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

• Published in: 中国海洋湖沼学报：英文版 2017, Vol.35 (2), p.225-234
• Main Author: 韩兆力 肖世俊 刘贤德 刘洋 李佳凯 谢仰杰 王志勇
• Format: Article
• Language: English
• Subjects: SSR标记; 免疫相关基因; 分子标记; 大黄鱼; 开发; 生长; 转录组; 鉴定
• ISSN: 0254-4059; 1993-5005

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. eroeea 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 transeriptome 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 ofL. eroeea.