Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq | |
Feng, Xiu1; Jia, Yintao1; Zhu, Ren1; Chen, Kang1,2; Chen, Yifeng1 | |
2019-08-01 | |
Source Publication | DNA RESEARCH
![]() |
ISSN | 1340-2838 |
Volume | 26Issue:4Pages:353-363 |
Abstract | 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. |
Keyword | single-molecule sequencing transcriptome alternative splicing gene expression Gymnocypris selincuoensis |
DOI | 10.1093/dnares/dsz014 |
Indexed By | SCI |
Language | 英语 |
WOS Research Area | Genetics & Heredity |
WOS Subject | Genetics & Heredity |
WOS ID | WOS:000493011000006 |
WOS Keyword | GENE-EXPRESSION ; CARP ; ADAPTATION ; LAKE ; INTEGRATION ; GENERATION ; CYPRINIDAE ; ALIGNMENT ; PROFILES ; FEATURES |
Publisher | OXFORD UNIV PRESS |
Citation statistics | |
Document Type | 期刊论文 |
Identifier | http://ir.ihb.ac.cn/handle/342005/35292 |
Collection | 水生生物多样性与资源保护研究中心_期刊论文 |
Corresponding Author | Chen, Yifeng |
Affiliation | 1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China |
Recommended Citation GB/T 7714 | Feng, Xiu,Jia, Yintao,Zhu, Ren,et al. Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq[J]. DNA RESEARCH,2019,26(4):353-363. |
APA | Feng, Xiu,Jia, Yintao,Zhu, Ren,Chen, Kang,&Chen, Yifeng.(2019).Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq.DNA RESEARCH,26(4),353-363. |
MLA | Feng, Xiu,et al."Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq".DNA RESEARCH 26.4(2019):353-363. |
Files in This Item: | ||||||
File Name/Size | DocType | Version | Access | License | ||
Feng-2019-Characteri(1017KB) | 期刊论文 | 作者接受稿 | 开放获取 | CC BY-NC-SA | View Application Full Text |
Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.
Edit Comment