Characterization and complexity of transcriptome in Gymnocypris przewalskii using single-molecule long-read sequencing and RNA-seq
文献类型： 外文期刊
作者： Li, Xindan 1 ; Wu, Jinming 1 ; Xiao, Xinping 1 ; Rong, Yifeng 1 ; Yang, Haile 1 ; Li, Junyi 1 ; Zhou, Qiong 1 ; Zhou, Weiguo 3 ; Shi, Jianquan 3 ; Qi, Hongfang 3 ; Du, Hao 1 ;
作者机构： 1.Chinese Acad Fishery Sci, Key Lab Freshwater Biodivers Conservat, Minist Agr, Wuhan 430223, Hubei, Peoples R China
2.Shanghai Ocean Univ, Coll Marine Sci, Shanghai 201306, Peoples R China
3.Rescue & Rehabil Ctr Naked Carps Lake Qinghai, Xining 810016, Qinghai, Peoples R China
关键词： Gymnocypris przewalskii; single-molecule sequencing; alternative splicing; gene expression; full-length transcriptome
期刊名称：DNA RESEARCH （ 影响因子：4.477； 五年影响因子：5.358 ）
ISSN： 1340-2838
年卷期： 2021 年 28 卷 3 期
页码：
收录情况： SCI
摘要： The Tibetan Schizothoracinae fish Gymnocypris przewalskii has the ability to adapt to the extreme plateau environment, making it an ideal biological material for evolutionary biology research. However, the lack of well-annotated reference genomes has limited the study of the molecular genetics of G. przewalskii. To characterize its transcriptome features, we first used long-read sequencing technology in combination with RNA-seq for transcriptomic analysis. A total of 159,053 full-length (FL) transcripts were captured by Iso-Seq, having a mean length of 3,445 by with N50 value of 4,348. Of all FL transcripts, 145,169 were well-annotated in the public database and 134,537 contained complete open reading frames. There were 4,149 pairs of alternative splicing events, of which three randomly selected were defined by RT-PCR and sequencing, and 13,293 long non-coding RNAs detected, based on all-vs.-all BLAST. A total of 118,185 perfect simple sequence repeats were identified from FL transcripts. The FL transcriptome might provide basis for further research of G. przewalskii.
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