Yongquan Zhang

The complete mitochondrial genome sequence of white-spotted char (Salvelinus leucomaenis)

Abstract The complete sequence of the mitochondrial genome of the white-spotted char (Salvelinus leucomaenis) was determined to be 16,658u2009bp in length, which contains the control region (CR), the origin of light-strand replication (OL), 22 transfer RNA genes, 2 ribosomal genes and 13 protein-coding genes. Overall, base composition of the complete mitochondrial DNA was 28.20% A, 26.51% T, 28.39% C, 16.90% G, with 54.71% AT.

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.

Population genetic structure of taimen, Hucho taimen (Pall.), in China

Abstract Hucho taimen (Pall.) is one of the largest salmonid species, and has been classified as an endangered species in China since 1998. In recent years, its wild stocks, habitats, and spawning grounds have been severely damaged by environmental degradation and human intervention. To protect and exploit this treasured species effectively and sustainably, the genetic diversity and structure of taimen populations in China was investigated using AFLP, microsatellite markers, and partial sequences of mtDNA genes. This paper summarizes these studies on the genetic diversity and structure of taimen populations in China.