Sequencing, de novo assembly and characterization of the spotted scat <italic style="font-style: italic">Scatophagus argus</italic>(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs

Wei YANG; Huapu CHEN; Xuefan CUI; Kewei ZHANG; Dongneng JIANG; Siping DENG; Chunhua ZHU; Guangli LI

doi:10.1007/s00343-018-7090-0

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Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs

Biology | Updated：2023-05-19

- Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs
- Chinese Journal of Oceanology and Limnology Vol. 36, Issue 4, Pages: 1329-1341(2018)
- Affiliations：
  
  1.Zhanjiang City Key Laboratory of Marine Ecology and Environment, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
  2.Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
  3.Food and Environmental Engineering Department, Yangjiang Vocational and Technical College, Yangjiang 529566, China
- Author bio：
  
  LI Guangli, guangligdou@163.com
- Funds：
- DOI：10.1007/s00343-018-7090-0
  CLC：
- Received：24 March 2017，
  
  Accepted：03 May 2017，
  
  Online First：19 June 2017，
  
  Published：2018-07
- Accepted：
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Wei YANG, Huapu CHEN, Xuefan CUI, et al. Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs[J]. Chinese Journal of Oceanology and Limnology, 2018, 36(4): 1329-1341.
DOI：

Wei YANG, Huapu CHEN, Xuefan CUI, et al. Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs[J]. Chinese Journal of Oceanology and Limnology, 2018, 36(4): 1329-1341. DOI： 10.1007/s00343-018-7090-0.

摘要

Abstract

Spotted scat (

Scatophagus argus

) is an economically important farmed fish

particularly in East and Southeast Asia. Because there has been little research on reproductive development and regulation in this species

the lack of a mature artificial reproduction technology remains a barrier for the sustainable development of the aquaculture industry. More genetic and genomic background knowledge is urgently needed for an in-depth understanding of the molecular mechanism of reproductive process and identification of functional genes related to sexual differentiation

gonad maturation and gametogenesis. For these reasons

we performed transcriptomic analysis on spotted scat using a multiple tissue sample mixing strategy. The Illumina RNA sequencing generated 118 510 486 raw reads. After trimming

de novo assembly was performed and yielded 99 888 unigenes with an average length of 905.75 bp. A total of 45 015 unigenes were successfully annotated to the Nr

Swiss-Prot

KOG and KEGG databases. Additionally

23 783 and 27 183 annotated unigenes were assigned to 56 Gene Ontology (GO) functional groups and 228 KEGG pathways

respectively. Subsequently

2 474 transcripts associated with reproduction were selected using GO term and KEGG pathway assignments

and a number of reproduction-related genes involved in sex differentiation

gonad development and gametogenesis were identified. Furthermore

22 279 simple sequence repeat (SSR) loci were discovered and characterized. The comprehensive transcript dataset described here greatly increases the genetic information available for spotted scat and contributes valuable sequence resources for functional gene mining and analysis. Candidate transcripts involved in reproduction would make good starting points for future studies on reproductive mechanisms

and the putative sex differentiation-related genes will be helpful for sex-determining gene identification and sex-specific marker isolation. Lastly

the SSRs can serve as marker resources for future research into genetics

marker-assisted selection (MAS) and conservation biology.

关键词

Keywords

references

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Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs

DOI：10.1007/s00343-018-7090-0

摘要

Abstract

关键词

Keywords

references