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De novo assembly of Schizothorax waltoni transcriptome to identify immune-related genes and microsatellite markers

文献类型： 外文期刊

作者： Ye, Hua 2 ; Zhang, Zhengshi 1 ; Zhou, Chaowei 1 ; Zhu, Chengke 1 ; Yang, Yuejing 1 ; Xiang, Mengbin 1 ; Zhou, Xinghua; 1 ;

作者机构： 1.Southwest Univ, Coll Anim Sci, Chongqing 402460, Peoples R China

2.Key Lab Aquat Sci Chongqing, Key Lab Freshwater Fish Reprod & Dev, Minist Educ, Chongqing 400175, Peoples R China

3.Sichuan Acad Agr Sci, Fisheries Res Inst, Chengdu 611731, Sichuan, Peoples R China

期刊名称：RSC ADVANCES （ 影响因子：3.361； 五年影响因子：3.39 ）

ISSN： 2046-2069

年卷期： 2018 年 8 卷 25 期

页码：

收录情况： SCI

摘要： Schizothorax waltoni (S. waltoni) is one kind of the subfamily Schizothoracinae and an indigenous economic tetraploid fish to Tibet in China. It is rated as a vulnerable species in the Red List of China's Vertebrates, owing to overexploitation and biological invasion. S. waltoni plays an important role in ecology and local fishery economy, but little information is known about genetic diversity, local adaptation, immune system and so on. Functional gene identification and molecular marker development are the first and essential step for the following biological function and genetics studies. For this purpose, the transcriptome from pooled tissues of three adult S. waltoni was sequenced and analyzed. Using paired-end reads from the Illumina Hiseq4000 platform, 83103 transcripts with an N50 length of 2337 bp were assembled, which could be further clustered into 66975 unigenes with an N50 length of 2087 bp. The majority of the unigenes (58934, 87.99%) were successfully annotated by 7 public databases, and 15 KEGG pathways of immune-related genes were identified for the following functional research. Furthermore, 19497 putative simple sequence repeats (SSRs) of 1-6 bp unit length were detected from 14690 unigenes (21.93%) with an average distribution density of 1:3.28 kb. We identified 3590 unigenes (5.36%) containing more than one SSR, providing abundant potential polymorphic markers in functional genes. This is the first reported high-throughput transcriptome analysis of S. waltoni, and it would provide valuable genetic resources for the functional genes involved in multiple biological processes, including the immune system, genetic conservation, and molecular marker-assisted breeding of S. waltoni.

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