基因组SNP揭示少根根霉种群结构

少根根霉在自然界分布广泛,是重要的食品发酵菌,又是著名的机会致病菌,在形态和生化上多样性丰富,包括原变种、德氏变种和东京变种等3个分类学变种,原型、德氏型、东京型和鲁氏型等4个形态型,以及乳酸组和富马苹果酸组等2个生化组。DNA分子多样性更为丰富。但这些多样性之间缺乏系统的关联研究。本研究选择能代表以上多样性的67个菌株,通过全基因组重测序提取ITS、IGS rDNA和SNP多态性位点进行分子系统发育和群体结构分析,结果将少根根霉分为4个主要的系统发育分支,分支1和2是姐妹群关系,共同构成德氏变种,另外两个分支分别对应东京变种和原变种。鲁氏形态型多系,源自原变种和德氏变种。群体结构分析表明在少根根霉物种内,德氏变种首先分歧出来,然后东京变种和原变种发生分化,最后3个变种分化出各自的亚群;这些亚群表明少根根霉物种正沿着8个相互杂交的分子群体进行演化。本研究首次利用基因组范围的信息支持所有的生态群、分类学变种、形态型、生化组和系统发育分支仍然属于同一个物种,物种分化尚未完成,同时实现了对少根根霉多个DNA分子群体的解析并推导出其演化规律。

Genomic SNPs reveal population structure of Rhizopus arrhizus

Rhizopus arrhizus is widely distributed in nature, important in food fermentation and well-known as opportunistic pathogens. It is diverse in morphology and biochemistry, including three taxonomic varieties (arrhizus, delemar and tonkinensis), four morphological types (arrhizus, delemar, tonkinensis and rouxii) and two biochemical groups (lactic acid, LA; and fumaric-malic acid, FMA). This species is more diverse in DNA molecules. However, the relationship among all these diversities lacks a systematic research. Based on the internal transcribed spacer (ITS), intergenic spacer (IGS) of nuclear ribosomal DNA and single nucleotide polymorphisms (SNPs) extracted from whole-genome resequencing, this study analyzed the phylogeny and population structure of R. arrhizus represented by strains covering the diversities above. Results showed that R. arrhizus was divided into four main phylogenetic clades. The sister clades 1 and 2 constituted the variety delemar, and the other two clades corresponded with the varieties tonkinensis and arrhizus, respectively. The morphological type rouxii was polyphyletic in the clades of varieties arrhizus and delemar. Analyses about the population structure within R. arrhizus indicated that the variety delemar diverged first, then the variety tonkinensis and arrhizus, and finally subgroups of these three varieties each; these subgroups indicated that R. arrhizus is evolving molecularly along eight hybrid populations. For the first time, this study molecularly analyzed several R. arrhizus populations and deduced its evolution through genome-wide information, and confirmed that all ecological populations, taxonomic varieties, morphological types, biochemical groups and phylogenetic clades were conspecific, and no speciation occurrence.