梅、杏、桃EST同源序列特征分析及EST-SNP发掘

Characterization and mining of EST-SNP from homologous EST sequences of Prunus mume,P.armeniaca and P.persica

通过生物信息学手段,下载GenBank数据库中已公布的梅、杏、桃3个物种EST序列各4 660、15 388、82 583条,利用CAP 3软件拼接后序列分别为4 456、5 595和24 243条。经比对发现,同源序列592条,同源序列的总长度为235 576 bp,平均长度和同源性分别为437.67 bp和97.50%;进行Blast比对后发现,所有同源序列中有340个具有相应的功能注释,183个为未知功能蛋白,其余69个为没有相应序列信息的新基因;在所有同源序列中共发现8 818个SNP,总频率为每SNP26.71 bp,并以转换和颠换为主。同时,对3个物种的同源序列进行两两比较发现,SNP数量明显少于这三者比较的结果。利用所有SNP对梅、杏、桃3个特种进行聚类分析,结果表明,梅、杏的亲缘关系较近,而两者与桃亲缘关系较远。

In this research,4 660,15 388,82 583 were downloaded from the published EST database among Prunus mume,P.armeniaca and P.persica in GenBank,and 4 456,5 595 and 24 243 congtigs were respectively obtained after splicing from original EST sequences,by using CAP 3 software.592 homologous sequences were found with a total length of 235 576 bp,and the average length and homology were 437.67 bp and 97.50%,respectively.The Blast results also showed that 340 of them had the corresponding functional annotation,183 were unknown proteins,and the remaining 69 had new gene sequence information.The amount and frequency of nucleotides were further analyzed,where 8 818 SNPs were found having a total frequency of 26.71 bp per SNP,which mainly comprised transitions and transversions.The amount of SNP compared in pairs was significantly less than the number among the homologous sequences.In addition,the cluster analysis result by using the obtained SNP information showed that the relationship between P.mume and P.armeniaca was closer,and they were distantly related with P.persica,which would provide representative information for understanding the characteristics of genetic evolution,of the three comparative genomics and phylogenetic relationship among these three species.