There were 108 SSRs primers.

Armillaria spp. are devastating forest pathogens. Due to its low pathogenicity and abundant genetic variation, Armillaria gallica exhibited a unique and beneficial symbiosis with Gastrodia elata, which was used as a traditional Chinese medicine. However, the variation and population structure of A. gallica populations have rarely been investigated. Hence, we analyzed the evolution and variation in simple sequence repeats (SSRs) in three Armillaria genomes: A. gallica, A. cepistipes, and A. ostoyae to assess the genetic diversity and population structure of 14 A. gallica strains. Genome analysis revealed that SSRs were more abundant in the intergenic region than the intron and exon region, as was the SSR density. Compared with other two genomes, SSR density was the lowest in exon region and largest in the intron region of A. gallica, with significant variation in genic region. There were 17 polymorphic markers in A. gallica genome was identified, with 26.7% in genic region, which is higher than that of 18.8% in the intergenic region. Moreover, a total of 50 alleles and 42 polymorphic loci were detected among these A. gallica strains. The averaged polymorphism information content (PIC) was 0.4487, ranged from 0.2577 to 0.6786. Both principal coordinate analysis (PCoA) and population structure analyses based on the genotype data of SSRs divided the strains into two clusters. The cluster I included all the strains from high-altitude G. elata producing areas and some low-altitude areas, while the strains in Cluster II originated from low-altitude G. elata producing areas. These results indicated that substantial genome-specific variation in SSRs within the genic region of A. gallica and provide new insights for further studies on the evolution and breeding of A. gallica.蜜环菌属（Armillaria）真菌是一类毁灭性森林病原菌。其中高卢蜜环菌（Armillaria gallica）因致病力较弱且遗传变异丰富，可与传统中药材天麻（Gastrodia elata）形成独特的互利共生关系。但目前针对高卢蜜环菌种群的变异与种群结构研究尚较为匮乏。为此，本研究对3种蜜环菌的基因组——高卢蜜环菌（Armillaria gallica）、cepistipes蜜环菌（Armillaria cepistipes）以及奥氏蜜环菌（Armillaria ostoyae）——的简单序列重复（simple sequence repeats，SSR）演化与变异特征展开分析，以评估14株高卢蜜环菌菌株的遗传多样性与种群结构。基因组分析结果显示，SSR在基因间区的丰度及密度均高于内含子区与外显子区。相较于另外两种蜜环菌，高卢蜜环菌的外显子区SSR密度最低，内含子区SSR密度最高，且其基因区SSR存在显著变异。本研究在高卢蜜环菌基因组中共鉴定得到17个多态性标记，其中26.7%的标记位于基因区，占比高于基因间区的18.8%。此外，在供试的14株高卢蜜环菌菌株中共检测到50个等位基因与42个多态性位点。其平均多态信息含量（polymorphism information content，PIC）为0.4487，取值范围为0.2577至0.6786。基于SSR基因型数据的主坐标分析（principal coordinate analysis，PCoA）与种群结构分析均将供试菌株划分为两个类群：类群I包含所有来自高海拔天麻产区及部分低海拔产区的菌株，而类群II菌株均来源于低海拔天麻产区。本研究结果表明，高卢蜜环菌基因区的SSR存在显著的基因组特异性变异，可为后续高卢蜜环菌的演化与育种研究提供新的理论视角与研究思路。