基于重测序的23份香菇种质资源全基因组序列分析

Whole- genome squence analysis of 23 Lentinula edodes germplasms based on genome re-sequencing

摘要

为了对河南香菇主产区的主栽品种进行鉴定，并分析其遗传多样性，将河南主栽的23份香菇种质资源进行重测序，对单核苷酸多态性(single nucleotide polymorphism, SNP)和小片段插入缺失(insertion-deletion, InDel)等数据进行统计和分析，并基于SNP变异对23份香菇资源进行遗传结构分析、进化树构建和主成分分析。结果表明，在23份香菇样本中，比对到参考基因组上的reads数目占总数的比例范围为72.53%~90.60%，样品平均测序深度范围为12.83~19.99，覆盖率范围为91.89%~99.32%。SNP位点共计14 115 075个，InDel共计1 909 516个。23份香菇样本的群体遗传结构及系统发育分析表明其包含3个谱系，遗传距离0.054 90~0.656 89，推测它们至少有3个祖先遗传成分。结合主成分分析法明确各菌种间的亲缘关系远近，证明了菌种分支具有明显的地域性。综合分析表明，以基因序列相似度、遗传距离差异及亲缘关系远近为主要依据特点，有助于对香菇地方品种命名和其特征特性关系的认识，促进优异种质资源的交流与利用。

Abstract

To identify and analyze the genetic diversity of Lentinula edodes isolated from the main producing area in Henan province, the study resequenced the genomes of 23 cultivated L. edodes germplasm resources. The researchers analyzed the single nucleotide polymorphism (SNP) and insertion-deletion (InDel) data, and finished the genetic structure analysis, phylogenetic tree construction and principal component analysis based on the SNP variation. The proportion of reads matched to the reference genome ranged from 72.53% to 90.60% among the samples, with an average sequencing depth ranging from 12.83 to 19.99 and coverage rates ranging from 91.89% to 99.32%. The researchers identified a total of 14 115 075 SNP sites and 1 909 516 InDel sites. The results revealed the presence of three lineages with genetic distances ranging from 0.054 90 to 0.656 89, indicating the existence of at least three ancestral genetic components. Based on the principal component analysis, the relative distance of each strain was confirmed, which proved that the strain branches had obvious regional characteristics.The comprehensive analysis considered the similarity of gene sequences, genetic distance differences, and the relationships among relatives as the main characteristics. The understanding of these characteristics could facilitate the exchange and utilization of excellent germplasm resources. Additionally, the study provided insights into the relationship between the naming of local varieties and their genetic characteristics.

关键词

香菇 / 重测序 / 单核苷酸多态性 / 插入缺失变异 / 群体遗传结构

Key words

Lentinula edodes / Resequencing / Single nucleotide polymorphism / Insertion-deletion variation / Population genetic structure

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基金资助

河南省重点研发与推广专项(212102110056)