Volume 15 Issue 1
Feb.  2019
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HUANG Yong, GONG Wangbao, CHEN Haigang, XIONG Jianli, SUN Xihong. Sequencing and bioinformatic analysis for transcriptome of Micropterus salmoides based on RNA-seq[J]. South China Fisheries Science, 2019, 15(1): 106-112. DOI: 10.12131/20180066
Citation: HUANG Yong, GONG Wangbao, CHEN Haigang, XIONG Jianli, SUN Xihong. Sequencing and bioinformatic analysis for transcriptome of Micropterus salmoides based on RNA-seq[J]. South China Fisheries Science, 2019, 15(1): 106-112. DOI: 10.12131/20180066
shu

Sequencing and bioinformatic analysis for transcriptome of Micropterus salmoides based on RNA-seq

  • 1.

    College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China

  • 2.

    Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China

  • 3.

    Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China

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  • Received Date: April 09, 2018
  • Revised Date: June 14, 2018
  • Accepted Date: July 24, 2018
  • Available Online: December 04, 2018
    Graphical Abstract
    • Abstract

  • The transcripts of Micropterus salmoides were obtained by RNA-seq technology to conduct a transcriptomic analysis. A total of 35 659 unigenes were generated by de novo assembly with an average length of 738 bp and N50 of 1 052 bp. The unigenes were assessed for length distribution and GC content. The sequencing data were of high quality and reliability. A total of 15 832, 21 279, 14 524, 16 973, 15 024 and 11 185 unigenes were annotated from the KOG, Nr, Pfam, Swiss-Prot, GO and KEGG databases, respectively, among which 5 617 were annotated in all the databases and 17 253 were annotated in at least one database. Blasted with KEGG pathway, 11 185 unigenes were annotated, belonging to 267 categories. Of all the pathways, the number of unigenes joining in the signal transduction was the most (1 349, 12.06%). Finally, 4 030 SSRs were identified. The results provide rich data to understand transcriptome information of M. salmoides and lay the foundation for further research on functional gene cloning, genomics, genetic diversity analysis, molecular marker exploitation and genetic improvement in M. salmoides.

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    • References (23)
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