Cite this paper:
HAN Zhaofang, XIAO Shijun, LIU Xiande, LIU Yang, LI Jiakai, XIE Yangjie, WANG Zhiyong. De novo characterization of Larimichthys crocea transcrip-tome for growth-/immune-related gene identification and massive microsatellite (SSR) marker development[J]. Journal of Oceanology and Limnology, 2017, 35(2): 225-234

De novo characterization of Larimichthys crocea transcrip-tome for growth-/immune-related gene identification and massive microsatellite (SSR) marker development

HAN Zhaofang, XIAO Shijun, LIU Xiande, LIU Yang, LI Jiakai, XIE Yangjie, WANG Zhiyong
Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, China Fisheries College, Jimei University, Xiamen 361021, China
Abstract:
The large yellow croaker, Larimichthys crocea is an important marine fish in China with a high economic value. In the last decade, the stock conservation and aquaculture industry of this species have been facing severe challenges because of wild population collapse and degeneration of important economic traits. However, genes contributing to growth and immunity in L. crocea have not been thoroughly analyzed, and available molecular markers are still not sufficient for genetic resource management and molecular selection. In this work, we sequenced the transcriptome in L. crocea liver tissue with a Roche 454 sequencing platform and assembled the transcriptome into 93 801 transcripts. Of them, 38 856 transcripts were successfully annotated in nt, nr, Swiss-Prot, InterPro, COG, GO and KEGG databases. Based on the annotation information, 3 165 unigenes related to growth and immunity were identified. Additionally, a total of 6 391 simple sequence repeats (SSRs) were identified from the transcriptome, among which 4 498 SSRs had enough flanking regions to design primers for polymerase chain reactions (PCR). To access the polymorphism of these markers, 30 primer pairs were randomly selected for PCR amplification and validation in 30 individuals, and 12 primer pairs (40.0%) exhibited obvious length polymorphisms. This work applied RNA-Seq to assemble and analyze a live transcriptome in L. crocea. With gene annotation and sequence information, genes related to growth and immunity were identified and massive SSR markers were developed, providing valuable genetic resources for future gene functional analysis and selective breeding of L. crocea.
Key words:    Larimichthys crocea|transcriptome|functional genes|SSR markers   
Received: 2015-11-18   Revised: 2016-01-04
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Articles by HAN Zhaofang
Articles by XIAO Shijun
Articles by LIU Xiande
Articles by LIU Yang
Articles by LI Jiakai
Articles by XIE Yangjie
Articles by WANG Zhiyong
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