The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
University of Chinese Academy of Sciences, Beijing, China.
DNA Res. 2019 Aug 1;26(4):353-363. doi: 10.1093/dnares/dsz014.
The lakes on the Qinghai-Tibet Plateau (QTP) are the largest and highest lake group in the world. Gymnocypris selincuoensis is the only cyprinid fish living in lake Selincuo, the largest lake on QTP. However, its genetic resource is still blank, limiting studies on molecular and genetic analysis. In this study, the transcriptome of G. selincuoensis was first generated by using PacBio Iso-Seq and Illumina RNA-seq. A full-length (FL) transcriptome with 75,435 transcripts was obtained by Iso-Seq with N50 length of 3,870 bp. Among all transcripts, 75,016 were annotated to public databases, 64,710 contain complete open reading frames and 2,811 were long non-coding RNAs. Based on all- vs.-all BLAST, 2,069 alternative splicing events were detected, and 80% of them were validated by reverse transcription polymerase chain reaction (RT-PCR). Tissue gene expression atlas showed that the number of detected expressed transcripts ranged from 37,397 in brain to 19,914 in muscle, with 10,488 transcripts detected in all seven tissues. Comparative genomic analysis with other cyprinid fishes identified 77 orthologous genes with potential positive selection (Ka/Ks > 0.3). A total of 56,696 perfect simple sequence repeats were identified from FL transcripts. Our results provide valuable genetic resources for further studies on adaptive evolution, gene expression and population genetics in G. selincuoensis and other congeneric fishes.
青藏高原上的湖泊是世界上最大和最高的湖泊群。细鳞裂腹鱼是生活在青藏高原上最大湖泊色林错中的唯一鲤科鱼类。然而，其遗传资源仍然是空白，限制了对分子和遗传分析的研究。在这项研究中，我们首次使用 PacBio Iso-Seq 和 Illumina RNA-seq 生成了细鳞裂腹鱼的转录组。通过 Iso-Seq 获得了全长（FL）转录组，其 N50 长度为 3,870 bp。在所有转录本中，75,016 个被注释到公共数据库，64,710 个包含完整的开放阅读框，2,811 个是长非编码 RNA。基于所有对所有 BLAST 的分析，检测到 2,069 个可变剪接事件，其中 80%通过逆转录聚合酶链式反应（RT-PCR）得到验证。组织基因表达图谱显示，在大脑中检测到的表达转录本数量从 37,397 个到肌肉中的 19,914 个不等，在所有七个组织中检测到 10,488 个转录本。与其他鲤科鱼类的比较基因组分析鉴定出了 77 个具有潜在正选择（Ka/Ks > 0.3）的直系同源基因。从 FL 转录本中总共鉴定出 56,696 个完美的简单序列重复。我们的研究结果为进一步研究细鳞裂腹鱼和其他同属鱼类的适应性进化、基因表达和群体遗传学提供了有价值的遗传资源。
