一株粗糙脉孢菌的分离、鉴定及其基因组变异和功能分析

Isolation, identification, genome variation and functional analysis of a strain form Neurospora crassa

摘要:

【背景】粗糙脉孢菌LY03是从武平传统“红菌豆腐”中分离得到的主要发酵菌株。【目的】研究粗糙脉孢菌LY03菌株的基因组信息，揭示武平传统“红菌豆腐”发酵特性。【方法】采用形态学观察、ITS鉴定、重测序及框架图测序对所分离的LY03菌株进行鉴定和基因组信息解析。【结果】武平传统“红菌豆腐”中分离得到的主要发酵菌株LY03确定为粗糙脉孢菌，将其在中国普通微生物菌种保藏管理中心进行专利保藏，保藏号为CGMCC 3.19233。LY03菌株比对到参考基因组上的总read数目为95.85%，测序对应深度的位点占全基因组76.13%；各变异类型在内含子区域均无变异，主要变异存在于基因组的外显子区域，具体变异数量为：单核苷酸多态性位点(single nucleotide polymorphism，SNP)位点变异总数203 128个、插入缺失(insertion/deletion，InDel)突变总和26 859个、拷贝数变异 (copy number variation，CNV)增加和减少的拷贝总数1 039个、结构变异(structure variation，SV)注释的变异总数777个；LY03菌株基因组序列长度为30 538 737 bp、(G+C)mol%为52.24%、编码5 550个基因、编码基因占比24.3%，参与了氨基酸代谢(amino acid metabolism)、碳水化合物代谢(carbohydrate metabolism)、能量产生与转化(energy production and conversion)等多种物质的代谢途径转化过程。【结论】对武平传统“红菌豆腐”主要发酵菌株的鉴定及基因组信息分析有利于揭示其产品发酵的特性及其发酵菌株遗传信息的本质，并为将来产品发酵性能的提高及推广提供理论依据。

Abstract:

[Background] Neurospora crassa LY03 was the main fermentation strain isolated from traditional “Red fungus tofu” in Wuping. [Objective] The genomic information of Neurospora crassa LY03 strain was studied to reveal the fermentation characteristics of traditional “Red fungus tofu” in Wuping. [Methods] Morphological observation, ITS identification, resequencing and frame diagram sequencing were used to identify the isolated LY03 strains and analyzed the genome information. [Results] The main fermentation strain LY03 isolated from traditional “Red fungus tofu” in Wuping was identified as Neurospora crassa, and preserved in the China General Microbiological Culture Collection Center with preservation number CGMCC 3.1923. The total number of reads in LY03 strain compared to the reference genome was 95.85%, and the site of sequencing corresponding depth accounted for 76.13% of the whole genome. There was no variation in the intronic region of each variant type, and the main variation existed in the exon region of the genome, and the specific number of variation was as follows: The total number of SNP site variants was 203 128, InDel mutations was 26 859, copies increased and decreased by CNV was 1 039, variation in SV comments was 777. The genome sequence length of LY03 strain was 30 538 737 bp, (G+C)mol% was 52.24%, encoding 5 550 genes, accounting for 24.3% of the coding genes, which was involved in the metabolic pathway transformation of amino acid metabolism, carbohydrate metabolism, energy production and conversion and other substances. [Conclusion] The identification and genome information analysis of the main fermentation strains of traditional “Red fungus tofu” in Wuping are helpful to reveal the fermentation characteristics of the products and the essence of the genetic information of the fermentation strains, and to provide a theoretical basis for the improvement of the fermentation performance and the popularization of the products in the future.