Armillaria species (Basidiomycota, Physalacriaceae) are well known as plant pathogens related to serious root rot disease on various trees in forests and plantations. Interestingly, some Armillaria species are essential symbionts of the rare Chinese medicinal herb Gastrodia elata, a rootless and leafless orchid used for over 2000 years. In this work, an 87.3-M draft genome of Armillaria gallica 012m strain, which was symbiotic with G. elata, was assembled. The genome includes approximately 23.6% repetitive sequences and encodes 26,261 predicted genes. In comparison with other four genomes of Armillaria, the following gene families related to pathogenicity/saprophytic phase, including cytochrome P450 monooxygenases, carbohydrate-active enzyme AA3, and hydrophobins, were significantly contracted in A. gallica 012m. These characteristics may be beneficial for G. elata to get less injuries. The genome-guided analysis of differential expression between rhizomorph (RH) and vegetative mycelium (VM) showed that a total of 2549 genes were differentially expressed, including 632 downregulated genes and 1917 upregulated genes. In the RH, most differentially expressed genes (DEGs) related to pathogenicity were significantly upregulated. To further elucidate gene function, Gene Ontology enrichment analysis showed that the upregulated DEGs significantly grouped into monooxygenase activity, hydrolase activity, glucosidase activity, extracellular region, fungal cell wall, response to xenobiotic stimulus, response to toxic substance, etc. These phenomena indicate that RH had better infection ability than VM. The infection ability of RH may be beneficial for G. elata to obtain nutrition, because the rhizomorph constantly infected the nutritional stems of G. elata and formed the hyphae that can be digested by G. elata. These results clarified the characteristics of A. gallica 012m and the reason why the strain 012m can establish a symbiotic relationship with G. elata in some extent from the perspective of genomics.

中文翻译：

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蜜环菌 012m 基因组序列草图：洞察其与天麻共生关系

蜜环菌属物种（担子菌门，Physalacriaceae）是众所周知的植物病原体，与森林和人工林中各种树木的严重根腐病有关。有趣的是，一些蜜环属植物是稀有中药天麻的重要共生体，天麻是一种使用了 2000 多年的无根无叶兰花。在这项工作中，组装了与 G. elata 共生的 Armillaria Gallica 012m 菌株的 87.3-M 基因组草图。该基因组包括大约 23.6% 的重复序列并编码 26,261 个预测基因。与蜜环菌的其他四个基因组相比，以下与致病性/腐生期相关的基因家族，包括细胞色素 P450 单加氧酶、碳水化合物活性酶 AA3 和疏水蛋白，在 A. Gallica 012m 中显着收缩。这些特性可能有利于 G. elata 减少受伤。根状茎（RH）和营养菌丝体（VM）之间差异表达的基因组引导分析表明，共有2549个基因差异表达，其中632个下调基因和1917个上调基因。在 RH 中，大多数与致病性相关的差异表达基因 (DEG) 显着上调。为了进一步阐明基因功能，基因本体富集分析表明，上调的DEGs显着分为单加氧酶活性、水解酶活性、葡萄糖苷酶活性、细胞外区域、真菌细胞壁、对异生物质刺激的反应、对有毒物质的反应等。这些现象表明， RH比VM具有更好的感染能力。RH 的感染能力可能对 G. elata 获得营养，因为根状体不断侵染G. elata 的营养茎，形成可被G. elata 消化的菌丝。这些结果从基因组学的角度阐明了 A. Gallica 012m 的特性以及菌株 012m 能够在一定程度上与 G. elata 建立共生关系的原因。