基于银鲳RNA-seq数据中SSR标记的信息分析

Bioinformatic Analysis of SSR Markers Based on RNA-seq of Pampus argenteus

[目的]开发银鲳分子标记技术。[方法]通过对银鲳(Pampus argenteus)进行高通量转录组测序(RNA-seq)获得银鲳转录组原始试验数据,经过拼接后,获得3 715 603条unigene序列。采用生物信息学分析软件MISA对所有unigene进行简单重复序列(simple sequence repeat,SSR)位点鉴定。同时,利用软件对银鲳转录组SSR的多态性进行评价。[结果]银鲳转录组水平上,共鉴定出107 007个SSR位点,分布在97 289条unigene中,发生频率为2.62%,SSR平均密度为476个/Mbp。在银鲳转录组SSRs中,单核苷酸与二核苷酸重复序列为主要重复类型,分别占总SSRs的48.14%和34.10%。银鲳转录组数据中SSR序列共包括424种重复基元类型,单核苷酸重复基元A占较高比例,占同一重复类型SSRs的49.57%,二核苷酸重复基元TG/AC和三核苷酸重复基元GAG/AAC是优势重复基元,分别占同一重复类型SSRs的42.43%和9.61%。重复序列长度在12 bp以上的SSR标记位点数占总SSR的76.95%,具有丰富的多态性。[结论]银鲳SSRs位点具有极大的可开发性,可为银鲳遗传多样性研究、遗传图谱构建及分子辅助育种提供有效工具。

Objective] To develop molecular marker technology of Pampus argenteus.[Method] Transcriptomic sequencing was performed for molecular marker technology development on Pampus argenteus, and 3 715 603 unigene was found after assembling.The Microsatellite （ MISA） software was used to identify SSRs from unigenes.Meanwhile, SSR polymorphisms were evaluated using software.[ Result] 107 007 SSRs were identified, distributed in 97 289 unigenes, which accounted for 2.62% of the whole unigenes and the distribution density of the transcriptomic SSRs from transcriptome were 476/Mbp.The nucleotides were repeated and the dinucleotide were the maintypes, accounting for 48.14% and 34.10%, respectively, of all the SSRs.In total, we found 424 different types of repeat motifs, in which the repeats with A、TG/AC and GAG/AAC as the most frequent motifs, accounting for 49.57%、42.43%and 9.61%, respectively, of the SSR repeat motifs.Statis-tics got from repetitive sequence length more than 12 bp SSR markers accounting for 76.95% of all the SSRs, it was very rich polymorphism. [ Conclusion] The study also assessed the potential of the transcriptomic SSRs for further use and research.These results provide a useful tool for studies in genetic diversity, genetic mapconstruction and molecular assisted breeding of Pampus argenteus.