秀珍菇全基因组SSR位点分析及其在遗传多样性评估中的应用

Genome-wide SSR characterization and its application in evaluating the genetic diversity of Pleurotus pulmonarius

利用GenBank数据库中秀珍菇(Pleurotus pulmonarius)的全基因组序列进行简单重复序列(SSR)位点挖掘。在秀珍菇PM_ss5基因组中共检测出2348个SSR位点,相对丰度为平均1 Mb中含有59个SSR位点;所有SSR位点中,以二核苷酸SSR为主(51.8%),三核苷酸SSR次之(27.7%);经鉴定的秀珍菇SSR位点包含141种碱基基序,优势碱基基序为GA/TC、CT/AG;SSR长度变化范围为10~156 bp,其中,10~15 bp的SSR位点占比为77.2%;在秀珍菇和其他4种侧耳属真菌基因组中,都是以短核苷酸SSR为主,秀珍菇二核苷酸SSR占比高于其他侧耳属菌株;利用筛选的53对多态性引物对18个秀珍菇菌株进行遗传多样性分析,结果发现参试菌株表现出中度遗传多样性,平均Shannon信息指数为0.38,平均Nei’s基因多样性为0.23,平均有效等位基因数为1.35。

Using the whole genome sequence of PM_ss5 downloaded from GenBank database,genome-wide simple sequence repeats(SSRs)of Pleurotus pulmonarius were mined and characterized.A total of 2348 SSR loci were detected in PM_ss5 genome,with a relative abundance of 59 SSRs per Mb.Among all SSR loci,the di-nucleotide repeats were the dominant(51.8%),followed by the tri-nucleotide repeats(27.7%).The identified SSR loci contained 141 base motifs,among which the dominant base motifs were GA/TC and CT/AG.The length of SSRs ranged from 10 to 156 bp,and 77.2%of the identified SSRs were 10 to 15 bp.The SSR patterns in P.pulmonarius were also compared with those of other four species of Pleurotus.The short nucleotide repeats were dominant SSRs in all five Pleurotus spp.,with the di-nucleotide SSRs accounting for higher rate in P.pulmonarius.Then,53 pairs of polymorphic SSR primers were designed and selected to analyze the genetic diversity of the 18 varieties of P.pulmonarius,which showed P.pulmonarius owned moderate genetic diversity,and the average numbers of effective alleles,Nei’s genetic diversity and Shannon index were 1.35,0.23 and 0.38,respectively.