Wang Ying, Yang Liandong, Wu Bo, Song Zhaobin, He Shunping
The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, China.
Gene. 2015 Jul 10;565(2):211-20. doi: 10.1016/j.gene.2015.04.023. Epub 2015 Apr 11.
Triplophysa dalaica, endemic species of Qinghai-Tibetan Plateau, is informative for understanding the genetic basis of adaptation to hypoxic conditions of high altitude habitats. Here, a comprehensive gene repertoire for this plateau fish was generated using the Illumina deep paired-end high-throughput sequencing technology. De novo assembly yielded 145, 256 unigenes with an average length of 1632 bp. Blast searches against GenBank non-redundant database annotated 74,594 (51.4%) unigenes encoding for 30,047 gene descriptions in T. dalaica. Functional annotation and classification of assembled sequences were performed using Gene Ontology (GO), clusters of euKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. After comparison with other fish transcriptomes, including silver carp (Hypophthalmichthys molitrix) and mud loach (Misgurnus anguillicaudatus), 2621 high-quality orthologous gene alignments were constructed among these species. 61 (2.3%) of the genes were identified as having undergone positive selection in the T. dalaica lineage. Within the positively selected genes, 13 genes were involved in hypoxia response, of which 11 were listed in HypoxiaDB. Furthermore, duplicated hif-α (hif-1αA/B and hif-2αA/B), EGLN1 and PPARA candidate genes involved in adaptation to hypoxia were identified in T. dalaica transcriptome. Branch-site model in PAML validated that hif-1αB and hif-2αA genes have undergone positive selection in T.dalaica. Finally, 37,501 simple sequence repeats (SSRs) and 19,497 high-quality single nucleotide polymorphisms (SNPs) were identified in T. dalaica. The identified SSR and SNP markers will facilitate the genetic structure, population geography and ecological studies of Triplophysa fishes.
达里湖高原鳅是青藏高原特有物种，对理解适应高海拔栖息地低氧条件的遗传基础具有重要意义。在此，利用Illumina深度双末端高通量测序技术生成了该高原鱼类的综合基因库。从头组装产生了145,256个单基因，平均长度为1632 bp。针对GenBank非冗余数据库的Blast搜索注释了74,594个（51.4%）单基因，这些单基因编码达里湖高原鳅中的30,047个基因描述。使用基因本体论（GO）、真核直系同源群簇（KOG）和京都基因与基因组百科全书（KEGG）分析对组装序列进行功能注释和分类。与其他鱼类转录组（包括鲢鱼（Hypophthalmichthys molitrix）和泥鳅（Misgurnus anguillicaudatus））比较后，在这些物种之间构建了2621个高质量的直系同源基因比对。其中61个（2.3%）基因被鉴定为在达里湖高原鳅谱系中经历了正选择。在正选择基因中，有13个基因参与低氧反应，其中11个列于HypoxiaDB中。此外，在达里湖高原鳅转录组中鉴定出了参与低氧适应的重复hif-α（hif-1αA/B和hif-2αA/B）、EGLN1和PPARA候选基因。PAML中的分支位点模型验证了hif-1αB和hif-2αA基因在达里湖高原鳅中经历了正选择。最后，在达里湖高原鳅中鉴定出37,501个简单序列重复（SSR）和19,497个高质量单核苷酸多态性（SNP）。所鉴定的SSR和SNP标记将有助于达里湖高原鳅属鱼类的遗传结构、种群地理学和生态学研究。
