De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA‐Seq is a useful tool for obtaining genetic information and developing genetic markers for nonmodel species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA‐Seq analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them to de novo assemble a high‐quality transcriptome with a N50 size of 1,060 bp. In the assembly, 82% of the transcripts were annotated using several databases, and 14,666 of the transcripts contained a full open reading frame. The assembly covered 75% of the transcripts of Atlantic salmon and 57.3% of the protein‐coding genes of rainbow trout. To learn about the genome evolution, we performed a systematic comparative analysis across 11 teleosts including eight salmonids and found 313 unique gene families in taimen. Using Atlantic salmon and rainbow trout transcriptomes as the background, we identified 250 positive selection transcripts. The pathway enrichment analysis revealed a unique characteristic of taimen: It possesses more immune‐related genes than Atlantic salmon and rainbow trout; moreover, some genes have undergone strong positive selection. We also developed a pipeline for identifying microsatellite marker genotypes in samples and successfully identified 24 polymorphic microsatellite markers for taimen. These data and tools are useful for studying conservation genetics, phylogenetics, evolution among salmonids, and selective breeding for threatened taimen.

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“…We adopted general methods suggested by Trinity (Haas et al., 2013) and Fu et al. (Fu & He, 2012) to assess the assembly quality.…”

Section: Methodsmentioning

confidence: 96%

De novo assembly and characterization of the Hucho taimen transcriptome

Tong

Xü

Zhang

et al. 2017

Ecology and Evolution

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“…After quality control and filtering of reads, all RNA libraries were de novo assembled together as a primary all-isolate transcriptome using Trinity (rel_2.25.13) 75,76 (Supplementary Table 5). Meanwhile, 16 tissue-specific transcriptomes were individually de novo assembled using Trinity (Supplementary Tables 1, 5, and 6).…”

Section: Methodsmentioning

confidence: 99%

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression

et al. 2017

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More than 380 million years of evolution have produced >46,000 extant spider species, exhibiting an incredible diversity of silks used for prey capture and reproduction [1][2][3] . Spider silks can be stronger than steel and tougher than Kevlar, yet are much lighter weight than these manmade materials 4 . Silks vary in extensibility 5 , are temperature resilient 6 , can enable electrical conduction 7 , and can inhibit bacterial growth while being nearly invisible to the human immune system 8 . Thus, novel materials derived from spider silks offer tremendous potential for medical and industrial innovation. To take advantage of their desirable properties, we must learn more about spider silk genetic structure, functional diversity, and production.A female orb-weaving spider can have up to seven morphologically differentiated types of silk glands, each believed to extrude a distinct class of silk with biophysical characteristics resulting from the expression of a unique combination of silk genes in that gland 9,10 . The silk classes of a typical 'gluey silk' orb-weaver (Araneoidea) female include (i) major ampullate silk, which exhibits great tensile strength and is employed in draglines, bridgelines, and web radii 11,12 ; (ii) minor ampullate silk, used for inelastic temporary spirals during web building 11,12 ; (iii) cement-like piriform silk that bonds fibers together and to other substrates 13,14 ; (iv) strong, yet flexible aciniform silk used for prey wrapping and egg case insulation 15 ; (v) tubuliform and cylindriform silk that constitutes the tough outer layer of egg cases 16,17 ; (vi) flagelliform silk that exhibits unparalleled extensibility and is used in the capture spiral 18,19 ; and (vii) the viscous and sticky aggregate silk that aids in prey capture [20][21][22][23][24] . Many spider species produce just a subset of these silk classes, and some produce yet other silk types, including cribellate silk 25 . Each species possesses an assortment of specialized gland types that are thought to produce distinct classes of silks to fit specific needs 9,26,27 .Spider silks are composed primarily of spidroin proteins (where a 'spidroin' is a spider fibroin [28][29][30][31] ) that, by convention, have been named and classified according to the specific silk gland in which they were first discovered. Spidroin proteins have conserved N-and C-terminal domains that flank long runs of repeated motifs 32-34 , the composition and number of which confer specific physical properties to silks 27 . Yet, despite decades of research on orb-weaver silks, there is incomplete knowledge of all the spidroins within an orb-weaver species.Adding to the sampling of sequences obtained from targeted investigations, the assembly of the velvet spider (Stegodyphus mimosarum) genome yielded 19 spidroins, the largest collection from any single species 27 . Owing to the challenges of assembling arrays of repeats, several of the S. mimosarum spidroin sequences are incomplete, without the sequences encoding N-and C-terminal domains anchored ...

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“…As the closest assembled genome ( P. equestris , Cai et al., 2015) is highly divergent from Dactylorhiza (their most recent common ancestor lived 55–70 Ma, Givnish et al., 2015), we have assembled de novo with Trinity (Haas et al., 2013) a combined reference transcriptome for both Dactylorhiza species (for details see Appendix S1 and Fig. S2).…”

Section: Methodsmentioning

confidence: 99%

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

et al. 2017

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The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and Dactylorhiza fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage‐specific adaptive evolution of protein‐coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post‐transcriptional regulation via sRNAs. Finally, D. incarnata appears to suffer from insufficient sRNA control over the activity of RNA‐dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.

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De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Cited by 7,316 publications

References 50 publications

De novo assembly and characterization of the Hucho taimen transcriptome

De novo assembly and characterization of the Hucho taimen transcriptome

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

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