Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500, Kunming, China.
BMC Genomics. 2023 May 23;24(1):275. doi: 10.1186/s12864-023-09384-4.
Armillaria species are plant pathogens, but a few Armillaria species can establish a symbiotic relationship with Gastrodia elata, a rootless and leafless orchid, that is used as a Chinese herbal medicine. Armillaria is a nutrient source for the growth of G. elata. However, there are few reports on the molecular mechanism of symbiosis between Armillaria species and G. elata. The genome sequencing and analysis of Armillaria symbiotic with G. elata would provide genomic information for further studying the molecular mechanism of symbiosis.
The de novo genome assembly was performed with the PacBio Sequel platform and Illumina NovaSeq PE150 for the A. gallica Jzi34 strain, which was symbiotic with G. elata. Its genome assembly contained ~ 79.9 Mbp and consisted of 60 contigs with an N50 of 2,535,910 bp. There were only 4.1% repetitive sequences in the genome assembly. Functional annotation analysis revealed a total of 16,280 protein coding genes. Compared with the other five genomes of Armillaria, the carbohydrate enzyme gene family of the genome was significantly contracted, while it had the largest set of glycosyl transferase (GT) genes. It also had an expansion of auxiliary activity enzymes AA3-2 gene subfamily and cytochrome P450 genes. The synteny analysis result of P450 genes reveals that the evolutionary relationship of P450 proteins between A. gallica Jzi34 and other four Armillaria was complex.
These characteristics may be beneficial for establishing a symbiotic relationship with G. elata. These results explore the characteristics of A. gallica Jzi34 from a genomic perspective and provide an important genomic resource for further detailed study of Armillaria. This will help to further study the symbiotic mechanism between A. gallica and G. elata.
蜜环菌属的物种是植物病原体，但有少数蜜环菌属的物种可以与天麻建立共生关系，天麻是一种无根无叶的兰花，被用作中药。蜜环菌是天麻生长的营养来源。然而，关于蜜环菌属和天麻之间共生的分子机制的报道很少。对与天麻共生的蜜环菌进行基因组测序和分析，将为进一步研究共生的分子机制提供基因组信息。
使用 PacBio Sequel 平台和 Illumina NovaSeq PE150 对与天麻共生的 A. gallica Jzi34 菌株进行了从头基因组组装。其基因组组装包含约 79.9 Mbp，由 60 个 contigs 组成，N50 为 2,535,910 bp。基因组组装中只有 4.1%的重复序列。功能注释分析共揭示了 16,280 个蛋白编码基因。与其他五个蜜环菌属基因组相比，该基因组的碳水化合物酶基因家族明显收缩，而其拥有最大的糖基转移酶 (GT) 基因集。它还具有辅助活性酶 AA3-2 基因亚家族和细胞色素 P450 基因的扩张。P450 基因的共线性分析结果表明，A. gallica Jzi34 与其他四个蜜环菌属的 P450 蛋白之间的进化关系很复杂。
这些特征可能有利于与天麻建立共生关系。这些结果从基因组角度探讨了 A. gallica Jzi34 的特点，为进一步详细研究蜜环菌属提供了重要的基因组资源。这将有助于进一步研究蜜环菌与天麻之间的共生机制。
