Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

Abstract

The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

“…It is believed that the genus Ganoderma encompasses more than 250 distinct species ( Wang et al, 2012 ; Kües et al, 2015 ; Jargalmaa et al, 2017 ; Sun et al, 2022c ). At present, the genomics and cultivation of Ganoderma genus are receiving increasing attention, promoting the development and utilization of Ganoderma resources ( Si et al, 2021 ; Sun et al, 2022b ). It has been observed that some species from the Ganoderma genus can be detrimental to woody plants, such as G .…”

Whole-genome sequencing and comparative genomic analyses of the medicinal fungus Sanguinoderma infundibulare in Ganodermataceae

“…2020 ). Currently, 18 species have been included in the genus Sanguinoderma worldwide ( Sun, Lebreton, et al 2022 ). Among them, Sanguinoderma infundibulare B.K.…”

Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis onColtricia

“…With the reduction of genome sequencing costs and the rapidly increasing numbers of fungal genome data, more studies have focused on the innovation and evolution of fungal life modes using omics data analyses ( Floudas et al 2012 ; Sipos et al 2017 ; Naranjo-Ortiz and Gabaldón 2019 ; Lebreton et al 2021 ; Lofgren et al 2021 ; Sun et al 2022 ; Wu et al 2022c ). Comparative genomic analyses have suggested that white rot fungi differ from brown rot fungi by their CAZymes repertoire ( Floudas et al 2012 ).…”