De novo assembly and characterization of the Hucho taimen transcriptome

Abstract

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.

Keywords: Hucho taimen; RNA‐Seq; comparative transcript analysis; microsatellite markers; positive selection.

Figure 1

Yong fish (age 3+) of Hucho taimen. Photographed by Wei Xu, with permission

Figure 2

Length distribution of contigs and unigenes

Figure 3

GO term distribution of taimen transcripts

Figure 4

Distribution of taimen transcripts classified by COG function

Figure 5

Homologous analysis among taimen and other three teleosts. (a, b) Distribution of the synonymous substitution rates (Ks) of homologous genes for interspecies (a) and intraspecies and (b) a comparison of taimen, rainbow trout, Atlantic salmon, and northern pike. We used homologous pairs with Ks values <0.6 (a) and <3.5 (b) to plot the Ks distribution curves. Vertical dashed lines in (a) marked the Ks values (0.062, 0.070, 0.074, respectively) of peaks

Figure 6

Net Venn diagram of gene families among eight species. Net Venn diagram was drawn using VennPainter (Lin et al., 2016); numbers in overlapped ellipse represented the number of gene families shared by species, numbers in nonoverlapped ellipse represented the number of unique gene families of a species; 12,979 families were shared by the eight species; 313 families occurred only in taimen

Figure 7

Phylogenetic tree of salmonids and other related teleosts. Single‐copy orthologs were used to reconstruct the phylogenetic tree with PhyML and MrBayes, and the model JTT+I+G+F was used; the topologies of phylogenetic trees inferred by PhyML and MrBayes were consistent; numbers with a black color on the branch are the bootstrap values, and divergent ages were calculated with MCMCtree program in PAML package. The 95% confidence interval for age is shown in square brackets in red. Gray vertical lines are reference lines of ages. TMRA, the most recent ancestor