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.

中文翻译：

---

利用单分子长读测序和RNA-seq技术对青藏高原selnocypris selincuoensis的转录组进行表征和分析。

青藏高原（QTP）上的湖泊是世界上最大，最高的湖泊群。裸inc亚目（Gymnocypris selincuoensis）是生活在QTP上最大的湖塞林科湖上的唯一鲤科鱼类。但是，其遗传资源仍然空白，限制了分子和遗传分析的研究。在这项研究中，首先使用PacBio Iso-Seq和Illumina RNA-seq产生了G. selincuoensis的转录组。通过Iso-Seq获得具有N，3,870 bp N50长度的全长（FL）转录组。在所有转录本中，有75,016条被注释到公共数据库中，有64,710条包含完整的开放阅读框，而2,811条是长的非编码RNA。基于所有BLAST与全部BLAST，检测到2,069个其他剪接事件，其中80％通过逆转录聚合酶链反应（RT-PCR）进行了验证。组织基因表达图谱显示，检测到的表达转录本数量从脑中的37,397个到肌肉中的19,914个不等，在所有七个组织中均检测到10,488个。与其他鲤科鱼类的比较基因组分析确定了77个直系同源基因具有潜在的阳性选择（Ka / Ks> 0.3）。从FL转录物中鉴定出总共56,696个完美的简单序列重复序列。我们的结果为进一步研究selincuoensis和其他同系鱼类的适应进化，基因表达和种群遗传学提供了宝贵的遗传资源。与其他鲤科鱼类的比较基因组分析确定了77个直系同源基因具有潜在的阳性选择（Ka / Ks> 0.3）。从FL转录物中鉴定出总共56,696个完美的简单序列重复序列。我们的结果为进一步研究selincuoensis和其他同系鱼类的适应进化，基因表达和种群遗传学提供了宝贵的遗传资源。与其他鲤科鱼类的比较基因组分析确定了77个直系同源基因具有潜在的阳性选择（Ka / Ks> 0.3）。从FL转录物中鉴定出总共56,696个完美的简单序列重复序列。我们的结果为进一步研究selincuoensis和其他同系鱼类的适应进化，基因表达和种群遗传学提供了宝贵的遗传资源。