Draft genomic sequence ofArmillaria gallica012m: insights into its symbiotic relationship withGastrodia elata

Armillariaspecies (Basidiomycota, Physalacriaceae) are well known as plant pathogens related to serious root rot disease on various trees in forests and plantations. Interestingly, someArmillariaspecies are essential symbionts of the rare Chinese medicinal herbGastrodia elata, a rootless and leafless orchid used for over 2000 years. In this work, an 87.3-M draft genome ofArmillaria gallica012m strain, which was symbiotic withG. elata, was assembled. The genome includes approximately 23.6% repetitive sequences and encodes 26,261 predicted genes. In comparison with other four genomes ofArmillaria, the following gene families related to pathogenicity/saprophytic phase, including cytochrome P450 monooxygenases, carbohydrate-active enzyme AA3, and hydrophobins, were significantly contracted inA. gallica012m. These characteristics may be beneficial forG. elatato 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 forG. elatato obtain nutrition, because the rhizomorph constantly infected the nutritional stems ofG. elataand formed the hyphae that can be digested byG. elata. These results clarified the characteristics ofA. gallica012m and the reason why the strain 012m can establish a symbiotic relationship withG. elatain some extent from the perspective of genomics.