Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
College of Life Sciences, Shandong Normal University, Jinan, China.
Genome Biol Evol. 2023 Aug 1;15(8). doi: 10.1093/gbe/evad136.
To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.
为了阐明外生菌根（EcM）珊瑚菌属物种在外生菌根菌目生态多样化中的基因组特征，我们对 15 个新基因组进行了测序，特别关注了 EcM 珊瑚菌属物种。结合已发表的数据，共比较分析了 32 个基因组，包括 31 个外生菌根菌目和一个外群。与寄生和腐生成员相比，EcM 物种的植物细胞壁降解酶基因数量显著减少，转座元件、基因组大小、小分泌蛋白和分泌蛋白酶显著增加。EcM 物种仍然保留了一些分泌碳水化合物活性酶（CAZymes），并且失去了降解木质素和纤维素的关键分泌 CAZymes，但具有很强的降解含有几丁质和肽聚糖的微生物细胞壁的能力。在 Gymnosperms 和 Angiosperms 上生长的真菌之间，分泌 CAZymes 没有显著差异，这表明外生菌根菌目中的分泌 CAZymes 是在宿主树木分化为裸子植物和被子植物之前进化而来的。然而，外生菌根菌目的寄生和腐生物种在许多基因组特征上非常相似，这反映了它们作为白腐真菌的密切系统发育关系。系统基因组学和分子钟分析表明，EcM 属珊瑚菌形成了一个位于外生菌科基部的分支，其分化时间晚于腐生物种。而且珊瑚菌仍然保留了一到两个 AA2 家族的基因。这些表明珊瑚菌的祖先似乎起源于具有白腐能力的腐生祖先。本研究为 EcM 物种提供了新的基因组数据，并通过比较基因组学和系统基因组学分析，对外生菌根菌目内的生态多样化提供了新的见解。
