基于桑葚转录组测序的SSR位点分析

Analysis on SSR Locis in Mulberry Fruit Transcriptome

采用转录组测序技术对三个时期的桑葚进行转录组测序,建立桑葚的EST数据库。基于生物信息学方法分析桑葚转录组数据库的简单重复序列位点。从51895条Unigenes中共检索出23641条Unigenes含有44867个简单重复序列位点,共计252种基序类型。在所有基序类型中,以A/T与AT/AT型出现次数最多。单核苷酸基序类型与二核苷酸基序类型出现频率最高,共计75.69%。基序长度以10~20 bp为主,重复次数集中5~18次。设计27149对引物,随机选择20对引物,通过PCR验证,在4个桑树品种中展现出良好的重现性与通用性。桑葚转录组SSR位点类型丰富,具备开发出适宜于果桑选育的分子标记的潜力。

In order to establi shing EST database,mulberry fruits of three development stages were carried out RNA-Seq.SSR loci were analyzed by bioinformatics.The results showed 23641 of 51895 Unigenes contained 44867 SSR loci which belong to 252 SSR motifs.A/T and AT/AT type took a higher proportion of all SSR motifs,with mononucleotide and dinucleotide SSRs being the most frequent,amount to 75.69%.SSR motif lengths and repetition numbers mainly varied from 10~20 bp,and 5~18,respectively.27149 primer pairs were developed and 20 pairs were selected randomly,the reproducibility and reproducibility were confirmed by PCR with four mulberry varieties.Abundant SSR motif types,included in mulberry fruit transcriptome,had the potential molecular markers suited for mulberry variety breeding.