Table 10 - uploaded by Murray P Cox
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Fungi of family Clavicipitaceae serve as models for evolution on the symbiotic continuum from pathogenic to mutualistic. Clavicipitaceous fungi associate with plants, invertebrates, and other fungi. Most plant-associated Clavicipitaceae systemically colonize shoots, but the fungal fruiting structures are localized to inflorescences, florets, buds,...
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... Periglandula is a recently discovered fungal genus that belongs to the Clavicipitaceae in Hypocreales [1]. The family Clavicipitaceae is known to include epibiotic, endophytic, and parasitic fungi associated with monocotyledonous plants in the families Cyperaceae, Poaceae, and Juncaceae [2][3][4]. One distinguishable character of the fungi in this family is their role in ergoline (syn. ...
Periglandula is a fungal genus that is associated with plants in the family Convolvulaceae. They produce medicinally important constituents called ergot alkaloids, which are stored in their host plants. Previously, the fungi were reported to mainly interact with young leaves and seeds of Convolvulaceae species. However, knowledge about how ergot alkaloid-producing fungi interact with their host plants is still lacking. Therefore, we investigated the interaction of Periglandula fungus with different plant parts of Ipomoea asarifolia, using molecular, histochemical, anatomical and micromorphological techniques. Our findings confirm the presence of Periglandula ipomoeae on six out of the eight plant parts examined (young folded leaves, mature leaves, flower buds, mature flowers, young seeds and mature seeds). The fungus was mostly distributed along external plant surfaces, and particularly on areas that were relatively unexposed. Our results suggest that the density of fungal mycelium varies depending on glandular trichome density and the growth stage of the host plant. Detection of the fungus in the flowers of its host plant, for the first time, fills a missing link in understanding how vertical transmission of Periglandula species occurs.
... Non-redundant fungal protein datasets (Table S1) [79][80][81][82][83], the Alternaria genome database (https:// mycocosm. jgi. ...
Plant diseases caused by fungal pathogens are typically initiated by molecular interactions between ‘effector’ molecules released by a pathogen and receptor molecules on or within the plant host cell. In many cases these effector-receptor interactions directly determine host resistance or susceptibility. The search for fungal effector proteins is a developing area in fungal-plant pathology, with more than 165 distinct confirmed fungal effector proteins in the public domain. For a small number of these, novel effectors can be rapidly discovered across multiple fungal species through the identification of known effector homologues. However, many have no detectable homology by standard sequence-based search methods. This study employs a novel comparison method (RemEff) that is capable of identifying protein families with greater sensitivity than traditional homology-inference methods, leveraging a growing pool of confirmed fungal effector data to enable the prediction of novel fungal effector candidates by protein family association. Resources relating to the RemEff method and data used in this study are available from https://figshare.com/projects/Effector_protein_remote_homology/87965 .
... The characteristics of this sample have been studied in detail (Tanaka, 2009(Tanaka, , 2010. The culture isolate (MAFF 241224) from the sample has been whole-genome sequenced and used in some studies (Schardl et al., 2013;Schardl et al., 2014). Additionally, ITS sequence analysis showed that there was almost no intraspecific variation among A. take in Japan ( Supplementary Fig. S2). ...
The genus Aciculosporium (Clavicipitaceae, Hypocreales, Ascomycota) was established in 1908 for A. take, which is the causal fungus of witches’ broom of bamboo. Although the original description was valid at that time, a type specimen for A. take has not been designated. To standardize the use of this genus and species name, a neotypification and reference specimen of A. take is are proposed. Multilocus phylogenetic analyses based on DNA sequences from 28S rDNA, TEF, Tub2, Mcm7, and RPB2 revealed that A. sasicola is from a different lineage to A. take, and other material specimens from wavyleaf basket grass (Oplismenus undulatifolius) represent a distinct species proposed here as Aciculosporium oplismeni sp. nov. Chemical analysis using mass spectrometry and nuclear magnetic resonance spectroscopy, etc. showed that A. take produces four proline-containing cyclic dipeptides, which are moieties of ergot alkaloids, . although However, ergot alkaloids, lolines, peramine, indole-diterpenes, and lolitrem were not detected in the culture solvent. The presentis study offers clarification of the lineage and morphology of this genus.
... Ophiocordycipitaceae are composed of species mostly known as parasitic fungi of insects. 51 This family was previously noted as sister taxa of Clavicipitaceae, 52 a major group of fungi consists of plant parasites and endophytes of grasses. 53 To the best of our knowledge, our study is the first to significantly report high occurence of Ophiocordycipitaceae in roots implying that this group of fungal taxa has the potential to be plant pathogens or symbionts similar to Clavicipitaceae. ...
Cycads have developed a complex root system categorized either as normal or coralloid roots. Past literatures revealed that a great diversity of key microbes is associated with these roots. This recent study aims to comprehensively determine the diversity and community structure of bacteria and fungi associated with the roots of two Cycas spp. endemic to China, Cycas debaoensis Zhong & Chen and Cycas fairylakea D.Y. Wang using high-throughput amplicon sequencing of the full-length 16S rRNA (V1-V9 hypervariable) and short fragment ITS region. The total DNA from 12 root samples were extracted, amplified, sequenced, and analyzed. Resulting sequences were clustered into 61 bacteria and 2128 fungal OTUs. Analysis of community structure revealed that the coralloid roots were dominated mostly by the nitrogen-fixer Nostocaceae but also contain other non-diazotrophic bacteria. The sequencing of entire 16S rRNA gene identified four different strains of cyanobacteria under the heterocystous genera Nostoc and Desmonostoc. Meanwhile, the top bacterial families in normal roots were Xanthobacteraceae, Burkholderiaceae, and Bacillaceae. Moreover, a diverse fungal community was also found in the roots of cycads and the predominating families were Ophiocordycipitaceae, Nectriaceae, Bionectriaceae, and Trichocomaceae. Our results demonstrated that bacterial diversity in normal roots of C. fairylakea is higher in richness and abundance than C. debaoensis. On the other hand, a slight difference, albeit insignificant, was noted for the diversity of fungi among root types and host species as the number of shared taxa is relatively high (67%). Our results suggested that diverse microbes are present in roots of cycads which potentially interact together to support cycads survival. Our study provided additional knowledge on the microbial diversity and composition in cycads and thus expanding our current knowledge on cycad-microbe association. Our study also considered the possible impact of ex situ conservation on cyanobiont community of cycads.
... Atkinsonella hypoxylon is an ascomycete in the tribe Balansieae and is related to grass associated endophytic fungi that can have large ecological and economic impacts because of the toxic effects of fungal produced alkaloids on grazing animals and insects (Bacon, Porter, Robbins, & Luttrell, 1977;Schardl et al., 2014). The interactions of these fungi with plant hosts can range from pathogenic to highly mutualistic. ...
... The interactions of these fungi with plant hosts can range from pathogenic to highly mutualistic. Some species are endobiotic, exhibiting growth in the intercellular spaces, while others such as A. hypoxyon grow primarily on the plant surface and spaces between plant tissue layers and are considered epibiotic (Schardl et al., 2014). Numerous grass host exhibiting biotic and abiotic stress resistances have been associated with endophyte infection including drought tolerance, nematode resistance, enhanced growth, disease resistance, insect resistance, antiherbivory resistance, and tolerance of heat and low-light intensity (Kuldau & Bacon, 2008). ...
... Since the completion of these studies the ITS regions of fungal ribosomal DNA (rDNA) have become widely used to distinguish fungal species and isolates within a species (Martin & Rygiewicz, 2005;White Jr et al., 1990). Additionally, genome sequences of several plant associated clavicipitaceae fungi including A. hypoxylon have been completed (Schardl et al., 2014) making reliable species-specific nonfunctional DNA-based markers such as SSRs available for genetic diversity assessments. ...
Poverty oat grass [Danthonia spicata (L.) P. Beauv. ex Roem. & Schult.] is a perennial bunch‐type grass native to North America. Poverty oat grass is often present in managed turfgrass areas of the United States where cool‐season grasses are adapted and has potential for development as a seeded low‐input turfgrass option. Naturally occurring poverty oat grass plants occasionally exhibit choke on the flowering stems because of a proliferation of fungal hyphae by the ascomycete Atkinsonella hypoxylon (Peck) Diehl. (family Clavicipitaceae). Twenty‐five A. hypoxylon isolates were cultured from choke‐exhibiting poverty oat grass plants collected from five different populations. DNA variation was evaluated at the 5.8S ribosomal ribonucleic acid (rRNA) internal transcribed spacer (ITS) first (ITS‐1) and second (ITS‐2) regions and 10 simple sequence repeat (SSR) loci. Five single nucleotide polymorphisms (SNPs) in the ITS‐1 region and an addition–deletion in the ITS‐2 region identified two isolate groups present in four of the five populations. The 10 SSR loci exhibited 28 scorable alleles and support the two groupings with variation appearing as random mutations and high linkage disequilibrium providing no evidence for sexual recombination within or between the two identified groups.
... Spatafora et al. (2007) demonstrated the evidences of host switching within the hypocrealean families. Therefore, some of the most recently emerged grass endophytes, such as Balansia, Claviceps and Epichloe, group alongwith well-known entomopathogens in the family Clavicipitaceae, such as Metarhizium, Hypocrella and Aschersonia (Schardl et al. 2014). The Clavicipitaceae can be characterised by either lilac, pallid, or strongly pigmented green, yellow or occasionally red stromata (Sung et al. 2007a). ...
Soil is a reservoir of numerous microorganisms critical for the sustainable functioning of natural and managed ecosystems. Entomopathogenic bacteria and fungi are natural enemies of pest-insects, whose utility in agroecosystems has been studied since decades. These entomopathogens spend significant time period in soil, either as saprotrophs, active conidia, resting spores or dormant endospores. In this chapter, we focus on: (a) the different bacterial and fungal species exhibiting entomopathogenicity; (b) insect-hosts and pathology; and (c) their survival in soil. Studying these aspects is of the utmost importance in fully exploiting the potential of these microorganisms. The bacterium Bacillus thuringiensis and fungi from the orders Entomophthorales and Hypocreales are discussed in more details, pertaining to the amount of literature and their dominance in the microbial biopesticide industry.
... The genes encoding each class of alkaloid have been identified, and for most genes, the relative step they encode within each biosynthetic pathway is known (9,14,15). Peramine synthesis is encoded by a single gene, perA (16), whereas the ergot alkaloids (EAS), indole-diterpenes (IDT), and lolines (LOL) each have multiple genes associated in gene clusters (9,17). Much of the alkaloid diversity present in Epichloë is due to presence or absence of the alkaloid biosynthesis genes, which makes it possible to predict synthesized alkaloids based on detection of genes encoding key pathway steps (10,12,13,18,19). ...
Severe problems of livestock intoxication from Epichloë -infected forage grasses have been reported from New Zealand, Australia, and the United States, but much less frequently from Europe, and particularly not from Germany. Nevertheless, it is important to monitor infection rates and alkaloids of grasses with Epichloë fungi to estimate possible intoxication risks. Most studies focus on agricultural grass species like Lolium perenne and Festuca arundinacea , but other cool-season grass species can also be infected. We show that in Germany, infection rates and alkaloids differ between grass species and that some of the alkaloids can be toxic to livestock. Changes in grassland management due to changing climate, especially with a shift toward grasslands dominated with Epichloë -infected species such as Lolium perenne , may result in greater numbers of intoxicated livestock in the near future. We therefore suggest regular monitoring of grass species for infections and alkaloids and call for maintaining heterogenous grasslands for livestock.
... The sexual species of genus Epichlo€ e are characterized based on their morphology, phylogeny and mating compatibility. As Epichlo€ e species are heterothallic, gametes carrying the opposite mating type are required for cell fusion and successful mating ( Schardl et al., 2014;White and Bultman, 1987). The heterothallic mating system is controlled by a single genetic locus discriminating two mating types (bipolar), which enforces mating between distinct haploid genotypes and has fostered implementation of a biological species concept ( . ...
Mate recognition mechanisms resulting in assortative mating constitute an effective reproductive barrier that may promote sexual isolation and speciation. While such mechanisms are widely documented for animals and plants, they remain poorly studied in fungi. We used two interfertile species of Epichloë (Clavicipitaceae, Ascomycota), E. typhina and E. clarkii, which are host-specific endophytes of two sympatrically occurring grasses. The life cycle of these obligatory outcrossing fungi entails dispersal of gametes by a fly vector among external fungal structures (stromata). To test for assortative mating, we mimicked the natural fertilization process by applying mixtures of spermatia from both species and examined their reproductive success. Our trials revealed that fertilization is non-random and preferentially takes place between conspecific mating partners, which is indicative of assortative mating. Additionally, the viability of hybrid and non-hybrid ascospore offspring was assessed. Germination rates were lower in E. clarkii than in E. typhina and were reduced in ascospore progeny from treatments with high proportions of heterospecific spermatia. The preferential mating between conspecific genotypes and reduced hybrid viability represent important reproductive barriers that have not been documented before in Epichloë. Insights from fungal systems will deepen our understanding of the evolutionary mechanisms leading to reproductive isolation and speciation.
... Some studies have indicated co-divergence of endophyte and grass species and also some host species transfers (Jackson, 2004;Schardl et al., 2005Schardl et al., , 2008. The phylogenetic analysis of Schardl et al. (2008) on Epichloë species and their pooid grass hosts indicated host-endophyte co-divergence, and since then, an explosion of genome sequences for Epichloë species and related Clavicipitaceae has allowed more detailed phylogenetic analysis (Leuchtmann et al., 2014;Schardl et al., 2014;Chen et al., 2015). Strikingly, the deepest split identified in the Clavicipitaceae phylogenetic tree is to a clade of two species symbiotic with Achnatherum species belonging to the Stipeae tribe of grasses that itself splits early from most of the other pooid tribes. ...
The grass family Poaceae, with 11 500 species, is economically, ecologically, and evolutionarily one of the most successful species‐rich groups. Because of this, it represents a model family for the study of speciose taxa. Routine DNA sequencing has accelerated progress in the evolutionary study of grasses, leading to more stable taxonomic classifications; prototype DNA barcoding systems; and a better understanding of their biogeography, physiology, and ecology. This article examines the remaining challenges in the evolutionary and taxonomic study of grasses. These include assessing the monophyly of genera, improving species‐level phylogenetics, establishing a comprehensive DNA barcoding system, understanding diversification in geological time and geographical/ecological space, understanding morphological and physiological trait evolution (such as C4 photosynthesis, polyploidy, and spikelet morphology), and understanding co‐evolution with other organisms such as herbivores and endophytic/mycorrhizal microbes.
... The ecology and physiology of Epichloë endophytes are relatively wellunderstood, but few studies have investigated the evolution of Epichloë species using molecular methods (Song et al., 2016a). Here, we identified alkaloids-coding genes and analyzed codon usage bias in seven asexual Epichloë species and their alkaloidscoding genes with available coding sequences (CDSs) data (Schardl et al., 2013aSchardl et al., , 2014Pan, 2014;Chen et al., 2015): Epichloë amarillans E4668, Epichloë bromicola AL0434, Epichloë festucae E894, Epichloë glyceriae E277, Epichloë sylvatica E7368, Epichloë typhina E8 and Epichloë typhina subsp. poae E5819. ...
... The CDSs of seven Epichloë species were obtained from genome projects at University of Kentucky (www.endophyte.uky.edu/) (Schardl et al., 2013aSchardl et al., , 2014Pan, 2014;Chen et al., 2015). The Epichloë species that were used in this study were Epichloë amarillans E4668, Epichloë bromicola AL0434, Epichloë festucae E894, Epichloë glyceriae E277, Epichloë sylvatica E7368, Epichloë typhina E8, and Epichloë typhina subsp. ...
Codon usage bias plays an important role in shaping genomes and genes in unicellular species and multicellular species. Here, we first analyzed codon usage bias in seven Epichloë species and their peramine-coding genes. Our results showed that both natural selection and mutation pressure played a role in forming codon usage bias in seven Epichloë species. All seven Epichloë species contained a peramine-coding gene cluster. Interestingly, codon usage bias of peramine-coding genes were not affected by natural selection or mutation pressure. There were 13 codons more frequently found in Epichloë genome sequences, peramine-coding gene clusters and orthologous peramine-coding genes, all of which had a bias to end with a C nucleotide. In the seven genomes analyzed, codon usage was biased in highly expressed coding sequences (CDSs) with shorter length and higher GC content. Genes in the peramine-coding gene cluster had higher GC content at the third nucleotide position of the codon, and highly expressed genes had higher GC content at the second position. In orthologous peramine-coding CDSs, high expression level was not significantly correlated with CDS length and GC content. Analysis of selection pressure identified that the genes orthologous to peramine genes were under purifying selection. There were no differences in codon usage bias and selection pressure between peramine product genes and non-functional peramine product genes. Our results provide insights into understanding codon evolution in Epichloë species.
