18个双孢蘑菇核心种质的重测序初步分析

A Preliminary Report on Resequencing 18 Representative Strains of Agaricus bisporus

【目的】通过对双孢蘑菇不同类型核心种质的基因组重测序分析,探讨双孢蘑菇不同类型菌株间基因组存在的差异及开发相关分子标记。【方法】对双孢蘑菇国内外杂交菌株、野生菌株、高产型或优质型传统菌株、棕色菌株、不育菌株等共18株核心种质进行基因组重测序,应用不同的生物信息学处理软件,对测序得到的原始reads序列与双孢蘑菇参考基因组H97序列进行比对,同时基于比对结果进行SNP、SV检测,通过检测结果对多态性标记分布进行统计并实现DNA水平差异基因挖掘和差异基因功能注释等。【结果】样品测序共获得21.63 G数据量,Q30平均达到89.10%。样品的reads与参考基因组H97的比对效率平均为82.50%,基因组覆盖度为96.32%,平均深度分别在33X左右。基于测序数据与参考基因组的比对结果,共检测获得约813 768个SNP,53 840个InDel,平均每个个体获得924个SV变异。【结论】国内外菌株的亲缘关系表明As2796系列与U1系列是世界上并列的两大双孢蘑菇杂交品系。

【Objective】 By resequencing the genomes of representative strains of Agaricus bisporus, the genetic differentiations and molecular markers were investigated for taxonomic and analytical studies on the mushrooms.【Method】 Genes of 18 major strains of A. bisporus including hybrids and wild strains from local and foreign sources, traditional highly productive or good quality varieties, and brown-colored and sterile strains were resequenced. Various bioinformatics software programs were applied to align the readings with the reference A. bisporus genome data. From the aligned results, SNP and SV were obtained to statistically analyze the distribution of the genetic differentiations in search for DNA-based molecular markers and to decipher the functions of the genomes.【Result】 From the resequencing, 21.63 G data were obtained with an average Q30 reaching 89.10%. A matching rate of 82.50%, a coverage of 96.32%, and an average depth of 33 X were found between the readings and sequence of the H97 reference genome. From the alignment results, 813 768 SNPs and 53 840 InDels were obtained with an average of 924 SV variations for each strain.【Conclusion】 Of the various A. bisporus strains in the world,the Chinese As2796 and Dutch U1 lines seemed to be the two major commercial hybrids on the market.