Insights into the ecological diversification of the Hymenochaetales based on comparative genomics and phylogenomics with an emphasis on Coltricia.

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, ectomycorrhizal species have significantly reduced number of plant cell wall degrading enzyme (PCWDE) genes, and expanded transposable elements (TEs), genome sizes, small secreted proteins (SSPs) and secreted proteases. Ectomycorrhizal 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 reflects their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the ectomycorrhizal genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remain one to two genes of AA2 family. These indicates 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 ectomycorrhizal species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.