两个糙皮侧耳菌株的比较基因组学研究

Comparative genomic analyses of two Pleurotus ostreatus strains

随着糙皮侧耳基因组测序的完成,基因组数据的深入挖掘和利用成为研究重点。本研究基于较高质量的糙皮侧耳CCMSSC00389-1和CCMSSC03989-1基因组图谱,开展了种内比较基因组学分析。CCMSSC00389-1和CCMSSC03989-1的11条染色体序列表现出良好的共线性,且分别含有89.92%和91.68%的保守基因。对菌株特有基因的GO富集分析表明,两菌株各自分化出一些独特的调控方式或途径。CCMSSC00389-1和CCMSSC03989-1之间共存在931542个单核苷酸多态性位点,231654个插入/缺失和9221个结构变异。对与遗传变异重叠基因的GO富集分析表明,碳水化合物降解、物质运输/催化和调控/蛋白活性相关的基因分别容易发生SNP、In/Del和SV变异。CCMSSC00389-1中50.326kb缺失序列的断点两侧含有双链断裂修复(DSB)信号,推测DSB介导50.326kb序列的缺失。

With the completion of genome sequencing of Pleurotus ostreatus, deep exploration and utilization of genomic data have become the research focuses. In this study, intraspecific comparative genomic analysis was carried out based on high quality genomic assemblies of P. ostreatus strains CCMSSC00389-1 and CCMSSC03989-1. The 11 chromosome sequences of CCMSSC00389-1 and CCMSSC03989-1 showed good collinearity and contained 89.92% and 91.68% conserved genes respectively. GO enrichment analysis of the strain-specific genes indicated that each strain had some unique regulatory functions or pathways. There were 931 542 SNPs, 231 65 In/Dels and 9 221 SVs between genomes of CCMSSC00389-1 and CCMSSC03989-1. GO enrichment analysis of genetic variation-overlapped genes revealed that genes related to carbohydrate degradation were prone to have SNPs, genes related to transportation/catalysis of substances were prone to have In/Dels, and genes related to regulation/protein activity were prone to have SVs. A 50.326 kb deletion with double strand break repair(DSB) signatures in its two breakpoints was identified in CCMSSC00389-1, and DSB was predicted to mediate the 50.326 kb deletion.