IHB OpenIR  > 水生生物多样性与资源保护研究中心  > 期刊论文
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 PublicationDNA RESEARCH
ISSN1340-2838
Volume26Issue: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.

Keywordsingle-molecule sequencing transcriptome alternative splicing gene expression Gymnocypris selincuoensis
DOI10.1093/dnares/dsz014
Indexed BySCI
Language英语
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000493011000006
WOS KeywordGENE-EXPRESSION ; CARP ; ADAPTATION ; LAKE ; INTEGRATION ; GENERATION ; CYPRINIDAE ; ALIGNMENT ; PROFILES ; FEATURES
PublisherOXFORD UNIV PRESS
Citation statistics
Cited Times:6[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://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 AuthorChen, Yifeng
Affiliation1.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.
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