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Statistical summary of cDNA sequences of Pitcairnia albiflos and Pitcairnia staminea obtained for each sequenced tissue type
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We present the leaf and floral transcriptomes of two hybridizing bromeliad species that differ in their major pollinator systems. Here we identified candidate genes responsible for pollinator attraction and reproductive isolation in these two species. We searched for candidate genes involved in floral traits, such as color. Approximately 34 Gbp of...
Contexts in source publication
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... this study, we sequenced ~34 Gbp of data and 424 506 914 raw sequencing reads of good quality (Phred >20) from four normalized cDNA libraries (Table 1). The four libraries were prepared using RNA from flowers and leaves of two bromeliad species. ...
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... purging contigs below 300 bp, the de novo assembler Trinity ( Grabherr et al. 2011) produced 263 955 contigs that clus- tered into 110 977 nonredundant transcripts (unigenes). The mean size of the unigenes was 1085 bp (Table 1). ...
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... the cellular function category, the most abundant classes were cell part and organelle, whereas binding and cat- alytic activities were the classes with the highest number of assigned unigenes in the molecular function category. Table S1 (Supporting information) shows the GO classifi- cation of the assembled sequences at all levels per species and tissue. ...
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... sequences and primers designed. Table S1_The GOs classification all leaves. Table S2_Keeg pathways. ...
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Citations
... Also, the higher past Plathymenia reticulata: Muniz et al., 2022). In fact, interspecific gene flow can contribute to the pool of standing genetic variation and thus to diversification of species (Brawand et al., 2015;Seehausen, 2004) and showed to have an important role in diversification and adaptive radiation of bromeliads (Lexer et al., 2016;Loiseau et al., 2021;Palma-Silva, Ferro, et al., 2016;Palma-Silva, Leal, et al., 2016). ...
The study of mechanisms that generate new species is considered fundamental for broad areas of ecology and evolution. Speciation is a continuous process in which reproductive isolation is established, and it is of fundamental importance to understand the origins of the adaptations that contribute to this process. Hybrid zones are considered natural laboratories for the study of speciation and represent ideal systems for such studies. Here, we investigated genomic differentiation between hybridizing Neotropical species Pitcairnia staminea (G. Lodd.) and P. albiflos (Herb.). Using thousands of SNPs genotyped through RAD‐seq, we estimate effective population sizes, interspecific gene flow, as well as time of divergence between these two sister species and identify candidate genomic regions for positive selection that may be related to reproductive isolation. We selected different scenarios of speciation and tested them by using approximate Bayesian computation (ABC); we found evidence of divergence with gradual reduction in gene flow between these species over time, compatible with the hypothesis of speciation with gene flow between these Pitcairnia species. The parameter estimates obtained through ABC suggested that the effective population size of P. albiflos was around three times larger than that of P. staminea. Our divergence date estimates showed that these two species diverged during the Pliocene (4.7 Mya; CI = 1.3–8.5 Mya), which has likely allowed this species to accumulate genome‐wide differences. We also detected a total of 17 of 4165 loci which showed signatures of selection with high genetic differentiation (FST > 0.85), 12 of these loci were annotated in de novo assembled transcriptomes of both species, and 4 candidate genes were identified to be putatively involved in reproductive isolation. These four candidate genes were previously associated with the function of pollen development, pollen tube germination and orientation, abiotic stress, and flower scent in plants, suggesting an interplay between pre‐ and postpollination barriers in the evolution of reproductive isolation between such species. Graphic representation of the simulated scenarios of divergence between Pitcairnia albiflos and P. staminea tested using approximate Bayesian computation (ABC) framework. By contrasting different scenarios of speciation using ABC, we found evidence of divergence with gradual reduction in gene flow between these species over time, compatible with the hypothesis of speciation with gene flow between these Neotropical plant species.
... Transcriptome analyses have helped to reveal the genetic basis of antho-cyanin polymorphism in Parrya nudicaulis (Butler et al., 2014). These approach has also been useful to identify candidate genes responsible for pollinator attraction and reproductive isolation in hybridising bromeliad species (Palma-Silva et al., 2016), as well as, to detect the potential genes involved in the terpenoid biosynthesis pathway and terpene diversity in Eugenia uniflora L. (Guzman et al., 2014). ...
Psidium cattleyanum Sabine is an Atlantic Forest native species that presents some populations with red fruits and others with yellow fruits. This variation in fruit pigmentation in this species is an intriguing character that could be related to species evolution but still needs to be further explored. Our goal was to provide genomic information for these morphotypes to understand the molecular mechanisms of differences in fruit colour in this species. In this study, we performed a comparative transcriptome analysis of red and yellow morphotypes of P. cattleyanum, considering two stages of fruit ripening. The transcriptomic analysis performed encompassing leaves, unripe and ripe fruits, in triplicate for each morphotype. The transcriptome consensus from each morphotype showed 301,058 and 298,310 contigs from plants with yellow and red fruits, respectively. The differential expression revealed important genes that were involved in anthocyanins biosynthesis, such as the anthocyanidin synthase (ANS) and UDP-glucose:flavonoid-o-glucosyltransferase (UFGT) that were differentially regulated during fruit ripening. This study reveals stimulating data for the understanding of the pathways and mechanisms involved in the maturation and colouring of P. cattleyanum fruits and suggests that the ANS and UFGT genes are key factors involved in the synthase and pigmentation accumulation in red fruits.
... Comparative genomics (transcriptomics) involves characterizing the differences in gene expression, and it is commonly used in studies of adaptive evolution or evolutionary developmental biology [12][13][14]. Moreover, transcriptomic data are widely used to study nonmodel organisms [15][16][17]. In this study, we generated and annotated de novo transcriptome assemblies for both A. nidus and A. komarovii. ...
Epiphytic ferns have been found to flourish after angiosperms dominated forest communities, and they play important roles in rainforest canopies. How do epiphytic ferns adapt to tropical rainforest canopy habitats? At present, we know little about the molecular mechanism underlying this adaptation. Asplenium nidus is a well-known epiphytic fern that is closely related to the terrestrial species Asplenium komarovii . Here, RNA-seq and comparative transcriptomic analyses were performed to explore the underlying basis of the adaptation of A. nidus to extreme environments. A total of 44.04 and 44.57 Mb clean reads were obtained from A. nidus and A. komarovii , respectively, and they were assembled into 89,741 and 77,912 unigenes. Functional annotation showed that 52,305 (58.28% of the total genes for A. nidus ) and 45,938 (58.96% of the total genes for A. komarovii ) unigenes were annotated in public databases. Genes involved in stress responses and photosynthesis were found to have undergone positive selection in A. nidus . Compared to A. komarovii , transcription factors related to stress response, leaf development, and root development were found to be considerably expanded in A. nidus , especially in the ANR1 subclade of MADS-box family genes which played roles in lateral root development. This study improves our understanding of the adaptation of A. nidus to epiphytic habitats by forming unique strategies.
... smooth cayenne [10]. The Bromelioideae species Aechmea fasciata [11] and two Pitcairnioideae species, Pitcairnia albiflos and P. staminea [12], also had their transcriptome analyzed. For the ornamental bromeliad A. fasciata, shoot tip tissues of juvenile and adult plants were harvested to compare flower development induced by ethylene treatment, while mature flowers and leaves of Pitcairnia were compared to comprehend the speciation process between these two species. ...
Guzmania monostachia is an epiphytic tank bromeliad that displays the inducible CAM photosynthesis under stressful conditions and had the highest stomata density in the leaf apex, while the base portion has the highest density of trichomes, which are specialized structures used to acquire water and nutrients from the tank solution. In order to correlate the genetic factors behind these morpho-physiological characteristics along the leaf blade of G. monostachia, a comparative transcriptome analysis was performed to identify the functional enriched pathways and unigenes that could play a role in the apical, middle and basal leaf portions. A total of 653 million reads were used for de novo transcriptome assembly, resulting in 48,051 annotated unigenes. Analysis of differentially expressed genes (DEGs) among distinct leaf regions revealed that 806 DEGs were upregulated in the apex compared to the middle portion, while 9685 DEGs were upregulated in the apex and 9784 DEGs were upregulated in the middle portions compared to the base. Our outcomes correlated some DEGs and identified unigenes with their physiological functions, mainly suggesting that the leaf apex was related to the regulation of stomatal movement, production of chlorophyll, cellular response to stress, and H2O2 catabolic process. In contrast, the middle portion showed DEGs associated with the transport of amino acids. Furthermore, DEGs from the leaf base were mainly correlated with responses to nutrients and nitrogen compounds, regulation of potassium ion import, response to water deprivation, and trichome branching, indicating that, at least in part, this leaf portion can replace some of the root functions of terrestrial plants. Therefore, possibly candidate unigenes and enriched pathways presented here could be prospected in future experimental work, opening new possibilities to bioengineer non-inducible CAM plants and/or improve the fertilization use efficiency by increasing leaf nutrient acquisition of crop plants.
... More genomes need to be sequenced for both gastropod and non-gastropod molluscs, since the higher the number of genomes, the greater the inferential power that these data can provide. About half of the omics publications on gastropods are transcriptome datasets since these are relatively easy and inexpensive to generate, but without a reference genome their interpretation may be of lower quality due to sequencing error rate and polymorphism [275][276][277]. An increase in available genomic data will also facilitate more proteomic investigations. ...
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
... The number of non-redundant contigs exceeded the 23,669 to 31,809 contigs observed in Pitcairnia spp. (Palma-Silva et al., 2016) and the 41,052 contigs of A. comosus var. bracteatus (Ma et al., 2015), but was smaller than the 86,609 contigs reported in Aechmea fasciata (Li et al., 2016). ...
... This relatively low number of genes assigned to a pathway is likely the result of imperfect annotation caused by Blast2go, although genes were present in 144 different KEGG pathways. The over-representation of some categories in the GO analysis as well as genes in some KEGG pathways has also been seen in other leaf transcriptome annotations of bromeliads (Li et al., 2016;Ma et al., 2015;Palma-Silva et al., 2016). It was performed an additional COG functional analysis. ...
Vriesea carinata is an endemic bromeliad from the Brazilian Atlantic Forest. It has trichome and tank system in their leaves which allows to absorb water and nutrients. It belongs to Bromeliaceae family, which includes several species highly enriched of cysteine-proteases (CysPs). These proteolytic enzymes regulate processes as senescence, cell differentiation, pathogen-linked programmed cell death and mobilization of proteins. Although, their biological importance, there are not genomic resources in V. carinata that can help to identify and understand their molecular mechanisms involved in different biological processes. Thus high-throughput transcriptome sequencing of V. carinata is necessary to generate sequences for the purpose of gene discovery and functional genomic studies. In the present study, we sequenced and assembled the V. carinata transcriptome to the identification of CysPs. A total of 43,232 contigs were assembled for the leaf tissue. BLAST analysis indicated that 23,803 contigs exhibited similarity to non-redundant Viridiplantae proteins. 28.24% of the contigs were classified into the COG database, and gene ontology categorized them into 61 functional groups. A metabolic pathway analysis with KEGG revealed 9679 contigs assigned to 31 metabolic pathways. Among 16 full-length CysPs identified, 11 were evaluated in respect to their expression patterns in the leaf apex, base and inflorescence tissues. The results showed differential expression levels of legumain, metacaspase, pyroglutamyl and papain-like CysPs depending of the leaf region. These results provide a global overview of V. carinata gene functions and expression activities of CysPs in those tissues.
... Also, RNA-seq can be used for the simultaneous study of nucleotide variations, gene expression levels across different tissue types, disparate time periods, and ecologically relevant variables in high resolution and large dynamic ranges (Wang et al., 2009;Harris et al., 2015). Therefore, this approach accelerates the examination of expression differences in ecologically important traits (Bonneaud et al., 2011;Schvartzman et al., 2018), phenotypic and behavioral plasticity (Aubin-Horth and Renn, 2009;Brawand et al., 2014), and genes with potential adaptive significance in changing environments for non-model species (Niu et al., 2015;Harris et al., 2015;Todd et al., 2016;Palma-Silva et al., 2016). This new sequencing tool is also valuable for the investigation, validation, and assessment of allelic information [e.g., single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs)]. ...
Cinnamomum chago, an endangered species endemic to Yunnan province, possesses large economic and phylogenetic values in Lauraceae. However, the genomic information of this species remains relatively unexplored. In this study, we used RNAseq technology to characterize and annotate the C. chago transcriptome and identify candidate genes involved in special metabolic pathways and gene-associated simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP). A total of 129,097 unigenes, with a mean length of 667 bp and an N50 length of 1,062 bp, were assembled. Among these genes, 56,887 (44.07%) unigenes were successfully annotated using at least one database. Furthermore, 47 and 46 candidate genes were identified in terpenoid biosynthesis and fatty acid biosynthesis, respectively. A total of 22 candidate genes participated in at least one abiotic stress response of C. chago. Additionally, a total of 25,654 SSRs and 640 SNPs were also identified. Based on these potential loci, 55 novel expressed sequence tag (EST)-SSR primers were successfully developed. This work provides comprehensive transcriptomic data that can be used to establish a valuable information platform for gene prediction, signaling pathway investigation, and molecular marker development for C. chago and other related species. Such a platform can facilitate further studies on germplasm conservation and utilization of Lauraceae species.
... However, the relative lack of genomic data for invasive plants, which represent mostly non-model species, hinders research on this group of organisms at the molecular level. As the development of transcriptome sequencing technology offers a convenient and efficient means to obtain genome resources in non-model species [16][17][18], it provides an opportunity for comparative study of closely related invasive and non-invasive congeners, as an effective approach to identify the genetic basis and mechanisms of invasive success [9,19,20]. ...
Background
Mikania micrantha H.B.K. (Asteraceae) is one of the world’s most invasive weeds which has been rapidly expanding in tropical Asia, including China, while its close relative M. cordata, the only Mikania species native to China, shows no harm to the local ecosystems. These two species are very similar in morphology but differ remarkably in several ecological and physiological traits, representing an ideal system for comparative analysis to investigate the genetic basis underlying invasion success. In this study, we performed RNA-sequencing on the invader M. micrantha and its native congener M. cordata in China, to unravel the genetic basis underlying the strong invasiveness of M. micrantha. For a more robust comparison, another non-invasive congener M. cordifolia was also sequenced and compared.
Results
A total of 52,179, 55,835, and 52,983 unigenes were obtained for M. micrantha, M. cordata, and M. cordifolia, respectively. Phylogenetic analyses and divergence time dating revealed a relatively recent split between M. micrantha and M. cordata, i.e., approximately 4.81 million years ago (MYA), after their divergence with M. cordifolia (8.70 MYA). Gene ontology classifications, pathway assignments and differential expression analysis revealed higher representation or significant up-regulation of genes associated with photosynthesis, energy metabolism, protein modification and stress response in M. micrantha than in M. cordata or M. cordifolia. Analysis of accelerated evolution and positive selection also suggested the importance of these related genes and processes to the adaptability and invasiveness of M. micrantha. Particularly, most (77 out of 112, i.e. 68.75%) positively selected genes found in M. micrantha could be classified into four groups, i.e., energy acquisition and utilization (10 genes), growth and reproduction (13 genes), protection and repair (34 genes), and signal transduction and expression regulation (20 genes), which may have contributed to the high adaptability of M. micrantha to various new environments and the capability to occupy a wider niche, reflected in its high invasiveness.
Conclusions
We characterized the transcriptomes of the invasive species M. micrantha and its non-invasive congeners, M. cordata and M. cordifolia. A comparison of their transcriptomes provided insights into the genetic basis of the high invasiveness of M. micrantha.
Electronic supplementary material
The online version of this article (10.1186/s12864-018-4784-9) contains supplementary material, which is available to authorized users.
... ABA can independently improve anthocyanin accumulation and also has a synergic effect with sugar [56,57]. ABA regulates anthocyanin biosynthesis via MYB, bHLH and bZIP [58][59][60]. In this work, one DEG with the function of ABA receptor PYL4 in ABA signal pathway was down-regulated. ...
In this study, a red mutant was obtained through in vitro regeneration of a wild purple potato. High-performance liquid chromatography and Mass spectrometry analysis revealed that pelargonidin-3-O-glucoside and petunidin-3-O-glucoside were main anthocyanins in the mutant and wild type tubers, respectively. In order to thoroughly understand the mechanism of anthocyanin transformation in two materials, a comparative transcriptome analysis of the mutant and wild type was carried out through high-throughput RNA sequencing, and 295 differentially expressed genes (DEGs) were obtained. Real-time qRT-PCR validation of DEGs was consistent with the transcriptome date. The DEGs mainly influenced biological and metabolic pathways, including phenylpropanoid biosynthesis and translation, and biosynthesis of flavone and flavonol. In anthocyanin biosynthetic pathway, the analysis of structural genes expressions showed that three genes, one encoding phenylalanine ammonia-lyase, one encoding 4-coumarate-CoA ligase and one encoding flavonoid 3′,5′-hydroxylasem were significantly down-regulated in the mutant; one gene encoding phenylalanine ammonia-lyase was significantly up-regulated. Moreover, the transcription factors, such as bZIP family, MYB family, LOB family, MADS family, zf-HD family and C2H2 family, were significantly regulated in anthocyanin transformation. Response proteins of hormone, such as gibberellin, abscisic acid and brassinosteroid, were also significantly regulated in anthocyanin transformation. The information contributes to discovering the candidate genes in anthocyanin transformation, which can serve as a comprehensive resource for molecular mechanism research of anthocyanin transformation in potatoes.
... Neotropical plant radiations provide a perfect system for examining potential gene flow among closely related species. The Bromeliaceae, in particular, have been used as a model group in studies of evolution of reproductive isolation and speciation in Neotropical regions (Schulte et al. 2010;Palma-Silva et al. 2011, 2015, 2016aWagner et al. 2015;Lexer et al. 2016;Zanella et al. 2016), mainly due to its high diversity and recent adaptive radiation (Benzing 2000;Givnish et al. 2011Givnish et al. , 2014. ...
Reproductive isolation is of fundamental importance for maintaining species boundaries in sympatry. Here, we examine the genetic and morphological differences between two closely related bromeliad species: Vriesea simplex and Vriesea scalaris. Furthermore, we examined the occurrence of natural hybridization and discuss the action of reproductive isolation barriers. Nuclear genomic admixture suggests hybridization in sympatric populations, although interspecific gene flow is low among species in all sympatric zones (Nem < 0.5). Thus, morphological and genetic divergence (10.99 %) between species can be maintained despite ongoing natural hybridization. Cross-evaluation of our genetic and morphological data suggests that species integrity is maintained by the simultaneous action of multiple barriers, such as divergent reproductive systems among species, differences in floral traits and low hybrid seed viability.
