基于转录组测序的缺须盆唇鱼微卫星标记特征分析

Characteristics Analysis of SSR Markers Based on Transcriptomic Sequenceing of Placocheilus cryptonemus

缺须盆唇鱼(Placocheilus cryptonemus)是云南省怒江流域特有的一种高原经济鱼类。通过在Illumina HiSeq 2500平台上对缺须盆唇鱼进行转录组测序(RNA-seq)分析,利用MicroSAtellite(MISA)微卫星识别工具对1~6个碱基重复、碱基数在10 bp以上的微卫星进行鉴定。结果表明,在缺须盆唇鱼转录组中共发现分布在36764条Unigene上的30500个SSR位点,包含序列的SSR数量为18078,发生频率为49.17%。获得的单纯SSR中共有215种重复基元,其中单核苷酸重复基元类型数量最多,为88个,六碱基重复的SSR最少,其他的重复从二、三、四、五、六碱基开始,SSR的形成呈现递减规律。SSR位点的重复次数主要发生在6~10次和11~15次重复之间,发生频率分别为38.59%和36.02%。本研究对缺须盆唇鱼的转录组数据进行测序鉴定,得到了数量较多的SSR标记,同时对得到的缺须盆唇鱼SSR数据特点进行归纳总结。本研究不仅提供了一个有价值的转录组资源,而且建立了一套SSR标记,可以为缺须盆唇鱼的基础研究、应用研究提供有效的分子标记。

Placocheilus cryptonemus is a kind of plateau economic fish endemic to Nujiang river basin,Yunnan Province,China.Transcriptome sequencing of Placocheilus cryptonemus was performed on Illumina HiSeq 2500 platform,and the MicroSAtellite(MISA)software was used to identify microsatellites with 1~6 bases repeated and base number over 10 bp.The results showed that a total of 30500 SSR sites were found at the transcriptome level,distributing in 36764 Unigene,and the number of SSRs containing sequences was 18078,with the occurrence frequency of 49.17%.In the obtained simple SSR,there were 215 types of repeat primitive,among which the number of single nucleotide repeat primitive types was the largest(88).SSRs with repeated 2,3,4,5 and 6 bases shawed an obvious decreasing rule,and SSRs with repeated 6 bases were the least.The frequency of SSR repetition mainly occurred between 6~10 and 11~15 repetitions,with the frequency of 38.59%and 36.02%,respectively.This study performed transcriptome sequencing analysis of Placocheilus cryptonemus,obtained a large number of SSR markers,and summarized SSR distribution characteristics of P.cryptonemus.This study not only provided a valuable transcriptomic resource,but also established a set of SSR markers,which can provide effective molecular markers for basic and applied research of Placocheilus cryptonemus.