Ye Hua, Zhang Zhengshi, Zhou Chaowei, Zhu Chengke, Yang Yuejing, Xiang Mengbin, Zhou Xinghua, Zhou Jian, Luo Hui
College of Animal Science, Southwest University Chongqing 402460 China
Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China.
RSC Adv. 2018 Apr 16;8(25):13945-13953. doi: 10.1039/c8ra00619a. eCollection 2018 Apr 11.
() 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 , owing to overexploitation and biological invasion. 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 was sequenced and analyzed. Using paired-end reads from the Illumina Hiseq4000 platform, 83 103 transcripts with an N50 length of 2337 bp were assembled, which could be further clustered into 66 975 unigenes with an N50 length of 2087 bp. The majority of the unigenes (58 934, 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, 19 497 putative simple sequence repeats (SSRs) of 1-6 bp unit length were detected from 14 690 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 , 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 .
（）是裂腹鱼亚科的一种，是中国西藏特有的经济四倍体鱼类。由于过度开发和生物入侵，它在《》中被列为易危物种。（）在生态和当地渔业经济中发挥着重要作用，但关于其遗传多样性、局部适应性、免疫系统等方面的信息知之甚少。功能基因鉴定和分子标记开发是后续生物学功能和遗传学研究的首要且关键步骤。为此，对三只成年（）的混合组织转录组进行了测序和分析。利用Illumina Hiseq4000平台的双端读数，组装了83103个转录本，N50长度为2337 bp，可进一步聚类为66975个单基因，N50长度为2087 bp。大多数单基因（58934个，87.99%）通过7个公共数据库成功注释，并鉴定出15条免疫相关基因的KEGG途径用于后续功能研究。此外，从14690个单基因（21.93%）中检测到19497个推定的1 - 6 bp单位长度的简单序列重复（SSR），平均分布密度为1:3.28 kb。我们鉴定出3590个包含多个SSR的单基因（5.36%），为功能基因提供了丰富的潜在多态性标记。这是首次报道的（）的高通量转录组分析，它将为参与多种生物学过程的功能基因提供有价值的遗传资源，包括（）免疫系统、遗传保护和分子标记辅助育种。
