Data from: De novo assembly and characterization of the Hucho taimen transcriptome

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 non-model 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 1060
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 8 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.