest that the changed chromosome number is the result of a fusion between genomic segments corresponding to C. elegans chromosomes I and III. ...
... B. malayi has ive chromosome pairs, and comparisons of genes linked in B. malayi against C. elegans suggest that the changed chromosome number is the result of a fusion between genomic segments corresponding to C. elegans chromosomes I and III. However, since the related ilarioid of Setaria is reported as having n=6 [57], the fusion could have occurred in the onchocercine lineage. ...
... Nematodes are one of the most abundant metazoans on the Earth and particularly in marine, freshwater, and soil habitats (Mitreva et al., 2005;Boag and Yeates, 1998). Soil is an excellent habitat for nematodes, and 100g of soil may contain several thousands of them (Háněl and Čerevková, 2010). ...
... S5 sample had 18 bands in DGGE gel. Most of these bands (6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18) concentrated in denaturant gradient ranged from 30% to 40% of gel (Fig. 1). Band 12 and 13 had strongest intensity indicating that species presented by these bands could be dominant species in S5 community. ...
... Therefore, Band 15 species may belong to genus Xiphinema.Genus Dorylaimoides (containing Band 9) and genus Xiphinema (containing Band 15) both belong to Dorylaimida order, so that they form a node distinct from genus Mylonchulus (containing Band 8) belong to Monochida order. Species in these order form clade A in phylogenetic tree.Clade B consisted ofBand 10,11,12,13, 16 and 18. With 100% of identity, Rotylenchulus reniformis (Band 7), Meloidogyne incognita (Band 13), Tylenchulus semipenetrans (Band 16), Helicotylenchus multicinctus (Band 18), we used their SSU sequences to re-construct the molecular tree. ...
Soil nematodes play an important role in indication for assessing soil environments and ecosystems. Previous studies of nematode community analyses based on molecular identification have shown to be useful for assessing soil environments. Here we applied PCR-DGGE method for molecular analysis of five soil nematode communities (designed as S1 to S5) collected from four provinces in Southeastern Vietnam (Binh Duong, Ba Ria Vung Tau, Binh Phuoc and Dong Nai) based on SSU gene. By sequencing DNA bands derived from S5 community sample, our data show 15 species containing soil nematode, other nematode and non-nematode (fungi) species. Genus Meloidogyne was found as abundant one. The genetic relationship of soil nematode species in S5 community were determined by Maximum Likelihood tree re-construction based on SSU gene. This molecular approach is applied for the first time in Vietnam for identification of soil nematode communities.
... All ecosystems contain the diverse group of creatures known as nematodes; there are estimated to be up to one million global species of nematodes (Mitreva et al. 2005). Some have evolved parasitic lifestyles, while others are free-living (Singh et al. ...
... Worm Base, a sizable database for nematode research created by Harris et al. (2010) for Caenorhabditis elegans, now has evidence on various plant parasitic nematodes, including further current sequences of several root knot nematode. Since the 86 Mb and 54 Mb M. hapla genomes were sequenced in 2008, another 19 genomic draughts representing six species have been identified (Abad et al. 2008;Opperman et al. 2008), allowing evolutionary and genomic assessments (Lunt et al. 2014;Mitreva et al. 2005). ...
Root-knot nematodes (RKNs) cause approximately 72% of global crop yield loss and have a vast host range of above 2000 plants. The interaction of nematode with other disease-causing agents increases the disease severity and makes the management strategies difficult. Meloidogyne-based disease complexes (MDCs) with plant pathogenic fungi and bacteria are a major constraint in vegetable production. Meloidogyne species show close interaction with phytopathogenic fungi in tomatoes. Interaction with fungi, including Fusarium spp., Sclerotium, Alternaria dauci, and Rhizoctonia spp., in vegetables, leads to a greater reduction in plant health. They drastically reduced plant growth. Interaction of nematodes with other pathogens is prime necessary for proper disease management. Thus, plants infected with nematodes increase disease severity and influence disease development and etiology.
... Nematodes are animals that belong to the phylum Nematoda. In existence for almost a billion years, these are multicellular animals [2]. Several nematodes are parasites of plants and animals, but others may live independently [3]. ...
... In 2008, the 86 Mb and 54 Mb genomes of M. incognita and M. hapla, respectively, were sequenced [36,45]. Genomic and phylogenetic comparisons are made possible by the discovery of 19 more genome drafts for 6 species at (https://www.ebi.ac.uk/ena/browser/view/PRJNA340324, accessed on 29 January 2023) [2,43]. This database includes data about the functional genomes, transcriptomics, and proteomics of all parasitic nematodes. ...
Citation: Khan, A.; Chen, S.; Fatima, S.; Ahamad, L.; Siddiqui, M.A. Biotechnological Tools to Elucidate the Mechanism of Plant and Nematode Interactions. Plants 2023, 12, 2387. https://doi. Abstract: Plant-parasitic nematodes (PPNs) pose a threat to global food security in both the developed and developing worlds. PPNs cause crop losses worth a total of more than USD 150 billion worldwide. The sedentary root-knot nematodes (RKNs) also cause severe damage to various agricultural crops and establish compatible relationships with a broad range of host plants. This review aims to provide a broad overview of the strategies used to identify the morpho-physiological and molecular events that occur during RKN parasitism. It describes the most current developments in the transcriptomic, proteomic, and metabolomic strategies of nematodes, which are important for understanding compatible interactions of plants and nematodes, and several strategies for enhancing plant resistance against RKNs. We will highlight recent rapid advances in molecular strategies, such as gene-silencing technologies, RNA interference (RNAi), and small interfering RNA (siRNA) effector proteins, that are leading to considerable progress in understanding the mechanism of plant-nematode interactions. We also take into account genetic engineering strategies, such as targeted genome editing techniques, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system, and quantitative trait loci (QTL), to enhance the resistance of plants against nematodes.
... Nematodes are a diverse group of animals that inhabit all ecosystems; it is considered that as many as one million cosmopolitan species exist (Mitreva et al. 2005). Many are freeliving, but others have developed parasitic lifestyles . ...
... ac. uk/ ena/ brows er/ view/ PRJNA 340324) (Mitreva et al. 2005;Lunt et al. 2014). ...
Root-knot nematodes (RKN) are sedentary parasites of the roots of plants and are considered some of the most damaging pests in agriculture. Since RKN target the root vascular system, they provoke host nutrient deprivation and defective water transport, causing above-ground symptoms of growth stunting, wilting, chlorosis, and reduced crop yields. In Mexico RKN infestations are primarily dealt with by treating with synthetic chemically based nematicides that are preferred by farmers over available bioproducts. However, due to environmental and human health concerns chemical control is increasingly restricted. Biological control of RKNs can help reduce the use of chemical nematicides as it is achieved with antagonistic organisms, mainly bacteria, fungi, other nematodes, or consortia of diverse microorganisms, which control nematodes directly by predation and parasitism at different stages: eggs, juveniles, or adults; or indirectly by the action of toxic diffusible inhibitory metabolites. The need to increase agricultural production and reduce negative environmental impact creates an opportunity for optimizing biological control agents to suppress nematode populations, but this endeavour remains challenging as researchers around the world try to understand diverse control mechanisms, nematode and microbe life cycles, ecology, metabolite production, predatory behaviours, molecular and biochemical interactions, in order to generate attractive products with the approval of local regulatory bodies. Here, we provide a brief review of the biology of the genus Meloidogyne, biological control strategies, and a comparison between chemical and bioproducts in the Mexican market, and guidelines emitted by national agencies to ensure safety and effectiveness of new developments.
... Nematodes show exceptional abundance among eukaryotes, composing 80% of all animals numerically [1] , and demonstrate a great variety of lifestyles [1,2,3] from free-living bacterivores to obligate parasitic forms [2,3,4] . Within the framework of such lifestyle diversity, they have managed to forge a myriad of associations with viruses, bacteria, fungi, and eukaryotic animals including invertebrates and vertebrates. ...
... Nematodes show exceptional abundance among eukaryotes, composing 80% of all animals numerically [1] , and demonstrate a great variety of lifestyles [1,2,3] from free-living bacterivores to obligate parasitic forms [2,3,4] . Within the framework of such lifestyle diversity, they have managed to forge a myriad of associations with viruses, bacteria, fungi, and eukaryotic animals including invertebrates and vertebrates. ...
... For example, nematode species causing health and welfare problems in livestock ruminants and equines are primarily found in clade V (Strongylida), whereas those of monogastric animals (e.g. birds, cats, dogs, humans and pigs) and one genus (Parascaris) of horses are mainly in clade III among the Ascaridida [3]. The genome of nematodes ranges in size from 50 to 250 Mb [4], but the variation across this phylum is probably even larger because genome size has so far only been estimated for a limited number of species. ...
... The alignment obtained was used to reconstruct the phylogeny selecting an evolutionary model based on the Bayesian information criterion (BIC) using the software prot-test3 (v. 3 , assuming a proportion of invariable sites (I) and rate variation modelled according to a gamma distribution (G). The branch support is given as bootstrap sampling proportions. ...
The nematode Ascaridia galli (order Ascaridida) is an economically important intestinal parasite responsible for increased food consumption, reduced performance and elevated mortality in commercial poultry production. This roundworm is an emerging problem in several European countries on farms with laying hens, as a consequence of the recent European Union (EU) ban on conventional battery cages. As infection is associated with slow development of low levels of acquired protective immunity, parasite control relies on repeated use of dewormers (anthelmintics). Benzimidazoles (BZ) are currently the only anthelmintic registered in the EU for use in controlling A. galli and there is an obvious risk of overuse of one drug class, selecting for resistance. Thus we developed a reference transcriptome of A. galli to investigate the response in gene expression before and after exposure to the BZ drug flubendazole (FLBZ). Transcriptional variations between treated and untreated A. galli showed that transcripts annotated as mitochondrial glutamate dehydrogenase and cytochrome P450 were significantly down-regulated in treated worms, whereas transcripts homologous to heat shock proteins (HSP), catalase, phosphofructokinase, and a multidrug resistance P-glycoprotein (PGP1) were significantly up-regulated in treated worms. Investigation of candidate transcripts responsible for anthelmintic resistance in livestock nematodes led to identification of several tubulins, including six new isoforms of beta-tubulin, and several ligand-gated ionotropic receptors and ABC-transporters. We discovered several transcripts associated with drug binding and processing genes, but further characterisation using a larger set of worms exposed to BZs in functional assays is required to determine how these are involved in drug binding and metabolism.
... Genomic tools and technologies have allowed the researchers to uncover the amazing biology of nematodes [27][28][29]. The genome of the EPN, Heterorhabditis bacteriophora TTO1-M31e strain has been sequenced [30] and is available in the public domain. ...
... Scanty information available on the Heterorhabditis IJ 'recovery' is not adequate to decipher the various molecular and physiological pathways specific to these IJs [33,49]. Additionally, it is suggested that genes expressed in survival or dispersal stages in nematodes, such as dauer, and EPN IJs, are more likely to be novel, compared with the genes expressed in adult or larval stages [29]. ...
Background
Nematodes are the most numerous animals in the soil. Insect parasitic nematodes of the genus Heterorhabditis are capable of selectively seeking, infecting and killing their insect-hosts in the soil. The infective juvenile (IJ) stage of the Heterorhabditis nematodes is analogous to Caenorhabditis elegans dauer juvenile stage, which remains in ‘arrested development’ till it finds and infects a new insect-host in the soil. H. indica is the most prevalent species of Heterorhabditis in India. To understand the genes and molecular processes that govern the biology of the IJ stage, and to create a resource to facilitate functional genomics and genetic exploration, we sequenced the transcriptome of H. indica IJs.
Results
The de-novo sequence assembly using Velvet-Oases pipeline resulted in 13,593 unique transcripts at N50 of 1,371 bp, of which 53 % were annotated by blastx. H. indica transcripts showed higher orthology with parasitic nematodes as compared to free living nematodes. In-silico expression analysis showed 30 % of transcripts expressing with ≥100 FPKM value. All the four canonical dauer formation pathways like cGMP-PKG, insulin, dafachronic acid and TGF-β were active in the IJ stage. Several other signaling pathways were highly represented in the transcriptome. Twenty-four orthologs of C. elegans RNAi pathway effector genes were discovered in H. indica, including nrde-3 that is reported for the first time in any of the parasitic nematodes. An ortholog of C. elegans tol-1 was also identified. Further, 272 kinases belonging to 137 groups, and several previously unidentified members of important gene classes were identified.
Conclusions
We generated high-quality transcriptome sequence data from H. indica IJs for the first time. The transcripts showed high similarity with the parasitic nematodes, M. hapla, and A. suum as opposed to C. elegans, a species to which H. indica is more closely related. The high representation of transcripts from several signaling pathways in the IJs indicates that despite being a developmentally arrested stage; IJs are a hotbed of signaling and are actively interacting with their environment.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-016-2510-z) contains supplementary material, which is available to authorized users.
... The recent characterisation of the draft genomes and transcriptomes of the barber's pole worm (Haemonchus contortus) [11,12], one of the most pathogenic nematodes of small ruminants (e.g., sheep and goats) worldwide [23], provides, for the first time, a solid foundation for detailed explorations of molecular pathways amenable to drug target discovery in a nematode that represents many species of a large order (Strongylida) of socioeconomically important pathogens. In addition, the relatively close relatedness of H. contortus with C. elegans [24,25], now arguably the best characterised metazoan organism [26], enables direct and detailed comparative analyses of such pathways. Of particular significance in this context are signalling pathways, because of their crucial roles in a plethora of developmental and physiological processes. ...
... Kinases prioritised as either "repurposing" targets or novel targets are highlighted in red and black, respectively. The group classification is indicated for each kinase; the total numbers of kinases with a particular score are indicated in square brackets phylogenetic relationship of these two nematodes [25], and contrasts results for the draft kinomes of parasitic nematodes representing different orders or clades that are reported to have substantially reduced kinase complements (n = 233-364), presumably having lost (or not gained) particular kinase families during nematode evolution [61]. The reduced number of kinases in parasitic nematodes compared with C. elegans might be explained by differences in the environmental conditions that these parasites are exposed to, as well as differences in their lifestyle, but it has also been proposed that the small numbers of kinases of some species (e.g., M. hapla and Tr. ...
Protein kinases regulate a plethora of essential signalling and other biological pathways in all eukaryotic organisms, but very little is known about them in most parasitic nematodes.
Methods:
Here, we defined, for the first time, the entire complement of protein kinases (kinome) encoded in the barber’s pole worm (Haemonchus contortus) through an integrated analysis of transcriptomic and genomic datasets using an advanced bioinformatic workflow.
Results:
We identified, curated and classified 432 kinases representing ten groups, 103 distinct families and 98 subfamilies. A comparison of the kinomes of H. contortus and Caenorhabditis elegans (a related, free-living nematode) revealed considerable variation in the numbers of casein kinases, tyrosine kinases and Ca^(2+) /calmodulin-dependent protein kinases, which likely relate to differences in biology, habitat and life cycle between these worms. Moreover, a suite of kinase genes was selectively transcribed in particular developmental stages of H. contortus, indicating central roles in developmental and reproductive processes. In addition, using a ranking system, drug targets (n = 13) and associated small-molecule effectors (n = 1517) were inferred.
Conclusions:
The H. contortus kinome will provide a useful resource for fundamental investigations of kinases and signalling pathways in this nematode, and should assist future anthelmintic discovery efforts; this is particularly important, given current drug resistance problems in parasitic nematodes.
... It is no longer necessary to justify obtaining a complete genome sequence for any given plant-parasitic nematode (PPN); that case has been made elsewhere on numerous occasions Bird & Opperman, 1998;Mitreva, Blaxter, Bird, & McCarter, 2005). Until very recently, the major barrier was cost. ...
... Importantly, early efforts to leverage the C. elegans genome annotation to curate data sets from parasitic nematodes proved highly effective for gene discovery. This is particularly true for RKN, which benefited from extensive expressed sequence tag (EST) sequencing projects in the USA and Europe (McCarter, Abad, Jones, & Bird, 2000;McCarter, Bird, Clifton, & Waterston, 2001;McCarter et al., 2003;Mitreva et al., 2005). ESTs correspond to the partial (sometimes complete) sequence of mRNAs and, as such, define the existence of the corresponding gene and confirm its expression. ...
The growing portfolio of sequenced plant-parasitic nematodes genomes is helping to drive the research agenda for the discipline of plant nematology. Comparative genomics has confirmed much of what had been deduced from expressed sequence tag sequencing, and expanded our understanding of the extent of horizontal gene transfer as a source of novelty during the evolution of parasitism. Full catalogues have been annotated for various phytolytic and other enzymes, and the evolutionary history of those genes deduced. Beyond these direct analyses, the genome sequences serve to underpin genetic, biochemical and physiological approaches, and we suspect that this will prove to be an invaluable legacy of genome sequencing.
... They have a conserved body 11 plan with similar structural organisation and cellular morphologies (Basyoni and Rizk 2016). 12 However, comparative analyses have highlighted the molecular and physiological diversity 13 within the phylum (Mitreva et al. 2005;Coghlan et al. 2019). Caenorhabditis elegans is a 14 Chromadorean that has been at the forefront of genetic research as a model species. ...
Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. A lack of genomic resources has limited the expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced, assembled, and annotated the whole genome of M. nigrescens using nanopore long-reads and 10X chromium link-reads. The assembly is 524 Mb in size consisting of 867 scaffolds. The N50 value is 2.42 Mb, and half of the assembly is in the 30 longest scaffolds. The assembly BUSCO score from the eukaryotic database (eukaryota_odb10) indicates that the genome is 86.7% complete and 5.1% partial. The genome has a high level of heterozygosity (6.6%) with a repeat content of 78.7%. mRNA-seq reads from different-sized nematodes (≤2 cm, 3.5-7 cm, and >7 cm body length) representing different developmental stages were also generated and used for the genome annotation. Using ab initio and evidence-based gene model predictions, 12,313 protein-coding genes and 24,186 mRNAs were annotated. These genomic resources will help researchers investigate the various aspects of the biology and host-parasite interactions of mermithid nematodes.
... Nematodes show great variability in karyotype, genome organisation, and reproductive modes [19,43,44]. Importantly, this diversity is present within species-rich clades and many transitions have multiple independent occurrences, such as the homoplastic origins of the XX/ XY system in filarial nematodes. ...
Heteromorphic sex chromosomes are usually thought to have originated from a pair of autosomes that acquired a sex-determining locus and subsequently stopped recombining, leading to degeneration of the sex-limited chromosome. The majority of nematodes species lack heteromorphic sex chromosomes and determine sex using an X-chromosome counting mechanism, with males being hemizygous for one or more X chromosomes (XX/X0). Some filarial nematode species, including important parasites of humans, have heteromorphic XX/XY karyotypes. It has been assumed that sex is determined by a Y-linked locus in these species. However, karyotypic analyses suggested that filarial Y chromosomes are derived from the unfused homologue of an autosome involved in an X-to-autosome fusion event. Here, we generated a chromosome-level reference genome for Litomosoides sigmodontis , a filarial nematode with the ancestral filarial karyotype and sex determination mechanism (XX/X0). By mapping the assembled chromosomes to the rhabditid nematode ancestral linkage (or Nigon) elements, we infer that the ancestral filarial X chromosome was the product of a fusion between NigonX (the ancestrally X-linked element) and NigonD (ancestrally autosomal). In the two filarial lineages with XY systems, there have been two independent autosome-to-X chromosome fusion events involving different autosomal Nigon elements. In both lineages, the region shared by the neo-X and neo-Y chromosomes is within the ancestrally autosomal portion of the X, confirming that the filarial Y chromosomes are derived from the unfused homologue of the autosome. Sex determination in XY filarial nematodes therefore likely continues to operate via the ancestral X-chromosome counting mechanism, rather than via a Y-linked sex-determining locus.
... Nematodes show great variability in karyotype, genome organisation, and reproductive modes (Mitreva et al. 2005;Denver et al. 2011;Gonzalez de la Rosa et al. 2021). Importantly this diversity is present within species-rich clades and many transitions have multiple independent occurrences, such as the homoplastic origins of the XX/XY system in filarial nematodes. ...
Heteromorphic sex chromosomes are usually thought to have originated from a pair of autosomes that acquired a sex-determining locus and subsequently stopped recombining, leading to degeneration of the sex-limited chromosome. In contrast, in rhabditid nematodes, sex is determined by an X-chromosome counting mechanism and males are hemizygous for one or more X chromosomes (XX/X0). Some species of filarial nematodes, including important parasites of humans, have heteromorphic XX/XY systems. It has been assumed that sex is determined by a Y-linked locus in these species. However, karyotypic analyses suggested that filarial Y chromosomes are derived from the unfused autosome following an X-to-autosome fusion. Here, we generated a chromosome-level reference genome for Litomosoides sigmodontis , a filarial nematode with the ancestral filarial karyotype and sex determination mechanism (XX/X0). We mapped the assembled chromosomes to the rhabditid nematode ancestral linkage (or Nigon) elements. We found that the L. sigmodontis X chromosome was formed from a fusion of NigonX (the ancestrally X-linked element) and NigonD (ancestrally autosomal) that occurred in the last common ancestor of all filarial nematodes. In the two filarial lineages with XY systems, the X chromosomes were formed from two recent and independent fusions of the ancestral X chromosome with different autosomal Nigon elements. In both lineages, the region shared by the neo-X and neo-Y chromosomes is within the ancestrally autosomal portion of the X, confirming that the filarial Y chromosomes are derived from unfused autosomes. Sex determination in XY filarial nematodes therefore likely continues to operate via the ancestral X-chromosome counting mechanism, rather than via a neo-Y-linked sex-determining locus.
... Nematodes were reported to be the second most numerous in the animal kingdom residing in multiple ecosystems, with up to one million species (Bongers and Bongers, 1998;Mitreva et al., 2005). Root-knot nematodes (RKN) were among the top ten plant parasitic nematodes in the world found in almost all vascular plants, causing severe crop losses through direct injury and transmission of pathogenic microorganisms (Chalivendra, 2021). ...
Introduction
Root-knot nematodes (RKN) disease is a devastating disease in Cucumis crops production. Existing studies have shown that resistant and susceptible crops are enriched with different rhizosphere microorganisms, and microorganisms enriched in resistant crops can antagonize pathogenic bacteria. However, the characteristics of rhizosphere microbial communities of Cucumis crops after RKN infestation remain largely unknown.
Methods
In this study, we compared the changes in rhizosphere bacterial communities between highly RKN-resistant Cucumis metuliferus (cm3) and highly RKN-susceptible Cucumis sativus (cuc) after RKN infection through a pot experiment.
Results
The results showed that the strongest response of rhizosphere bacterial communities of Cucumis crops to RKN infestation occurred during early growth, as evidenced by changes in species diversity and community composition. However, the more stable structure of the rhizosphere bacterial community in cm3 was reflected in less changes in species diversity and community composition after RKN infestation, forming a more complex and positively co-occurrence network than cuc. Moreover, we observed that both cm3 and cuc recruited bacteria after RKN infestation, but the bacteria enriched in cm3 were more abundant including beneficial bacteria Acidobacteria, Nocardioidaceae and Sphingomonadales. In addition, the cuc was enriched with beneficial bacteria Actinobacteria, Bacilli and Cyanobacteria. We also found that more antagonistic bacteria than cuc were screened in cm3 after RKN infestation and most of them were Pseudomonas (Proteobacteria, Pseudomonadaceae), and Proteobacteria were also enriched in cm3 after RKN infestation. We hypothesized that the cooperation between Pseudomonas and the beneficial bacteria in cm3 could inhibit the infestation of RKN.
Discussion
Thus, our results provide valuable insights into the role of rhizosphere bacterial communities on RKN diseases of Cucumis crops, and further studies are needed to clarify the bacterial communities that suppress RKN in Cucumis crops rhizosphere.
... In addition, crop damage caused by root-invading nematodes sometimes goes unnoticed by cultivators because of a lack of awareness of the symptoms created by parasitic nematodes, such as root galls, root lesions, and cysts. As a result, the banana crop is still threatened by nematodes in every place it is farmed (Mitreva et al. 2005). ...
Wairimu WJ, Kimenjul JW, Muiru WM, Wachira PM. 2022. Interactions between soil additives and a variety of naturally occurring nematode-demolishing fungi in banana fields of Meru and Embu Counties, Kenya. Cell Biol Dev 6: 82-93. Plant-parasitic nematodes pose a significant danger to banana production, as they reduce the productivity, quality, and lifetime of banana orchards. This study aimed to evaluate the diversity, quantity, and occurrence of nematode-demolishing fungi in banana production farms to use them to manage plant-parasitic nematodes. Also examined was the impact of organic and inorganic soil additives on nematode-demolishing fungi. The study region was divided into three agroecological zones: UM3 (Low), UM2 (Middle), and UM 1 (Upper). Ten farms were chosen randomly for a soil sample in each zone to determine the diversity and abundance of nematode-demolishing fungi. One farm was chosen randomly for soil additive treatments in each zone. The gathered soil samples were used to isolate and identify nematode-demolishing fungi at the species level. The diversity of nematode-demolishing fungi varied significantly between zones, with the highest variety and number of fungi found in the highest zone. Arthrobotrys, Monacrosporium, Nematoctonus, Harposporium, and Paecilomyces were the identified genera. Arthrobotrys was the most often isolated genus, with a frequency of 45%, followed by Harposporium, with a frequency of 18%. The remaining three genera each had a frequency of 9%. The A. dactyloides, A. oligospora, A. robusta, A. longispora, A. superba, H. anguillulae, H. crassum, Meria coniospora, Monacrosporium cionopagum, N. leiosporus, and P. lilacinus were among the species identified. The A. oligospora had captured and destroyed 98 plant parasite nematodes, whereas M. cionopagum and Dactyllela phymatopaga had eliminated 88 and 76 plant parasitic nematodes, respectively, within the same time frame. The amount of nematode-demolishing fungi was significantly different between the various soil additives, with chicken dung having the greatest number of 74 isolates, followed by cow manure, goat manure, the control treatment, and inorganic additive with 71, 69, 54, and 39 isolates, respectively. The amount of isolated nematode-demolishing fungi fluctuated throughout time, from 89 pre-treatment isolates to 122 after three months and 96 after six months. The variation of nematode-demolishing fungi over time was significantly different, demonstrating the impact of diverse soil additives on their existence. Arthrobotrys spp. is a suitable option for field efficacy studies since it was the most diversified, had the highest demolishing rate, and the organic additives facilitated its dispersion in banana plantations.
... As previously commented, phylogenetic relationships within the Nematoda have changed considerably with the use of genetic analyses (see the reviews by Mitreva et al., 2005;Blaxter, 2011;Blaxter and Koutsovoulos, 2015). Broad and pioneer phylogenetic works on nematode parasites included very few representatives that infect marine fish and have been reported in the American continent Hudspeth, 1998, 2000). ...
The ichthyofauna of the Atlantic and Pacific coasts off the American continent is very rich. Consequently, a high biodiversity of nematodes parasitizing these vertebrates is also expected. Currently, data on nematode parasites of marine fish off the Americas is fragmented. A review of all adult nematode species reported parasitizing marine fish from off the American continent is herein presented, as well as comments on their patterns of diversity, life cycles and advances in the taxonomic and phylogenetic knowledge. A total of 209 valid species, 19 species inquirendae and 6 dubious records have been recorded, the majority from the fish taxa Eupercaria and Perciformes. The families Sciaenidae, Serranidae and Lutjanidae, as well as the tropical and temperate Atlantic waters, exhibited the highest records of parasitic nematodes. The Cucullanidae, Philometridae and Cystidicolidae were the most speciose families of nematodes, which may be related to technological advances and relatively recent efforts of taxonomists, resulting in description of new taxa and the resolution of taxonomic problems. Numerous taxonomic questions still need resolution and, even though genetic data have been important for this process, the database is very scarce. This is the first review on all currently known nematode species parasitizing marine fish off the Americas and may serve as an important basis of reference for future approaches on these organisms.
... The nematode C. elegans was the first metazoan to have its genome sequenced in 1998, and Brugia malayi was the first parasitic nematode. Since then, many other genomes of nematodes have been published and sequenced (Howe et al., 2017;Kumar et al., 2012;Mitreva et al., 2005). The International Helminth Genomes Consortium did a study using 81 helminth genomes, combining 36 published genomes and 31 nematodes and 14 platyhelminth species that were newly produced (International Helminth Genomes Consortium, 2019). ...
The study of molecular systematics, where the concept was first introduced in Chap. 1, enables the elucidation of relationships among groups of organisms using molecular means. Molecular systematics allows us to unravel the evolutionary history embedded in the organism’s genetic material by reconstructing phylogenetic trees, which illuminate the driving forces behind speciation and biodiversity. This chapter focused on the molecular systematics of parasitic nematodes that afflict humans and animals, where the phylum Nematoda is the second-largest phylum in the kingdom Animalia. Relationships among the major groups were detailed, as evidenced through molecular phylogenetic studies performed over the decades. A summary of the major findings, together with significant milestones in elucidating parasitic nematode phylogenetic relationships, was discussed. With such vast species diversity, coupled with the complex nature of host-parasite relationships, a robust phylogenetic framework through the study of nematode molecular systematics is essential to make meaningful comparisons across taxa, for classification and the generation of evolutionary hypotheses for the phylum.
... Organisms do not always contain a single, static genome. Programmed genome rearrangements exist in many organisms, including ciliates (1), nematodes (2), lampreys (3) and zebra finches (4). Most cases involve excision, removal and rejoining of large regions of DNA to distinguish germline and somatic genomes. ...
Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax , Tetrahymena thermophila and Paramecium tetraurelia , but only the Oxytricha lineage has a massively scrambled genome whose assembly requires hundreds of thousands of precise DNA joining events. Here we study the emergence of genome complexity by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage.
We sequenced, assembled and annotated the germline and somatic genomes of Euplotes woodruffi and the germline genome of Tetmemena sp. , and compared their genome rearrangement features to that of the model ciliate Oxytricha trifallax . The germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha ’s: 13.6% of its gene loci rearrange via translocations and/or inversions. This study revealed that the earlier-diverged spirotrich, E. woodruffi , also has a scrambled genome, but approximately half as many loci (7.3%) are scrambled, supporting its position as a possible evolutionary intermediate in this lineage, in the process of accumulating complex genome rearrangements. Scrambled loci are more often associated with local duplications, supporting a simple model for the origin of scrambled genes via DNA duplication and decay.
... Possible explanations discussed by (Hillier et al. 2007) include: (1) a large effective population size, which would reduce the probability of translocations becoming fixed; (2) strong selection for maintaining the arm/center distinction of chromosomes, which may be disrupted by translocations; and (3) the possible existence of sequence motifs imparting chromosome-specific identity used in critical processes such as homologous pairing in meiosis. Possibly, similar considerations may explain the striking constancy in overall karyotype in Clade V members, most of whom have a chromosome number of 6 (Mitreva et al. 2005). It appears more plausible that postrepair selection, rather than strong innate bias against interchromosomal repair, might account for the constancy of karyotype, since interchromosomal translocations can be made relatively easily in C. elegans (e.g. ...
The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell biology, and genomics. A major factor in the success of C. elegans as a model organism has been the availability, since the late 1990s, of an essentially gap-free and well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss the structure, function, and biology of C. elegans chromosomes and then provide a general perspective on chromosome biology in other diverse nematode species. We highlight malleable chromosome features including centromeres, telomeres, and repetitive elements, as well as the remarkable process of programmed DNA elimination (historically described as chromatin diminution) that induces loss of portions of the genome in somatic cells of a handful of nematode species. An exciting future prospect is that nematode species may enable experimental approaches to study chromosome features and to test models of chromosome evolution. In the long term, fundamental insights regarding how speciation is integrated with chromosome biology may be revealed.
... This is further corroborated by our analysis of the exclusion of parasitic organisms from model training. As an illustration, we found that nematodes are one of the most important clades for the model, where nematodes have been previously identified to be highly divergent concerning their evolutionary distances regardless of parasitic status 51,52 Many human genes are still mostly uncharacterized. In recent years this problem garnered attention and solutions were rigorously discussed [15][16][17] . ...
Over the next decade, more than a million eukaryotic species are expected to be fully sequenced. This has the potential to improve our understanding of genotype and phenotype crosstalk, gene function and interactions, and answer evolutionary questions. Here, we develop a machine-learning approach for utilizing phylogenetic profiles across 1154 eukaryotic species. This method integrates co-evolution across eukaryotic clades to predict functional interactions between human genes and the context for these interactions. We benchmark our approach showing a 14% performance increase (auROC) compared to previous methods. Using this approach, we predict functional annotations for less studied genes. We focus on DNA repair and verify that 9 of the top 50 predicted genes have been identified elsewhere, with others previously prioritized by high-throughput screens. Overall, our approach enables better annotation of function and functional interactions and facilitates the understanding of evolutionary processes underlying co-evolution. The manuscript is accompanied by a webserver available at: https://mlpp.cs.huji.ac.il .
... They are classified in five major clades on the basis of morphological and evolutionary criteria (Blaxter et al., 1998). The relatively compactness of nematodes' genome, ranging from 50 to 600 Mbp (Coghlan, 2005) (Coghlan et al., 2019) allows to easily producing sequence data, although the high AT content (Mitreva et al., 2005) and the amount of satellite DNA (Subirana and Messeguer, 2013) are sometimes challenging in generating the sequencing data in many nematodes species. ...
The number of reports concerning horizontal transposon transfers (HTT) in metazoan species is considerably increased, alongside with the exponential growth of genomic sequence data However, our understanding of the mechanisms of such phenomenon is still at an early stage. Nematodes constitute an animal phylum successfully adapted to almost every ecosystem and for this reason could potentially contribute to spreading the genetic information through horizontal transfer. To date, few studies describe HTT of nematode retrotransposons. This is due to the lack of annotation of transposable elements in the sequenced nematode genomes, especially DNA transposons, which are acknowledged as the best horizontal travelers among mobile sequences. We have therefore started a survey of DNA transposons and their possible involvement in HTT in sequenced nematode genomes. Here, we describe 83 new Tc1/mariner elements distributed in 17 nematode species. Among them, nine families were possibly horizontally transferred between nematodes and the most diverse animal species, including ants as preferred partner of HTT.
The results obtained suggest that HTT events involving nematodes Tc1/mariner elements are not uncommon, and that nematodes could have a possible role as transposon reservoir that, in turn, can be redistributed among animal genomes. Overall, this could be relevant to understand how the inter-species genetic flows shape the landscape of genetic variation of organisms inhabiting specific environmental communities.
... Genome decay (gene loss and genome reduction) is a phenomenon known to occur widely in prokaryotes (Judelson et al. 2012;Mandadi and Scholthof 2015;Couce et al. 2017) and eukaryotes, perhaps the best examples of this being the loss of significant amounts of genomic and morphological complexity by Tardigrada (Smith et al. 2016) and Dicyemids (Kobayashi et al. 1999). However, similar examples can be also found throughout Nematoda (Mitreva et al. 2005). Such reductions are thought to arise from selection pressures associated with deletion bias (Mira et al. 2001), simplification (Smith et al. 2016), or increasing specialization (Smith et al. 2006;Cramer et al. 2011), including parasitism (Olson et al. 2012;Wiredu Boakye et al. 2017;Lammers et al. 2019). ...
Plectus murrayi is one of the most common and locally abundant invertebrates of continental Antarctic ecosystems. Because it is readily cultured on artificial medium in the laboratory and highly tolerant to an extremely harsh environment, P. murrayi is emerging as a model organism for understanding the evolutionary origin and maintenance of adaptive responses to multiple environmental stressors, including freezing and desiccation. The de novo assembled genome of P. murrayi contains 225.741 million base pairs and a total of 14,689 predicted genes. Compared to Caenorhabditis elegans, the architectural components of P. murrayi are characterized by a lower number of protein-coding genes, fewer transposable elements, but more exons, than closely related taxa from less harsh environments. We compared the transcriptomes of lab-reared P. murrayi with wild-caught P. murrayi and found genes involved in growth and cellular processing were up-regulated in lab-cultured P. murrayi, while a few genes associated with cellular metabolism and freeze tolerance were expressed at relatively lower levels. Preliminary comparative genomic and transcriptomic analyses suggest that the observed constraints on P. murrayi genome architecture and functional gene expression, including genome decay and intron retention, may be an adaptive response to persisting in a biotically simplified, yet consistently physically harsh environment.
... In the recent past, genome sequencing efforts for nematodes have generated the huge amount of genomic dataset. Their comparative genomic analysis has revealed the origin of large number of genes through horizontal gene transfer events from bacteria have enabled the tylenchid nematode to parasitize plants (Mitreva et al., 2005). Therefore, genomic resources have been proven to be a potential resource for understanding of molecular mechanism, relations and evolutionary dynamics with other nematodes as well organism. ...
Nematodes are the most abundant metazoans and highly diverse playing significant
role in nutrient recycling, successful bioagent of insect pest and most importantly
yield loss to crop. The model nematode (Caenorhabditis elegans) was first nematode
which genome sequenced in 1998 and given impetus for future endeavor to generate
genomic information for other nematodes particularly for PPNs. Comparative
genomics is one of the approaches to predict the genes shared with different species
and also to unravel the genes unique and novel to a particular species. In the present
study we have used a graph-based method by utilizing Orthovenn 2 tool for
orthologous analysis to compare and annotate the orthologous cluster between the
genome of Anguina tritici, Ditylenchus destructor and Meloidogyne incognita
... The southern root-knot nematode Meloidogyne incognita is the most widespread and is able to infect the roots of almost all cultivated plants, which possibly renders this species as one of the most damaging crop pathogens in the world (Trudgill and Blok 2001). (Mitreva et al. 2005). Plant-parasitic nematodes appear branched in bold. ...
Meloidogyne incognita is the most widespread and polyphagous plantparasitic nematode, a group of nematodes that cause more than $150 billion damage every year. As most control means based upon chemicals are banned from use, new control measures need to be developed. Completion of the genome sequence of this plant-parasitic nematode revealed a set of singularities compared to non-parasitic nematode genomes. One of the most striking features was the presence of a full arsenal of plant cell wall-degrading enzymes probably acquired via horizontal gene transfer. The structure of the genome itself, mostly present as two similar but distinct copies may also account for the parasitic success of this nematode in terms of host spectrum and global distribution. These findings announce mechanisms used for successful establishment of plant-parasitism in metazoan and open the way for the development of more efficient control measures.
... Such redundancy might result from features of genome evolution that are common to nematodes and other animals. Studies over the last decade revealed that nematode genomes are gene-rich and exhibit high rates of gene birth and death [60,66,67]. In particular, enzyme-encoding genes are subject to high evolutionary dynamics [62]. ...
Environment shapes development through a phenomenon called developmental plasticity. Deciphering its genetic basis has potential to shed light on the origin of novel traits and adaptation to environmental change. However, molecular studies are scarce, and little is known about molecular mechanisms associated with plasticity. We investigated the gene regulatory network controlling predatory vs. non-predatory dimorphism in the nematode Pristionchus pacificus and found that it consists of genes of extremely different age classes. We isolated mutants in the conserved nuclear hormone receptor nhr-1 with previously unseen phenotypic effects. They disrupt mouth-form determination and result in animals combining features of both wild-type morphs. In contrast, mutants in another conserved nuclear hormone receptor nhr-40 display altered morph ratios, but no intermediate morphology. Despite divergent modes of control, NHR-1 and NHR-40 share transcriptional targets, which encode extracellular proteins that have no orthologs in Caenorhabditis elegans and result from lineage-specific expansions. An array of transcriptional reporters revealed co-expression of all tested targets in the same pharyngeal gland cell. Major morphological changes in this gland cell accompanied the evolution of teeth and predation, linking rapid gene turnover with morphological innovations. Thus, the origin of feeding plasticity involved novelty at the level of genes, cells and behavior.
... observations of the C. elegans and C. briggsae genomes, which saw a 10-fold 460 difference in these rates (Stein et al. 2003). This overall pattern remains consistent even 461 when comparing C. elegans to more distantly related genera of nematodes (Guiliano et 462 al. 2002;Whitton et al. 2004;Mitreva et al. 2005). 463 ...
Caenorhabditis is a group of nematodes that contains the important model organism C. elegans. Several chromosome-level genome assemblies exist for species within this group, but it has been a challenge to fully assemble the genome...
The nematode Caenorhabditis elegans is one of the key model systems in biology, including possessing the first fully assembled animal genome. Whereas C. elegans is a self-reproducing hermaphrodite with fairly limited within-population variation, its relative C. remanei is an outcrossing species with much more extensive genetic variation, making it an ideal parallel model system for evolutionary genetic investigations. Here, we greatly improve on previous assemblies by generating a chromosome-level assembly of the entire C. remanei genome (124.8 Mb of total size) using long-read sequencing and chromatin conformation capture data. Like other fully assembled genomes in the genus, we find that the C. remanei genome displays a high degree of synteny with C. elegans despite multiple within-chromosome rearrangements. Both genomes have high gene density in central regions of chromosomes relative to chromosome ends and the opposite pattern for the accumulation of repetitive elements. C. elegans and C. remanei also show similar patterns of interchromosome interactions, with the central regions of chromosomes appearing to interact with one another more than the distal ends. The new C. remanei genome presented here greatly augments the use of the Caenorhabditis as a platform for comparative genomics and serves as a basis for molecular population genetics within this highly diverse species.
... Analyse par Inférence bayesienne des ARN18S des nématodes (A) et des protéines MIFs correspondantes (B). L'arbre des espèces des nématodes (A) est cohérent avec les phylogénies précédement publiées et acceptées [168][169][170]173]. Globodera pallida (en gris, en A) est la seule espèce de nématodes de cette analyse qui ne comporte aucune protéine MIF. ...
Les cytokines MIFs (Macrophage Migration Inhibitory Factor) sont des protéines multifonctionnelles qui, chez les mammifères, interviennent dans plusieurs processus majeurs tels que le contrôle du cycle et de la mobilité cellulaire, l’activation de la réponse immunitaire et l’inhibition de l’apoptose. Des travaux récents montrent que les protéines MIFs peuvent également jouer un rôle majeur dans l’immunité des invertébrés, et être utilisées par des organismes parasites d’animaux ou de végétaux pour inhiber les défenses de leurs hôtes respectifs, ce qui soulève la question de leur diversité, de leur histoire évolutive et des potentielles différences fonctionnelles. L’objectif général de ce travail de thèse était d’explorer la diversité et l’histoire évolutive des protéines MIFs à une échelle trans-règne, puis de rechercher leurs éventuelles différences fonctionnelles, en se focalisant sur les systèmes plantes-pathogènes. Nous avons tout d’abord identifié les MIFs chez 803 espèces de plantes, champignons, protistes, et métazoaires, et analysé leur présence/absence et histoire évolutive en fonction des taxa, de l’écologie et du mode de vie (libre ou parasitaire) des espèces. Nous avons montré que l’histoire évolutive des MIFs, chez les eucaryotes, est complexe et implique des duplications ancestrales ainsi que des pertes multiples ou des re-duplications récentes. Les plantes (espèces libres autotrophes) et les parasites de plantes (autres que champignons) possèdent un nombre médian de trois MIFs, alors que les espèces hétérotrophes et les parasites d’animaux ont un nombre de MIF plus faible et/ou plus variable. De plus, les protéines MIFs semblent essentielles et fortement conservées, avec de nombreux résidus sous sélection purifiante, chez certains groupes comme les plantes, alors que dans d’autres groupes, elles semblent facultatives (e.g. champignons) ou présentes en plusieurs copies divergentes (e.g. nématodes, insectes), ce qui suggère de potentielles néofonctionalisations. Nous avons ensuite analysé l’effet des protéines MIFs de plusieurs espèces sur la mort cellulaire en système végétal. Tous les organismes testés (plantes oomycètes, protozoaires, insectes et nématodes), y compris ceux n’ayant pas d’interaction avec les plantes, possèdent au moins une protéine MIF capable d’inhiber cette mort cellulaire. Cela suggère que l’inhibition de la mort cellulaire en plante ne correspond pas à une néofonctionalisation des MIFs de parasites de plantes, mais serait liée à des propriétés structurales et conservées des MIFs. Toutefois, aucun des paramètres étudiés (localisation subcellulaire) ou prédits in silico (présence de motifs, structures 3D, oligomérisation, modifications post-traductionnelles) ne semble lié à cette activité d’inhibition de la mort cellulaire. De futures études fonctionnelles poussées sont nécessaires à l’élucidation des relations structure/fonction de ces protéines complexes.
... We observed many more intra-than interchromosomal rearrangements, which is consistent with first comparative observations of the C. elegans and C. briggsae genomes, which saw a 10-fold difference in these rates (Stein et al. 2003). This overall pattern remains consistent even when comparing C. elegans to more distantly related genera of nematodes (Guiliano et al. 2002;Whitton et al. 2004;Mitreva et al. 2005). ...
The nematode Caenorhabditis elegans is one of the key model systems in biology, including possessing the first fully assembled animal genome. Whereas C. elegans is a self-reproducing hermaphrodite with fairly limited within-population variation, its relative C. remanei is an outcrossing species with much more extensive genetic variation, making it an ideal parallel model system for evolutionary genetic investigations. Here, we greatly improve on previous assemblies by generating a chromosome-level assembly of the entire C. remanei genome (124.8 Mb of total size) using long-read sequencing and chromatin conformation capture data. Like other fully assembled genomes in the genus, we find that the C. remanei genome displays a high degree of synteny with C. elegans despite multiple within-chromosome rearrangements. Both genomes have high gene density in central regions of chromosomes relative to chromosome ends and the opposite pattern for the accumulation of repetitive elements. C. elegans and C. remanei also show similar patterns of inter-chromosome interactions, with the central regions of chromosomes appearing to interact with one another more than the distal ends. The new C. remanei genome presented here greatly augments the use of the Caenorhabditis as a platform for comparative genomics and serves as a basis for molecular population genetics within this highly diverse species.
... This also helps to develop new approaches. Indeed, recently an in silico approach for discovering new filarial drug targets was developed in which comparative sequence analysis and functional genomics data from the related model nematode Caenorhabditis elegans are combined into subtractive filters that can be used to identify potentially essential nematode genes and generate a pool of pre-validated candidate targets [15][16][17]. Different techniques such as the RNA interference (RNAi) experiments and other functional studies serve as potential genomic tools to examine gene function from NTDs pathogen. Interestingly, sequencing of pathogen genomes, can contribute to describing nearly every aspect of transmission dynamics when some of the following information, date, location, clinical manifestation, or others data regarding the samples origin are including. ...
... The protein profile of the PCF of adult D. renale (Clade I) males and females is completely different from that of the equivalently-sized Ascaris and Toxocara spp. of clade III [35]. The last common ancestor of the two clades is thought to have lived between 500 and 650 million years ago [57]. The major proteins in PCF of these large gut-dwelling ascaridids are the lipid-binding NPAs (e.g. ...
Background
The giant kidney worm, Dioctophyme renale, is a debilitating and potentially lethal parasite that inhabits and destroys, typically host’s right kidney, and may also be found in ectopic sites. It is circumglobally distributed, mainly in dogs, and is increasingly regarded as a threat to other domestic animals and humans. There is little information on the parasite’s true incidence, or immune responses to it, and none on its biochemistry and molecular biology.
Results
We characterised the soluble proteins of body wall, intestine, gonads and pseudocelomic fluid (PCF) of adult parasites. Two proteins, P17 and P44, dominate the PCF of both male and females. P17 is of 16,622 Da by mass spectrometry, and accounts for the intense red colour of the adult parasites. It may function to carry or scavenge oxygen and be related to the ‘nemoglobins’ found in other nematode clades. P44 is of 44,460 Da and was found to associate with fatty acids by thin layer chromatography. Using environment-sensitive fluorescent lipid probes, P44 proved to be a hydrophobic ligand-binding protein with a binding site that is highly apolar, and competitive displacement experiments showed that P44 binds fatty acids. It may therefore have a role in distributing lipids within the parasites and, if also secreted, might influence local inflammatory and tissue responses. N-terminal and internal peptide amino-acid sequences of P44 indicate a relationship with a cysteine- and histidine-rich protein of unknown function from Trichinella spiralis.
Conclusions
The dominant proteins of D. renale PCF are, like those of large ascaridids, likely to be involved in lipid and oxygen handling, although there is evidence of strong divergence between the two groups.
... On the other hand, differences between CeTS and TsTS are the largest among all compared sequences. This can be attributed to, often overlooked, diversity of nematodes [113], especially considering relatively large evolutionary distance between C. elegans belonging to the clade V of Nematoda and T. spiralis from clade I [114][115][116]. Since most of the sequence differences pertain to amino acids of the same character, the local hydrogen bonding and/or hydrophobic interactions are mostly preserved, regardless of the enzyme origin. ...
... Their diversity and abundance are the result of their extraordinary ability to adapt, small size, resistant cuticle, and simple body plan [2]. Nematodes have independently evolved parasitism several times in all major clades [3][4][5] and it has been proposed that understanding the genomic adaptations to parasitism in one clade could give insight into how parasitism has evolved across the phylum [5,6]. Entomopathogenic nematodes (EPNs) represent an interesting group of parasitic nematodes, comprising the genera Heterorhabditis and Steinernema, which are lethal parasites of insects capable of infecting and killing a wide range of insects. ...
Background
The entomopathogenic nematode Steinernema carpocapsae has been used worldwide as a biocontrol agent for insect pests, making it an interesting model for understanding parasite-host interactions. Two models propose that these interactions are co-evolutionary processes in such a way that equilibrium is never reached. In one model, known as “arms race”, new alleles in relevant genes are fixed in both host and pathogens by directional positive selection, producing recurrent and alternating selective sweeps. In the other model, known as“trench warfare”, persistent dynamic fluctuations in allele frequencies are sustained by balancing selection. There are some examples of genes evolving according to both models, however, it is not clear to what extent these interactions might alter genome-level evolutionary patterns and intraspecific diversity. Here we investigate some of these aspects by studying genomic variation in S. carpocapsae and other pathogenic and free-living nematodes from phylogenetic clades IV and V.
Results
To look for signatures of an arms-race dynamic, we conducted massive scans to detect directional positive selection in interspecific data. In free-living nematodes, we detected a significantly higher proportion of genes with sites under positive selection than in parasitic nematodes. However, in these genes, we found more enriched Gene Ontology terms in parasites. To detect possible effects of dynamic polymorphisms interactions we looked for signatures of balancing selection in intraspecific genomic data. The observed distribution of Tajima’s D values in S. carpocapsae was more skewed to positive values and significantly different from the observed distribution in the free-living Caenorhabditis briggsae. Also, the proportion of significant positive values of Tajima’s D was elevated in genes that were differentially expressed after induction with insect tissues as compared to both non-differentially expressed genes and the global scan.
Conclusions
Our study provides a first portrait of the effects that lifestyle might have in shaping the patterns of selection at the genomic level. An arms-race between hosts and pathogens seems to be affecting specific genetic functions but not necessarily increasing the number of positively selected genes. Trench warfare dynamics seem to be acting more generally in the genome, likely focusing on genes responding to the interaction, rather than targeting specific genetic functions.
Electronic supplementary material
The online version of this article (doi:10.1186/s12862-017-0935-x) contains supplementary material, which is available to authorized users.
... Although Pennak (1978) referred to nematodes as to "the most highly adaptable organisms from ecological and physiological stand point," the question of why nematodes exhibit such widely tolerant character remains unsolved, primarily because the physiological and genetic flexibility of nematodes is currently far from being understood. An increasing amount of attention is now focusing on reconstructing nematode phylogeny and evolution (Mitreva, Blaxter, Bird, & McCarter, 2005), and these efforts may hopefully provide a satisfactory explanation in the near future concerning the capability of nematodes to survive extremely diverse environmental conditions (Adhikari, Tomasel, Li, Wall, & Adams, 2010). If so, their distribution may offer null models to untangle spatial from environmental constraints in species richness patterns for invertebrates in varied ecosystems and regions. ...
Nematode species are widely tolerant of environmental conditions and disperse passively.
Therefore, the species richness distribution in this group might largely depend
on the topological distribution of the habitats and main aerial and aquatic dispersal
pathways connecting them. If so, the nematode species richness distributions may
serve as null models for evaluating that of other groups more affected by environmental
gradients. We investigated this hypothesis in lakes across an altitudinal gradient in
the Pyrenees. We compared the altitudinal distribution, environmental tolerance, and
species richness, of nematodes with that of three other invertebrate groups collected
during the same sampling: oligochaetes, chironomids, and nonchironomid insects. We
tested the altitudinal bias in distributions with t-tests and the significance of narrowranging
altitudinal distributions with randomizations. We compared results between
groups with Fisher’s exact tests. We then explored the influence of environmental
factors on species assemblages in all groups with redundancy analysis (RDA), using 28
environmental variables. And, finally, we analyzed species richness patterns across altitude
with simple linear and quadratic regressions. Nematode species were rarely biased
from random distributions (5% of species) in contrast with other groups (35%,
47%, and 50%, respectively). The altitudinal bias most often shifted toward low altitudes
(85% of biased species). Nematodes showed a lower portion of narrow-ranging
species than any other group, and differed significantly from nonchironomid insects
(10% and 43%, respectively). Environmental variables barely explained nematode assemblages
(RDA adjusted R2 = 0.02), in contrast with other groups (0.13, 0.19 and
0.24). Despite these substantial differences in the response to environmental factors,
species richness across altitude was unimodal, peaking at mid elevations, in all groups.
This similarity indicates that the spatial distribution of lakes across altitude is a primary
driver of invertebrate richness. Provided that nematodes are ubiquitous, their distribution
offers potential null models to investigate species richness across environmental
gradients in other ecosystem types and biogeographic regions.
... Nematodes are also used increasingly as model organisms. Caenorhabditis elegans was the Wrst metazoan organism to have its complete genome sequenced (the C. elegans sequencing Consortium, 1998) and currently over 30 nematode genome sequencing projects are ongoing (Mitreva et al., 2005). However, no sequencing projects are underway for marine nematodes (e.g. ...
Phylogenetic reconstructions of relations within the phylum Nematoda are inherently difficult but have been advanced with the introduction of large-scale molecular-based techniques. However, the most recent revisions were heavily biased towards terrestrial and parasitic species and greater representation of clades containing marine species (e.g. Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, Enoplida, and Monhysterida) is needed for accurate coverage of known taxonomic diversity. We now add small subunit ribosomal DNA (SSU rDNA) sequences for 100 previously un-sequenced species of nematodes, including 46 marine taxa. SSU rDNA sequences for >200 taxa have been analysed based on Bayesian inference and LogDet-transformed distances. The resulting phylogenies provide support for (i) the re-classification of the Secernentea as the order Rhabditida that derived from a common ancestor of chromadorean orders Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, and Monhysterida and (ii) the position of Bunonema close to the Diplogasteroidea in the Rhabditina. Other, previously controversial relationships can now be resolved more clearly: (a) Alaimus, Campydora, and Trischistoma belong in the Enoplida, (b) Isolaimium is placed basally to a big clade containing the Axonolaimidae, Plectidae, and Rhabditida, (c) Xyzzors belongs in the Desmodoridae, (d) Comesomatidae and Cyartonema belongs in the Monhysterida, (e) Globodera belongs in the Hoplolaimidae and (f) Paratylenchus dianeae belongs in the Criconematoidea. However, the SSU gene did not provide significant support for the class Chromadoria or clear evidence for the relationship between the three classes, Enoplia, Dorylaimia, and Chromadoria. Furthermore, across the whole phylum, the phylogenetically informative characters of the SSU gene are not informative in a parsimony analysis, highlighting the short-comings of the parsimony method for large-scale phylogenetic modelling.
... For instance, the nematode Caenorhabditis elegans Maupas 1900 has for decades served as an animal model for researchers throughout the world [3,4,5]. In the wake of the success of C. elegans, other Nematoda species have been used to investigate a broader range of traits [6,7]. ...
The nematode Pristionchus pacificus is of growing interest as a model organism in evolutionary biology. However, despite multiple studies of its genetics, developmental cues, and ecology, the basic life-history traits (LHTs) of P. pacificus remain unknown. In this study, we used the hanging drop method to follow P. pacificus at the individual level and thereby quantify its LHTs. This approach allowed direct comparisons with the LHTs of Caenorhabditis elegans recently determined using this method. When provided with 5×109
Escherichia coli cells ml–1 at 20°C, the intrinsic rate of natural increase of P. pacificus was 1.125 (individually, per day); mean net production was 115 juveniles produced during the life-time of each individual, and each nematode laid an average of 270 eggs (both fertile and unfertile). The mean age of P. pacificus individuals at first reproduction was 65 h, and the average life span was 22 days. The life cycle of P. pacificus is therefore slightly longer than that of C. elegans, with a longer average life span and hatching time and the production of fewer progeny.
Nematodes are important biological models in genetics and genomics, with research driven by basic biological as well as applied questions. The presence of holocentric chromosomes, clades with frequent polyploidy and the phenomenon of programmed DNA elimination make nematode karyotypic diversity of particular interest. Here we present a catalogue of published karyotypes of nematode species, rationalising and normalising descriptions from the previous 135 years. Karyotypes of 257 species are presented in taxonomic context. Nuclear chromosome counts range from 2 to 60. Tylenchina is identified as particularly diverse in karyotype. We highlight that Rhabditida and especially parasitic Rhabditina are well-represented, but there is a paucity of data from Enoplea, Dorylaimia, and from free-living marine groups in Chromadorea. The data have been uploaded to the Genomes on a Tree (GoaT) datasystem (https://goat.genomehubs.org/) for integration with ongoing, large-scale genome sequencing efforts.
Plant-parasitic nematodes (PPNs) are vital soil organisms well-known to damage and reduce crop yield worldwide. Surveys were attempts to determine the impact of weed species on the communities and composition of nematodes in barley, wheat, quinoa, eggplant, and tomato crops in Alexandria and Ismailia regions of Egypt. During the surveys, eight occurring genera of nematodes were found namely; Meloidogyne spp, Pratylenchus spp, Helicotylenchus spp, Rotylenchulus spp, Xiphinema spp, Criconemoides spp, Ditylenchus spp, and Longidorus spp associated with the soil’s rhizosphere of 28 weed species belonging to 12 families. Among these weeds, Hordeum marinum and Sonchus oleraceus were good hosts to nematode species. Both wheat and barley had higher nematode diversity than quinoa in the winter season. Pratylenchus spp, Meloidogyne spp and Rotylenchulus spp can be considered vital potential PPNs with economic importance. Nematode abundances and structural indices varied greatly based on the host weed species, crop types and soil characteristics. A positive correlation was monitored among weeds, nematode frequencies and relative abundances as well as their crops. Finally, weed species are critical components in nematode communities that may increase the incidence and severity of nematode risks based on crop type and soil characteristics. Therefore weeds should be managed properly to diminish reservoir sites when developing nematode management options.
Plant-parasitic nematodes from the genera Globodera, Heterodera (cyst-forming nematodes), and Meloidogyne (root-knot nematodes) are notorious and serious pests of crops. They cause tremendous economic losses between US $80 and 358 billion a year. Nematodes infect the roots of plants and induce the formation of specialised feeding structures (syncytium and giant cells, respectively) that nourish juveniles and adults of the nematodes. The specialised secretory glands enable nematodes to synthesise and secrete effectors that facilitate migration through root tissues and alter the morphogenetic programme of host cells. The formation of feeding sites is associated with the suppression of plant defence responses and deep reprogramming of the development and metabolism of plant cells.
In this chapter, we focus on syncytia induced by the sedentary cyst-forming nematodes and provide an overview of ultrastructural changes that occur in the host roots during syncytium formation in conjunction with the most important molecular changes during compatible and incompatible plant responses to infection with nematodes.
Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement, a natural genome editing process that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax , Tetrahymena thermophila, and Paramecium tetraurelia , but only the Oxytricha lineage has a massively scrambled genome, whose assembly during development requires hundreds of thousands of precisely programmed DNA joining events, representing the most complex genome dynamics of any known organism. Here we study the emergence of such complex genomes by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage. This study compares six genomes from three species, the germline and somatic genomes for Euplotes woodruffi , Tetmemena sp ., and the model ciliate O. trifallax . We sequenced, assembled, and annotated the germline and somatic genomes of E. woodruffi, which provides an outgroup , and the germline genome of Tetmemena sp . We find that the germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha ’s: 13.6% of its gene loci require programmed translocations and/or inversions, with some genes requiring hundreds of precise gene editing events during development. This study revealed that the earlier diverged spirotrich, E. woodruffi , also has a scrambled genome, but only roughly half as many loci (7.3%) are scrambled. Furthermore, its scrambled genes are less complex, together supporting the position of Euplotes as a possible evolutionary intermediate in this lineage, in the process of accumulating complex evolutionary genome rearrangements, all of which require extensive repair to assemble functional coding regions. Comparative analysis also reveals that scrambled loci are often associated with local duplications, supporting a gradual model for the origin of complex, scrambled genomes via many small events of DNA duplication and decay.
Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. Lack of genomic resources has been a limiting factor for expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced, assembled, and annotated the whole genome of M. nigrescens using nanopore long-reads and 10X chromium link-reads. The assembly is 524 Mb in size consisting of 867 scaffolds. The N50 value is 2.42 Mb, and half of the assembly is in the 30 longest scaffolds. The assembly BUSCO score from the eukaryotic database (eukaryota_odb10) indicates that the genome is 86.7% complete and 5.1% partial. The genome has a high level of heterozygosity (6.6%) with a repeat content of 78.7%. mRNA-seq reads from different sized nematodes (≤2 cm, 3.5-7 cm, and >7 cm body length) representing different developmental stages were also generated and used for the genome annotation. Using ab initio and evidence-based gene model predictions, 12,313 protein-coding genes and 24,186 mRNAs were annotated. These genomic resources will help researchers investigate the various aspects of the biology and host-parasite interactions of mermithid nematodes.
Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Ecdysozoa by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Similar to bdelloid rotifers, nematodes and other animals of the water film, limno-terrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of HGT events, but how important this is in evolution, and in particular in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of Hypsibius dujardini , a limno-terrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of Ramazzottius varieornatus , a related species with tolerance to rapid desiccation. The two species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus . We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.
Cinnamon is the dried bark of Cinnamomum cassia Presl, and its main component is cinnamaldehyde (CA). Decades of synthetic pesticide use to control parasitic nematodes that can harm plants has seriously polluted the environment and poses a risk to soil ecology, highlighting the need to develop natural biological pesticides. Some species classified under Nematoda are highly similar, therefore we used the model organism C. elegans to explore the effect of cinnamaldehyde, a plant-derived natural product, on C. elegans viability. We found that the lethal dose of cinnamaldehyde for C. elegans treatment for 4 h at a concentration of 800 mg/L. Sequencing-based transcriptome data revealed differences between the cinnamaldehyde treatment and control groups. RNA-seq analysis showed that C. elegans exposed to cinnamaldehyde had significantly altered expression of metabolic genes, particularly for genes involved in glutathione metabolism (gst-1, gst-2, gst-4, gst-5, gst-6, gst-7, gst-8, gst-25, gst-30, gst-38, gst-44, and gcs-1). Therefore, glutathione metabolism is altered in C. elegans upon exposure to cinnamaldehyde. Based on the above results, treatment with 800 mg/L of cinnamaldehyde for 4 h was selected for all experiments in nematodes. Given these findings, cinnamaldehyde may be a promising natural alternative to synthetic pesticides for controlling plant parasitic nematodes with low cost, high efficiency, and diminished environmental pollution.
Neglected tropical diseases (NTDs) is a diverse group of communicable diseases that prevail in tropical and subtropical conditions in 149 countries. NTDs affect more than one billion people and cost developing economies billions of dollars every year. According to the World Health Organization (WHO), NTDs mainly affect populations living in poverty, without adequate sanitation, and in close contact with infectious vectors, domestic animals, and livestock. Migration, as well as climate change and variability, are key factors in NTD prevalence. Therefore, NTDs deserve more study. Recently, viruses transmitted by vectors (arboviruses) that affect not only people living in the tropics, but also travelers and migrating populations, have been causing epidemics. Examples of these viruses include Dengue, Chikungunya, Zika, Mayaro, and encephalitis viruses. These viruses emerge and reemerge in multiple regions of the world, as occurred in the Americas recently (2013-2017) with Chikungunya and Zika. This book aims to update the significant epidemiological and clinical research of NTDs in many aspects with a multinational perspective.
Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.
Kök-ur nematodları (Meloidogyne spp.), konukçu bitki ile özel ve karmaşık ilişkilere sahiptir. Nematod ve konukçusu arasındaki ilişkinin daha iyi anlaşılması, mücadele açısından yeni bakış açılarının oluşumuna yardımcı olacaktır. Bu amaçla, kök-ur nematodlarında parazitizm ve konukçu tepkileri ile ilgili hücresel ve moleküler temelli son araştırmalar derlenerek verilmiştir.
Root-knot nematodes (Meloidogyne spp.) have specialized and complex relationships with their host plants. A better understanding of interaction between nematode and their host will help to provide new point of view for root-knot nematode management. For this purpose, recently investigations on cellular and molecular basis of root-knot nematode parasitism and host response were reviewed.
Plant-parasitic nematodes cause a considerable amount of crop damage worldwide. These nematodes all have a stylet to damage plant cells mechanically, but through which they also secrete proteins important for their infection process. Most studies on genes encoding these so-called parasitism proteins were conducted on sedentary plant-parasitic nematodes which manipulate the plant to induce a specialized nematode feeding site. In this doctoral thesis parasitism genes of the less specialized migratory endoparasitic nematodes were investigated. The focus was on plant cell wall modifying enzymes that are being secreted by the nematode to enable migration through the rigid plant cell wall.
The main component of the plant cell wall is cellulose, the most abundant sugar polymer on earth. In nematodes, cellulases or endo-1,4-β-glucanases which can degrade cellulose were mainly identified in sedentary species. A large part of this thesis is about the characterization of endoglucanases in migratory endoparasitic nematodes, namely in the species Radopholus similis, Ditylenchus africanus and Pratylenchus coffeae. Additionally, a detailed model for the evolution of the gene structure of endoglucanases within nematodes was proposed.
The second most abundant sugar polymer in a plant cell wall is xylan. An endoxylanase from R. similis putatively able to degrade xylan was characterized. When this gene was downregulated in nematodes by RNAi, the infection on the plant was reduced by 60%, showing that the xylanase is important for the nematodes to infect their host plant.
Another technique to identify parasitism genes is expressed sequence tag analysis, by randomly sequencing pieces of genes that are being expressed by the nematode. This approach was applied to D. africanus and 4847 ESTs were analyzed.
Scientific research sometimes leads to unexpected discoveries. During an EST analysis of R. similis several ESTs were found with significant similarity to sequences from a Wolbachia endosymbiotic bacterium. This finding was further investigated and the presence of an intracellular Wolbachia bacterium in the nematode was demonstrated. Although this bacterium is often found in filarial nematodes, it is the first time it is discovered in a plant-parasitic nematode. Future research will be needed to determine what role this endosymbiont plays within the nematode.
The nematode Caenorhabditis elegans can be a powerful model system for the discovery and characterization of new anthelmintics. C. elegans is free-living and its use therefore circumvents the complications of culturing parasitic nematodes that are invariably dependent on a host to complete their life cycle. C. elegans is also small (1mm in length), hermaphroditic, and has a 3-day life cycle. These features make C. elegans a seemingly ideal high-throughput platform with which to discover novel anthelmintics. However, C. elegans has formidable xenobiotic defenses that have likely evolved to protect it from a plethora of chemical insults in its native environment. In this chapter, we will discuss the extent of C. elegans xenobiotic resistance and review strategies to circumvent this resistance in order to take full advantage of one of the most powerful animal models available.
The free-living nematode Caenorhabditis elegans (C. elegans) is a ubiquitous soil organism that plays a primary role in decomposition and nutrient recycling in the soil ecosystem. C. elegans is widely used as a model for studying fundamental processes of multicellular eukaryotes, due to its easy maintenance and handling in the laboratory. Because of these properties, several toxicity tests using C. elegans have been developed for ecological risk assessment. In these tests, several endpoints, including mortality, reproduction, growth, behavior, lifespan, and inductions of stress-response genes, are used to detect ecotoxicity of a variety of agents, such as metals, detergents, pesticides, and endocrine disrupting chemicals. This chapter describes the effects of various ecotoxicants on nematodes; ecotoxicity tests using C. elegans, including transgenic nematodes; and recent progress in C. elegans-based technology with regard to ecotoxicology, such as ecotoxicogenomics and high-throughput toxicity assays.
The 97-megabase genomic sequence of the nematode Caenorhabditis elegans reveals over 19,000 genes. More than 40 percent of the predicted protein products find significant matches in other organisms.
There is a variety of repeated sequences, both local and dispersed. The distinctive distribution of some repeats and highly
conserved genes provides evidence for a regional organization of the chromosomes.
We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
Nematodes are important: parasitic nematodes threaten the health of plants, animals and humans on a global scale; interstitial nematodes pervade sediment and soil ecosystems in overwhelming numbers; and Caenorhabditis elegans is a favourite experimental model system. A lack of clearly homologous characters and the absence of an informative fossil record have prevented us from deriving a consistent evolutionary framework for the phylum. Here we present a phylogenetic analysis, using 53 small subunit ribosomal DNA sequences from a wide range of nematodes. With this analysis, we can compare animal-parasitic, plant-parasitic and free-living taxa using a common measurement. Our results indicate that convergent morphological evolution may be extensive and that present higher-level classification of the Nematoda will need revision. We identify five major clades within the phylum, all of which include parasitic species. We suggest that animal parasitism arose independently at least four times, and plant parasitism three times. We clarify the relationship of C. elegans to major parasitic groups; this will allow more effective exploitation of our genetic and biological knowledge of this model species.
The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification
of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of
bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www.ncbi.nlm.nih.gov/COG). In addition, a supplement to the COGs is available, in which proteins encoded in the genomes of two multicellular eukaryotes,
the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and shared with bacteria and/or archaea were included. The new features added to the COG database include information pages
with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is
used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis.
Chromatin diminution in the nematodes Parascaris equorum and Ascaris lumbricoides leads to the formation of somatic cells that contain less DNA than the germ-line cells. We present molecular evidence for the coding potential of germ-line-specific DNA. We report on a cDNA clone that codes for a putative ribosomal protein (ALEP-1, for A. lumbricoides eliminated protein 1). That the corresponding gene is located in the eliminated portion of the genome indicates a difference in germ-line and somatic ribosomes of A. lumbricoides and P. equorum. Elimination of the ALEP-1 gene from all somatic cells in its fully active state may represent an alternative way to gene regulation.
Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes. Extensive horizontal transfer has occurred for operational genes (those involved in housekeeping), whereas informational genes (those involved in transcription, translation, and related processes) are seldomly horizontally transferred. Through phylogenetic analysis of six complete prokaryotic genomes and the identification of 312 sets of orthologous genes present in all six genomes, we tested two theories describing the temporal flow of horizontal transfer. We show that operational genes have been horizontally transferred continuously since the divergence of the prokaryotes, rather than having been exchanged in one, or a few, massive events that occurred early in the evolution of prokaryotes. In agreement with earlier studies, we found that differences in rates of evolution between operational and informational genes are minimal, suggesting that factors other than rate of evolution are responsible for the observed differences in horizontal transfer. We propose that a major factor in the more frequent horizontal transfer of operational genes is that informational genes are typically members of large, complex systems, whereas operational genes are not, thereby making horizontal transfer of informational gene products less probable (the complexity hypothesis).
Serine proteinase inhibitors (serpins) play a vital regulatory role in a wide range of biological processes, and serpins from viruses have been implicated in pathogen evasion of the host defence system. For the first time, we report a functional serpin gene from nematodes that may function in this manner. This gene, named Bm-spn-2, has been isolated from the filarial nematode Brugia malayi, a causative agent of human lymphatic filariasis. Polymerase chain reaction (PCR) and Western blot experiments indicate that Bm-spn-2 is expressed only by microfilariae (Mf), which are the long-lived blood-dwelling larval stage. A survey of the greater than 14,000 expressed sequence tags (ESTs) from B malayi deposited in dbEST shows that greater than 2% of the ESTs sequenced from Mf cDNA libraries correspond to Bm-spn-2. Despite its abundance in the microfilarial stage, Bm-spn-2 has not been found in any other point in the life cycle. The predicted protein encoded by Bm-spn-2 contains 428 amino acids with a putative signal peptide. Antibodies to recombinant Bm-SPN-2 protein react specifically with a 47.5-kD native protein in Mf extract. Bm-SPN-2 is one of the largest of the 93 known serpins, due to a 22 amino acid carboxy-terminal extension, and contains the conserved serpin signature sequence. Outside these regions, levels of homology are low, and only a distant relationship can been seen to a Caenorhabditis elegans serpin. The Bm-spn-2 gene contains 6 introns, 2 of which appear to be shared by both nematode species. The B malayi introns have an extended and conserved 3' splice site and are relatively large compared with C elegans. A panel of mammalian serine proteinases were screened and Bm-SPN-2 protein was found to specifically inhibit enzymatic activity of human neutrophil cathepsin G and human neutrophil elastase, but not a range of other serine proteinases. It is possible that Bm-SPN-2 could function as a stage-specific serpin in the blood environment of the microfilarial parasite in protection from human immunity and thus may be a good candidate for protective vaccine.
Larvae of Toxocara canis, a nematode parasite of dogs, infect humans, causing visceral and ocular larva migrans. In noncanid hosts, larvae neither grow nor differentiate but endure in a state of arrested development. Reasoning that parasite protein production is orientated to immune evasion, we undertook a random sequencing project from a larval cDNA library to characterize the most highly expressed transcripts. In all, 266 clones were sequenced, most from both 3' and 5' ends, and similarity searches against GenBank protein and dbEST nucleotide databases were conducted. Cluster analyses showed that 128 distinct gene products had been found, all but 3 of which represented newly identified genes. Ninety-five genes were represented by a single clone, but seven transcripts were present at high frequencies, each composing >2% of all clones sequenced. These high-abundance transcripts include a mucin and a C-type lectin, which are both major excretory-secretory antigens released by parasites. Four highly expressed novel gene transcripts, termed ant (abundant novel transcript) genes, were found. Together, these four genes comprised 18% of all cDNA clones isolated, but no similar sequences occur in the Caenorhabditis elegans genome. While the coding regions of the four genes are dissimilar, their 3' untranslated tracts have significant homology in nucleotide sequence. The discovery of these abundant, parasite-specific genes of newly identified lectins and mucins, as well as a range of conserved and novel proteins, provides defined candidates for future analysis of the molecular basis of immune evasion by T. canis.
Genome sequencing projects generate a wealth of information; however, the ultimate goal of such projects is to accelerate the identification of the biological function of genes. This creates a need for comprehensive studies to fill the gap between sequence and function. Here we report the results of a functional genomic screen to identify genes required for cell division in Caenorhabditis elegans. We inhibited the expression of approximately 96% of the approximately 2,300 predicted open reading frames on chromosome III using RNA-mediated interference (RNAi). By using an in vivo time-lapse differential interference contrast microscopy assay, we identified 133 genes (approximately 6%) necessary for distinct cellular processes in early embryos. Our results indicate that these genes represent most of the genes on chromosome III that are required for proper cell division in C. elegans embryos. The complete data set, including sample time-lapse recordings, has been deposited in an open access database. We found that approximately 47% of the genes associated with a differential interference contrast phenotype have clear orthologues in other eukaryotes, indicating that this screen provides putative gene functions for other species as well.
The stylet secretions produced by plant parasitic root-knot nematodes are thought to be pathogenicity factors involved in the invasion of the root tissue and in the induction and maintenance of feeding cells. A new procedure was established that allowed the direct qualitative analysis of proteins secreted by Meloidogyne incognita infective juveniles. Purified proteins whose isoelectric point (pI) ranged from 5.0 to 7.5 were separated by two-dimensional (2D) electrophoresis and the seven most abundant proteins were identified by micro-sequencing. A calreticulin (CRT) was isolated and transcription of its gene in infective juveniles and adults was demonstrated. Moreover, evidence for expression of the CRT in the subventral oesophageal glands of infective juveniles was obtained. The potential roles of this secreted protein in pathogenesis and the advantages of developing this strategy to obtain new insights into plant-nematode interactions are discussed.
An unusually high proportion of proteins encoded in Chlamydia genomes are most similar to plant proteins, leading to proposals that a Chlamydia ancestor obtained genes from a plant or plant-like host organism by horizontal gene transfer. However, during an analysis of bacterial–eukaryotic protein similarities, we found that the vast majority of plant-like sequences in Chlamydia are most similar to plant proteins that are targeted to the chloroplast, an organelle derived from a cyanobacterium. We present further evidence suggesting that plant-like genes in Chlamydia , and other Chlamydiaceae, are likely a reflection of an unappreciated evolutionary relationship between the Chlamydiaceae and the cyanobacteria-chloroplast lineage. Further analyses of bacterial and eukaryotic genomes indicates the importance of evaluating organellar ancestry of eukaryotic proteins when identifying bacteria-eukaryote homologs or horizontal gene transfer and supports the proposal that Chlamydiaceae, which are obligate intracellular bacterial pathogens of animals, are not likely exchanging DNA with their hosts.
[Supplementary Material is available online at http://www.genome.org and at http://www.pathogenomics.bc.ca/BAE-watch.html .]
Chromosomes are divided into domains of open chromatin, where genes have the potential to be expressed, and domains of closed chromatin, where genes are not expressed. Classic examples of open chromatin domains include 'puffs' on polytene chromosomes in Drosophila and extended loops from lampbrush chromosomes. If multiple genes were typically expressed together from a single open chromatin domain, the position of co-expressed genes along the chromosomes would appear clustered. To investigate whether co-expressed genes are clustered, we examined the chromosomal positions of the genes expressed in the muscle of Caenorhabditis elegans at the first larval stage. Here we show that co-expressed genes in C. elegans are clustered in groups of 2-5 along the chromosomes, suggesting that expression from a chromatin domain can extend over several genes. These observations reveal a higher-order organization of the structure of the genome, in which the order of the genes along the chromosome id correlated with their expression in specific tissues.
Regulation of body fat storage involves signalling between centres that regulate feeding in the brain and sites of fat storage and use in the body. Here we describe an assay for analysing fat storage and mobilization in living Caenorhabditis elegans. By using RNA-mediated interference (RNAi) to disrupt the expression of each of the 16,757 worm genes, we have systematically screened the C. elegans genome for genes necessary for normal fat storage. We identify 305 gene inactivations that cause reduced body fat and 112 gene inactivations that cause increased fat storage. Analysis of the fat-reducing gene inactivations in insulin, serotonin and tubby signalling mutants of C. elegans, which have increased body fat, identifies a core set of fat regulatory genes as well as pathway-specific fat regulators. Many of the newly identified worm fat regulatory genes have mammalian homologues, some of which are known to function in fat regulation. Other C. elegans fat regulatory genes that are conserved across animal phylogeny, but have not previously been implicated in fat storage, may point to ancient and universal features of fat storage regulation, and identify targets for treating obesity and its associated diseases.
A principal challenge currently facing biologists is how to connect the complete DNA sequence of an organism to its development and behaviour. Large-scale targeted-deletions have been successful in defining gene functions in the single-celled yeast Saccharomyces cerevisiae, but comparable analyses have yet to be performed in an animal. Here we describe the use of RNA interference to inhibit the function of approximately 86% of the 19,427 predicted genes of C. elegans. We identified mutant phenotypes for 1,722 genes, about two-thirds of which were not previously associated with a phenotype. We find that genes of similar functions are clustered in distinct, multi-megabase regions of individual chromosomes; genes in these regions tend to share transcriptional profiles. Our resulting data set and reusable RNAi library of 16,757 bacterial clones will facilitate systematic analyses of the connections among gene sequence, chromosomal location and gene function in C. elegans.
Haemonchus contortus is a nematode that infects small ruminants. It releases a variety of molecules, designated excretory/secretory products (ESP), into the host. Although the composition of ESP is largely unknown, it is a source of potential vaccine components because ESP are able to induce up to 90% protection in sheep. We used proteomic tools to analyze ESP proteins and determined the recognition of these individual proteins by hyperimmune sera. Following two-dimensional electrophoresis of ESP, matrix-assisted laser desorption ionization time-of-flight and liquid chromatography-tandem mass spectrometry were used for protein identification. Few sequences of H. contortus have been determined. Therefore, the data base of expressed sequence tags (dbEST) and a data base consisting of contigs from Haemonchus ESTs were also consulted for identification. Approximately 200 individual spots were observed in the two-dimensional gel. Comprehensive proteomics analysis, combined with bioinformatic search tools, identified 107 proteins in 102 spots. The data include known as well as novel proteins such as serine, metallo- and aspartyl proteases, in addition to H. contortus ESP components like Hc24, Hc40, Hc15, and apical gut GA1 proteins. Novel proteins were identified from matches with H. contortus ESTs displaying high similarity with proteins like cyclophilins, nucleoside diphosphate kinase, OV39 antigen, and undescribed homologues of Caenorhabditis elegans. Of special note is the finding of microsomal peptidase H11, a vaccine candidate previously regarded as a "hidden antigen" because it was not found in ESP. Extensive sequence variation is present in the abundant Hc15 proteins. The Hc15 isoforms are differentially recognized by hyperimmune sera, pointing to a possible specific role of Hc15 in the infectious process and/or in immune evasion. This concept and the identification of multiple novel immune-recognized components in ESP should assist future vaccine development strategies.
Plant parasitic nematodes are major pathogens of most crops. Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches. As an entrée to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ESTs) from second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita.
From these, 1,625 EST clusters were formed and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. L2 larvae, which represent the infective stage of the life cycle before plant invasion, express a diverse array of ligand-binding proteins and abundant cytoskeletal proteins. L2 are structurally similar to Caenorhabditis elegans dauer larva and the presence of transcripts encoding glyoxylate pathway enzymes in the M. incognita clusters suggests that root-knot nematode larvae metabolize lipid stores while in search of a host. Homology to other species was observed in 79% of translated cluster sequences, with the C. elegans genome providing more information than any other source. In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases.
With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses.
Serine proteinase inhibitors (serpins) play a vital regulatory role in a wide range of biological processes, and serpins from viruses have been implicated in pathogen evasion of the host defence system. For the first time, we report a functional serpin gene from nematodes that may function in this manner. This gene, named Bm-spn-2, has been isolated from the filarial nematode Brugia malayi, a causative agent of human lymphatic filariasis. Polymerase chain reaction (PCR) and Western blot experiments indicate that Bm-spn-2 is expressed only by microfilariae (Mf), which are the long-lived blood-dwelling larval stage. A survey of the greater than 14,000 expressed sequence tags (ESTs) from B malayi deposited in dbEST shows that greater than 2% of the ESTs sequenced from Mf cDNA libraries correspond to Bm-spn-2. Despite its abundance in the microfilarial stage, Bm-spn-2 has not been found in any other point in the life cycle. The predicted protein encoded byBm-spn-2 contains 428 amino acids with a putative signal peptide. Antibodies to recombinant Bm-SPN-2 protein react specifically with a 47.5-kD native protein in Mf extract. Bm-SPN-2 is one of the largest of the 93 known serpins, due to a 22 amino acid carboxy-terminal extension, and contains the conserved serpin signature sequence. Outside these regions, levels of homology are low, and only a distant relationship can been seen to a Caenorhabditis elegansserpin. The Bm-spn-2 gene contains 6 introns, 2 of which appear to be shared by both nematode species. The B malayi introns have an extended and conserved 3′ splice site and are relatively large compared with C elegans. A panel of mammalian serine proteinases were screened and Bm-SPN-2 protein was found to specifically inhibit enzymatic activity of human neutrophil cathepsin G and human neutrophil elastase, but not a range of other serine proteinases. It is possible that Bm-SPN-2 could function as a stage-specific serpin in the blood environment of the microfilarial parasite in protection from human immunity and thus may be a good candidate for protective vaccine.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Isolation and cloning of abundant reverse transcriptase-polymerase chain reaction (RT-PCR) products from the filarial nematode Brugia malayi using the conserved nematode spliced leader sequence and poly A as amplification targets has allowed us to identify abundant, stage specific transcripts from infective and post-infective larvae. The predicted protein products of the most prominent full-length transcripts from mosquito-derived L3 parasites are: (i) Bm-ALT-1, a homologue of a Dirofilaria immitis abundant larval protein; (ii) Bm-CPI-1, a cystatin-type cysteine protease inhibitor; (iii) Bm-ALT-3, a novel predicted 6 kDa glycine/tyrosine-rich protein; and (iv) Bm-TPH-1, a homologue of a mammalian translationally-controlled tumour protein. Some transcripts were not full-length but had mis-primed at A-rich stretches of coding sequence: the most abundant of these was Bm-col-3, a which encodes a collagen homologous to Bp-COL-1 of Brugia pahangi. Similar analysis of abundant spliced leader (SL)/oligo-dT products from fourth-stage larvae 9 days post-infection yielded two dominant transcripts: (i) Bm-cdd-1, which encodes a protein with homology to cytidine deaminase, differing at only one amino acid position from its homologue described in Brugia pahangi; and (ii) the same truncated form of Bm-col-3 found in L3 preparations. Expression of the major transcripts was assessed by PCR amplification of cDNA libraries derived from each stage of the life cycle. alt1, alt-3 and cpi-1 were all found to be specific to the L3 stage, while cdd-1 was found only in the L4 cDNA library. Expression of these larval-specific transcripts was not detected in either microfilarial or adult libraries.
T he completion of the Caenorhabditis elegans genome sequence represents a major milestone in a journey initiated by Sydney Brenner some 30 years ago. The goal then as now was to discover how genetic information specifies the development, anatomy, and behavior of a simple animal. Bringing the full
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Polymerase chain reaction (PCR) with degenerate primers was performed on cDNA from Pratylenchus penetrans to amplify a conserved region in β-1,4-endoglucanase genes. Two distinct genomic DNA fragments that encoded partial β-1,4-endoglucanase sequences were isolated. Two corresponding full-length cDNAs, designated Pp-eng-1 and Pp-eng-2, were obtained by 3′ and 5′ rapid amplification of cDNA ends. Pp-eng-1 and Pp-eng-2 consisted of 1521 nucleotides encoding 455 amino acids and 1179 nucleotides encoding 328 amino acids, respectively. The two cloned genes encoded family 5 β-1,4-endoglucanases. The predicted protein PP-ENG-1 contained a cellulose-binding domain (CBD), and the predicted protein PP-ENG-2 lacked a CBD.
Hookworms are gut-dwelling, blood-feeding nematodes that infect hundreds of millions of people, particularly in the
tropics. As part of a program aiming to define novel drug targets and vaccine candidates for human parasitic nematodes,
genes expressed in adults of the human hookworm Necator americanus were surveyed by the expressed sequence tag
approach. In total 161 new hookworm genes were identified. For the majority of these, a function could be assigned by
homology. The dataset includes proteases, protease inhibitors, a lipid binding protein, C-type lectins, an anti-bacterial
factor, globins and other genes of interest from a drug or vaccine development viewpoint. Three different classes of small,
secreted proteins were identified that may be involved in the host–parasite interaction, including potential potassium
channel blocking peptides. One third of the genes were novel. These included highly expressed, secreted (glyco)proteins
which may be part of the excretory–secretory products of these important pathogens. Of particular interest are a family
of 9 genes with similarity to the immunomodulatory protein, neutrophil inhibitory factor, that may play a role in
establishing an immunocompromised niche for this successful parasite.
Isolation and cloning of abundant reverse transcriptase-polymerase chain reaction (RT-PCR) products from the filarial nematode Brugia malayi using the conserved nematode spliced leader sequence and poly A as amplification targets has allowed us to identify abundant, stage specific transcripts from infective and post-infective larvae. The predicted protein products of the most prominent full-length transcripts from mosquito-derived L3 parasites are: (i) Bm-ALT-1, a homologue of a Dirofilaria immitis abundant larval protein; (ii) Bm-CPI-1, a cystatin-type cysteine protease inhibitor; (iii) Bm-ALT-3, a novel predicted 6 kDa glycine/tyrosine-rich protein; and (iv) Bm-TPH-1, a homologue of a mammalian translationally-controlled tumour protein. Some transcripts were not full-length but had mis-primed at A-rich stretches of coding sequence: the most abundant of these was Bm-col-3, a which encodes a collagen homologous to Bp-COL-1 of Brugia pahangi. Similar analysis of abundant spliced leader (SL)/oligo-dT products from fourth-stage larvae 9 days post-infection yielded two dominant transcripts: (i) Bm-cdd-1, which encodes a protein with homology to cytidine deaminase, differing at only one amino acid position from its homologue described in Brugia pahangi; and (ii) the same truncated form of Bm-col-3 found in L3 preparations. Expression of the major transcripts was assessed by PCR amplification of cDNA libraries derived from each stage of the life cycle. alt1, alt-3 and cpi-1 were all found to be specific to the L3 stage, while cdd-1 was found only in the L4 cDNA library. Expression of these larval-specific transcripts was not detected in either microfilarial or adult libraries.
The 97-megabase genomic sequence of the nematode Caenorhabditis elegans reveals over 19,000 genes. More than 40 percent of the predicted protein products find significant matches in other organisms. There is a variety of repeated sequences, both local and dispersed. The distinctive distribution of some repeats and highly conserved genes provides evidence for a regional organization of the chromosomes.
Expressed sequence tags (EST) have been widely used to assist in gene discovery in various organisms (e.g., Arabidopsis thaliana, Caenorhabditis elegans, Mus musculus, and Homo sapiens). In this paper we describe an EST project, which aims to investigate gene expression in Meloidogyne incognita at the onset of parasitism. Approximately 1000 5′-end sequence tags were produced from a cDNA library made of freshly hatched preparasitic second stage juveniles (J2). The EST were identified in the primary transformants of the cDNA library, and assigned to nine different functional groups, including (candidate) parasitism genes. A large fraction of the EST (45€did not have a putative homologue in public databases. Sixty five percent of the EST that could be clustered into a functional group had putative homologues in other nematode species. EST were found for virtually all parasitism related genes that have been cloned from M. incognita to date. In addition, several novel genes were tagged, including a xylanase and a chitinase gene. The efficiency of EST projects, which produce sequence data for thousands of genes in months time without any difficult pre-selections of mRNA pools, makes random sequencing cDNA libraries a superior method to identify candidates for parasitism related genes in plant-parasitic nematodes. The sequences in this paper are retrievable from Genbank with the accession numbers BE191640 to BE191741, BE217592 to BE217720, BE225324 to BE225598, BE238852 to BE239221, and BE240829 to BE240865
Diss. rer. nat. Freiburg/Schweiz, 1990 (Austausch beschränkt).
We have characterized the organization of the germline limited DNA of P. univalens by means of sequence analysis. The repeat unit of this satellite DNA is the pentanucleotide 5′TTGCA, although there is a
high degree of sequence variation. Repeat variants are not arranged in tandem but in a disperse, nonrandom manner. In the
somatic genome which arises from the germline genome through extensive genomic rearrangement early in development, copies
of these pentamers represent the telomeric repeats, indicated by their sensitivity to Bal 31 and their presence in a somatic
endlibrary. Unlike telomeric sequences from other species the P. univalens telomeres do not display consecutive guanines and no strand bias for that base, recently suggested as universal features
of eukaryotic telomeres. Investigation of fragments that carry pentameric repeats along with sequences of different type identifies
a 5 bp consensus sequence at the junction point. We suggest a model in which pentameric repeats originate via amplification
by a terminal transferase (telomerase) in both the germline and the somatic genome.
We report here a broad analysis of the excretory/secretory (E/S) products of adult Brugia malayi, collected by in-vitro cultivation of the parasite. Culture media and conditions were optimized, and non-essential amino acids were found to be crucial for efficient protein synthesis under cell- and serum-free culture conditions. A close correlation was found between total protein secretion, phosphorylcholine-bearing antigen release and lactate production on each day of culture, indicating that E/S molecules are actively secreted. Parasites cultured in vitro take 2-3 days to adjust to the new environment, and show peak levels of secretion at days 3 and 4. The active secretion of phosphorylcholine by the parasite therefore justifies the measurement of this molecule as an indication of active infection, possibly reflecting total worm burdens. By comparing metabolically labelled E/S from male and female worms, several molecules of low mol. wt, namely 10,000, 13,000, 14,000 and 22,000, together with high mol. wt components of above 12,000 were found to be female specific. Tracing the origin of the E/S products, several molecules were also found to be associated with the surface. Among these, there are at least two glycoproteins, 29,000 and 51,000 of which the 29,000 molecule is a major surface protein. The immunogenicity of the E/S was examined and antigenic cross-reactivity was found with sera from most filarial infections but not with non-filarial nematodiases such as hookworm or Trichinella. However, two molecules of low mol. wt, 15,000 and 19,000, were not recognized by anti-Onchocerca sera and appeared to be potential Brugia-specific diagnostic molecules. Possible functional roles of the adult E/S products were examined but we could find no evidence of protease activity in the E/S or glutathione S-transferase activity in either the E/S or in whole somatic extract.
While determining the 5' ends of C. elegans actin mRNAs, we have discovered a 22 nucleotide spliced leader sequence. The leader sequence is found on mRNA from three of the four nematode actin genes. The leader also appears to be present on some, but not all, nonactin mRNAs. The actin mRNA leader sequence is identical to the first 22 nucleotides of a novel 100 nucleotide RNA transcribed adjacent, and in the opposite orientation, to the 5S ribosomal gene. The evidence suggests that the actin mRNA leader sequence is acquired from this novel nucleotide transcript by an intermolecular trans-splicing mechanism.
Using air-dried preparations of the testis and ovary, karyotypes were analyzed and compared to each other in two species of filarial parasites, Brugia pahangi and B. malayi. Both species had a diploid number of 10 chromosomes and were karyotypically very similar. C-banding analyses disclosed that the sex-determining mechanism of these species was of the XY-XX type, where the X chromosome was the largest, and the Y chromosome was of medium-size.
Employing isoelectric focusing on immobilized pH gradients followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) we have obtained a map of C. elegans proteins, from a mixed culture containing all developmental stages, presenting over 2000 spots within the window of isoelectric points (pI) 3.5-9 and a molecular mass of 10-200 kDa. Edman microsequencing yielded successful results in 12 out of 24 analyzed spots. All but one of the N-terminal sequences retrieved C. elegans sequences in cosmid and/or expressed sequence tag clones. Structurally related protein sequences found in data banks included enzymes in energy metabolism (cytochrome oxydase, ATP synthase, enolase), a fatty acid-binding protein, a translationally controlled tumor protein, an unknown C. elegans protein, an acidic ribosomal protein, a titin-like protein, a G-protein beta chain, cyclophilin, and cathepsin D. Experimental determination of N-termini allowed us to define sites of signal cleavage providing further information on the physiological role of the newly found C. elegans proteins. This report demonstrates the possibility of two-dimensional gel electrophoresis and Edman microsequencing in the elucidation of C. elegans proteome.
Experimental introduction of RNA into cells can be used in certain biological systems to interfere with the function of an endogenous gene. Such effects have been proposed to result from a simple antisense mechanism that depends on hybridization between the injected RNA and endogenous messenger RNA transcripts. RNA interference has been used in the nematode Caenorhabditis elegans to manipulate gene expression. Here we investigate the requirements for structure and delivery of the interfering RNA. To our surprise, we found that double-stranded RNA was substantially more effective at producing interference than was either strand individually. After injection into adult animals, purified single strands had at most a modest effect, whereas double-stranded mixtures caused potent and specific interference. The effects of this interference were evident in both the injected animals and their progeny. Only a few molecules of injected double-stranded RNA were required per affected cell, arguing against stochiometric interference with endogenous mRNA and suggesting that there could be a catalytic or amplification component in the interference process.
A genetic interference phenomenon in the nematode Caenorhabditis elegans
has been described in which expression of an individual gene can be
specifically reduced by microinjecting a corresponding fragment of
double-stranded (ds) RNA. One striking feature of this process is a
spreading effect: interference in a broad region of the animal is
observed following the injection of dsRNA into the extracellular body
cavity. Here we show that C. elegans can respond in a gene-specific
manner to dsRNA encountered in the environment. C. elegans normally feed
on bacteria, ingesting and grinding them in the pharynx and subsequently
absorbing bacterial contents in the gut. We find that Escherichia coli
bacteria expressing dsRNAs can confer specific interference effects on
the nematode larvae that feed on them.
Studies in microbial evolution have focused on the origin and vertical transmission of genetic variation within populations experiencing limited recombination. Genomic analyses have highlighted the importance of horizontal genetic transfer in shaping the composition of microbial genomes, providing novel metabolic capabilities, and catalyzing the diversification of bacterial lineages.
Hookworms are gut-dwelling, blood-feeding nematodes that infect hundreds of millions of people, particularly in the tropics. As part of a program aiming to define novel drug targets and vaccine candidates for human parasitic nematodes, genes expressed in adults of the human hookworm Necator americanus were surveyed by the expressed sequence tag approach. In total 161 new hookworm genes were identified. For the majority of these, a function could be assigned by homology. The dataset includes proteases, protease inhibitors, a lipid binding protein, C-type lectins, an anti-bacterial factor, globins and other genes of interest from a drug or vaccine development viewpoint. Three different classes of small, secreted proteins were identified that may be involved in the host-parasite interaction, including potential potassium channel blocking peptides. One third of the genes were novel. These included highly expressed, secreted (glyco)proteins which may be part of the excretory-secretory products of these important pathogens. Of particular interest are a family of 9 genes with similarity to the immunomodulatory protein, neutrophil inhibitory factor, that may play a role in establishing an immunocompromised niche for this successful parasite.
Chromatin diminution in Parascaris univalens and Ascaris suum undoubtedly represents an interesting case of developmentally programmed DNA rearrangement in higher eukaryotes. It is a complex mechanism involving chromosomal breakage, new telomere addition and DNA degradation, and occurs in all presomatic cells. The process is rather specific with respect to its developmental timing and the chromosomal regions that are eliminated. The functional significance of chromatin diminution still remains an enigma. The fact, however, that single-copy, protein-coding genes are contained in the eliminated DNA demonstrates that in P. univalens and A. suum, there is a qualitative difference between germ-line and somatic genomes, and suggests that chromatin diminution may be used as a "throw-away" approach to gene regulation. We present a hypothesis as to how, during evolution, a partial genome duplication might have been linked to the process of chromatin diminution, in order to provide a selective advantage to parasitic DNA-eliminating nematodes.
Unlike eukaryotes, which evolve principally through the modification of existing genetic information, bacteria have obtained a significant proportion of their genetic diversity through the acquisition of sequences from distantly related organisms. Horizontal gene transfer produces extremely dynamic genomes in which substantial amounts of DNA are introduced into and deleted from the chromosome. These lateral transfers have effectively changed the ecological and pathogenic character of bacterial species.
Complete genomic sequence is known for two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and it will soon be known for humans. However, biological function has been assigned to only a small proportion of the predicted genes in any animal. Here we have used RNA-mediated interference (RNAi) to target nearly 90% of predicted genes on C. elegans chromosome I by feeding worms with bacteria that express double-stranded RNA. We have assigned function to 13.9% of the genes analysed, increasing the number of sequenced genes with known phenotypes on chromosome I from 70 to 378. Although most genes with sterile or embryonic lethal RNAi phenotypes are involved in basal cell metabolism, many genes giving post-embryonic phenotypes have conserved sequences but unknown function. In addition, conserved genes are significantly more likely to have an RNAi phenotype than are genes with no conservation. We have constructed a reusable library of bacterial clones that will permit unlimited RNAi screens in the future; this should help develop a more complete view of the relationships between the genome, gene function and the environment.
Genome-wide analysis of gene function is essential for the post-genome era, and development of efficient and economical technology suitable for it has been in demand. Here we report a large-scale inactivation of the expressed genes in the nematode Caenorhabditis elegans. For this purpose, we have established a high-throughput "RNAi-by-soaking" methodology by modifying the conventional RNAi method [1, 2]. A set of tag-sequenced, nonredundant cDNAs corresponding to approximately 10,000 genes [3] (representing half of the predicted genes [4]) was used for the systematic RNAi analysis. We have processed approximately 2500 genes to date. In development, 27% of them showed detectable phenotypes, such as embryonic lethality, post-embryonic lethality, sterility, and morphological abnormality. Of these, we analyzed the phenotypes of F1 sterility in detail, and we have identified 24 genes that might play important roles in germline development. Combined with the ongoing analysis of expression patterns of these cDNAs [3, 5], the functional information obtained in this work will provide a starting point for the further analysis of each gene. Another finding from this screening is that the incidence of essential genes is significantly lower in the X chromosome than in the autosomes.
Horizontal gene transfer (HGT) has long been recognized as a principal force in the evolution of genomes. Genome sequences of Archaea and Bacteria have revealed the existence of genes whose similarity to loci in distantly related organisms is explained most parsimoniously by HGT events. In most multicellular organisms, such genetic fixation can occur only in the germ line. Therefore, it is notable that the publication of the human genome reports 113 incidents of direct HGT between bacteria and vertebrates, without any apparent occurrence in evolutionary intermediates, that is, non-vertebrate eukaryotes. Phylogenetic analysis arguably provides the most objective approach for determining the occurrence and directionality of HGT. Here we report a phylogenetic analysis of 28 proposed HGT genes, whose presence in the human genome had been confirmed by polymerase chain reaction (PCR). The results indicate that most putative HGT genes are present in more anciently derived eukaryotes (many such sequences available in non-vertebrate EST databases) and can be explained in terms of descent through common ancestry. They are, therefore, unlikely to be examples of direct HGT from bacteria to vertebrates.
We have assembled data from Caenorhabditis elegans DNA microarray experiments involving many growth conditions, developmental stages, and varieties of mutants. Co-regulated
genes were grouped together and visualized in a three-dimensional expression map that displays correlations of gene expression
profiles as distances in two dimensions and gene density in the third dimension. The gene expression map can be used as a
gene discovery tool to identify genes that are co-regulated with known sets of genes (such as heat shock, growth control genes,
germ line genes, and so forth) or to uncover previously unknown genetic functions (such as genomic instability in males and
sperm caused by specific transposons).
To advance and facilitate molecular studies of Brugia malayi, one of the causative agents of human lymphatic filariasis, an expressed sequence tag (EST)-based gene discovery programme has been carried out. Over 22,000 ESTs have been produced and deposited in the public databases by a consortium of laboratories from endemic and non-endemic countries. The ESTs have been analysed using custom informatic tools to reveal patterns of individual gene expression that may point to potential targets for future research on anti-filarial drugs and vaccines. Many genes first discovered as ESTs are now being analysed by researchers for immunodiagnostic, vaccine and drug target potential. Building on the success of the B. malayi EST programme, significant EST datasets are being generated for a number of other major parasites of humans and domesticated animals, and model parasitic species.
We compared the genome of the nematode Caenorhabditis elegans to 13% of that of Caenorhabditis briggsae , identifying 252 conserved segments along their chromosomes. We detected 517 chromosomal rearrangements, with the ratio of translocations to inversions to transpositions being ∼1:1:2. We estimate that the species diverged 50–120 million years ago, and that since then there have been 4030 rearrangements between their whole genomes. Our estimate of the rearrangement rate, 0.4–1.0 chromosomal breakages/Mb per Myr, is at least four times that of Drosophila , which was previously reported to be the fastest rate among eukaryotes. The breakpoints of translocations are strongly associated with dispersed repeats and gene family members in the C. elegans genome.
[The following institution kindly provided reagents, samples or unpublished information as indicated in the paper: Genome Sequencing Center, Washington University School of Medicine, St. Louis.]
RNA interference is of value in determining gene function in many organisms. Plant parasitic nematodes are refractory to microinjection as a means of introducing RNA and do not show any oral uptake until they are within plants. We have used octopamine to stimulate uptake by preparasitic second stage juveniles of two cyst nematodes, Heterodera glycines and Globodera pallida. This new technique was used to facilitate uptake of double stranded RNA (dsRNA) together with fluoroscein isothiocyanate as a visual marker. Targeting cysteine proteinases did not reduce the number of parasites but caused a shift from the normal female/male ratio of 3:1 to 1:1 by 14 days postinfection (dpi). Exposure of H. glycines to dsRNA corresponding to a newly characterized protein with homology to C-type lectins did not affect sexual fate, but 41% fewer parasites were recovered from the plants. As expected, treatment with dsRNA corresponding to the major sperm protein (MSP) had no effect on either parasite development or sexual fate over 14 days. Northern analysis showed lower transcript abundance for the two targeted mRNAs that occur in J2, plus a later inhibition for MSP transcripts when males developed sperm at 15 dpi. These findings establish a procedure for RNAi of plant parasitic nematodes.
HOX GENES ARE IMPORTANT: their central role in anterior-posterior patterning provides a framework for molecular comparison of animal body plan evolution. The nematode Caenorhabditis elegans stands out as having a greatly reduced Hox gene complement. To address this, orthologs of C. elegans Hox genes were identified in six species from across the Nematoda, and they show that rapid homeodomain sequence evolution is a general feature of nematode Hox genes. Some nematodes express additional Hox genes belonging to orthology groups that are absent from C. elegans but present in other bilaterian animals. Analysis of the genomic environment of a newly identified Brugia malayi Hox6-8 ortholog (Bm-ant-1) revealed that it lay downstream of the Bm-egl-5 Hox gene and that their homeodomain exons are alternately cis spliced to the same 5' exon. This organization may represent an intermediate state in Hox gene loss via redundancy. The Hox clusters of nematodes are the product of a dynamic mix of gene loss and rapid sequence evolution, with the most derived state observed in the model C. elegans.
