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Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing

文献类型： 外文期刊

作者： Fang, D. -A. 1 ; Zhou, Y. -F. 2 ; Duan, J. -R. 2 ; Zhang, M. -Y. 2 ; Xu, D. -P. 2 ; Liu, K. 2 ; Xu, P. 1 ; Wei, Q. 3 ;

作者机构： 1.Nanjing Agr Univ, Wuxi Fisheries Coll, Wuxi, Peoples R China

2.Chinese Acad Fishery Sci, Freshwater Fisheries Res Ctr, Wuxi, Peoples R China

3.Chinese Acad Fishery Sci, Yangtze River Fisheries Res Inst, Minist Agr, Key Lab Freshwater Biodivers Conservat, Wuhan, Peoples R China

关键词： Coilia nasus;De novo transcriptome;SSR markers;Illumina sequencing

期刊名称：GENETICS AND MOLECULAR RESEARCH （ 影响因子：0.764； 五年影响因子：0.912 ）

ISSN： 1676-5680

年卷期： 2015 年 14 卷 4 期

页码：

收录情况： SCI

摘要： RNA-Seq technology has been widely applied to transcriptomics, genomics, molecular marker development, and functional gene studies. In the genome, microsatellites are simple sequence repeats (SSR) with a high degree of polymorphism that are used as DNA markers in many molecular genetic studies. Using traditional methods such as magnetic bead enrichment, only a few microsatellite markers have been isolated. Coilia nasus is an anadromous, small-to-moderately sized fish species that is famous as an important fishery resource. Here, we have identified a large number of microsatellites from the fish brains by using Illumina sequencing. About 20 million Illumina reads were assembled into 148,845 unigenes. A total of 13,038 SSR motifs were identified via analysis of 3,958,293,117 (3.96 Gb) nucleotides to produce a comprehensive transcript dataset for the C. nasus brain, including mono-, di-, tri-, tetra-, and penta-repeat motifs. The most abundant type of repeat motif was di-nucleotide (42.97%), followed by mono-nucleotide (38.86%), tri-nucleotide (16.21%), tetra-nucleotide (1.83%), and penta-nucleotide (0.05%) repeat units, which is similar to the results obtained in studies in other species. These data provide a base of sequence informa-tion to improve molecular-assisted markers to study C. nasus genetic diversity.

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