Simple sequence repeats (SSRs) in the Trametes versicolor genome were identified and characterized in terms of number,distribution and frequency using in silico approaches.SSR-containing genes were functionally annotated.The features of SSRs in T.versicolor were compared with those in other five species of Agaricomycetes,Agaricus bisporus,Bjerkandera adusta,Fomitopsis pinicola,Flammulina velutipes and Pycnoporus cinnabarinus.The results showed that 1 224SSRs were detected in the T.versicolor genome with the relative abundance of 27 SSRs per Mb.Trinucleotides were the most frequent motifs.SSRs were found to be more frequent in UTR,intergenic regions and introns,though 299 SSRs occur in the CDS,ranking second after intergenic regions.Through blast analysis against the nr database,485 SSR-containing genes were successfully annotated.Thus,115 of them could be assigned to the Gene Ontology (GO) terms of molecular function,biological process and cell component,and 108 to KEGG pathways of metabolism,genetic information processing,cellular processes and environmental information processing.Fifty-eight pairs of primers were designed mainly for species identification,and other 23 pairs of primers were mainly used to study active substance metabolism and assist the breeding.Compared with other agaricomycete genomes,T.versicolor has lower number and reduced abundance of SSRs.SSR number was found to be unrelated to genomic size while some specific SSR motifs were related to GC content among the above six species of Agaricomycetes.The results of this study will benefit future population genetics and evolution investigation of T.versicolor.%本研究采用生物信息学方法统计分析了云芝基因组中SSR位点的数量、分布及频率等信息,对云芝基因组中含SSR的基因进行了功能注释,与其他5种伞菌纲真菌(双孢蘑菇、黑管孔菌、红缘拟层孔菌、金针菇和鲜红密孔菌)基因组进行了比较.结果发现云芝基因组中共有1 224个SSR位点,相对丰度为27个/Mb,三核苷酸重复类型分布最频繁.其中编码基因序列中包含299个SSR,仅次于基因间区,但是在非编译区、基因间区和内含子中SSR分布更加频繁.通过与nr数据库比对,485个含SSR的基因获得注释,其中115个基因通过GO注释到分子功能、生物进程及细胞组分3类中,108个基因通过KEGG注释到新陈代谢、遗传信息处理、细胞过程和环境信息处理4类中.设计58对引物主要用于物种鉴定,另外23对引物主要用于活性物质代谢研究和辅助育种.与其他伞菌纲真菌相比,云芝所含SSR的数量及相对丰度较低,并证明SSR数量与基因组大小无关,而某些特定的重复类型与GC含量有关.本研究为云芝的种群遗传学及进化研究奠定了理论基础.
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