Sequencing, de novo assembly and characterization of the spotted scat <i>Scatophagus argus</i>(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs -- Journal of Oceanology and Limnology,2018,36(4):1329-1341

	Cite this paper:
	YANG Wei, CHEN Huapu, CUI Xuefan, ZHANG Kewei, JIANG Dongneng, DENG Siping, ZHU Chunhua, LI Guangli. Sequencing, de novo assembly and characterization of the spotted scat Scatophagus argus(Linnaeus 1766) transcriptome for discovery of reproduction related genes and SSRs[J]. Journal of Oceanology and Limnology, 2018, 36(4): 1329-1341

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

YANG Wei^1,3, CHEN Huapu^1,2, CUI Xuefan¹, ZHANG Kewei¹, JIANG Dongneng¹, DENG Siping¹, ZHU Chunhua¹, LI Guangli¹

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

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.

Key words: Scatophagus argus|illumina RNA-seq|reproduction|simple sequence repeat (SSR)

Received: 2017-03-24 Revised:

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