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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。
In this study, the bioinformatics methods were used to statistically analyze the number, distribution and frequency of SSR loci in the genome of Coriolus versicolor. Functional annotation of SSR-containing genes in the genome of Coriolus versicolor was carried out. Compared with other 5 species of Agaricus Agaricus bisporus, Corynebacterium mucronatus, Rhodosporidium, Flammulina velutipes and Pseudomonas aeruginosa) genomes were compared. A total of 1 224 SSR loci were found in the genome of Coriolus versicolor, with a relative abundance of 27 per Mb and the trinucleotide repeat types were most frequently distributed. Among them, 299 SSRs were found in the sequence of coding genes, second only to the intergenic region, but SSR distribution was more frequent in non-coding region, intergenic region and intron. One hundred and fifty five SSR-containing genes were annotated by comparison with the nr database, of which 115 were annotated with GO to molecular functions, biological processes, and cellular components. 108 genes were annotated through KEGG to metabolism, genetic information processing, Cell Processes and Environmental Information Processing. Fifty-eight pairs of primers were designed for species identification, and the other 23 pairs were primarily used for active metabolite research and assisted breeding. The amount and relative abundance of SSR contained in Yunzhi was lower than that of other Agaricomyces and it was proved that the number of SSR was not related to the size of the genome, while some specific repeat types were related to the content of GC. This study laid the theoretical foundation for the study of population genetics and evolution of Yunzhi.