Genome of Ganoderma Species Provides Insights Into the Evolution, Conifers Substrate Utilization, and Terpene Synthesis for Ganoderma tsugae.

Nan Jiang,Xiaohui Yuan,Shuang Hu,Yongping Fu,Shijun Xiao,Bing Peng,Zhenhao Li

doi:10.3389/fmicb.2021.724451

Abstract

Ganoderma tsugae is an endemic medicinal mushroom in Northeast China, providing important source of pharmaceutical product. Comparing with other Ganoderma species, wild G. tsugae can utilize coniferous wood. However, functional genes related to medicinal component synthesis and the genetic mechanism of conifer substrate utilization is still obscure. Here, we assembled a high-quality G. tsugae genome with 18 contigs and 98.5% BUSCO genes and performed the comparative genomics with other Ganoderma species. G. tsugae diverged from their common ancestor of G. lingzhi and G. sinense about 21 million years ago. Genes in G. tsugae-specific and G. tsugae-expanded gene families, such as salh, phea, cyp53a1, and cyp102a, and positively selected genes, such as glpk and amie, were functionally enriched in plant-pathogen interaction, benzoate degradation, and fanconi anemia pathway. Those functional genes might contribute to conifer substrate utilization of G. tsugae. Meanwhile, gene families in the terpene synthesis were identified and genome-wide SNP variants were detected in population. Finally, the study provided valuable genomic resources and offered useful hints for the functional gene mapping and investigation of key gene contributing to conifer cultivation substrate utilization and medicinal component biosynthesis.

Highlights

Ganoderma tsugae is a precious cultivated Ganoderma species in Northeast China, which has become an important source of pharmaceutical product (Hung et al, 2004; Wu et al, 2004)
The aims of this study are as follows: (1) generate a high-quality reference genome for G. tsugae to lay a solid foundation for further functional genomic studies; (2) provide hints for the mechanism of conifer substrate utilization by comparative genomic studies between G. tsugae and three broadleaf-tree parasitic Ganoderma species; (3) identify putative functional genes involved in the pharmaceutical compound synthesis in the genome; and (4) develop genome-wide molecular markers in a high-throughput manner from population sequencing for G. tsugae
G. tsugae, one of the Ganoderma species which was used in traditional Chinese medicine for more than 4,000 years, has been widely cultivated for pharmaceutical product in North

Summary

Introduction

Ganoderma tsugae is a precious cultivated Ganoderma species in Northeast China, which has become an important source of pharmaceutical product (Hung et al, 2004; Wu et al, 2004). Compared with other cultivated Ganoderma species, such as G. lingzhi and G. sinense, wild G. tsugae mainly distribute in the Changbai Mountain and grow on coniferous wood, such as Larix gmelinii, Abies nephrolepis, Abies fabri, etc. Previous studies mainly focused on the isolation and pharmaceutical functions of secondary metabolites in G. tsugae (Kıvrak, 2015; Ma et al, 2020). Identifying key genes for conifer substrate utilization and medicinal component synthesis would facilitate our understanding for the mechanism of habitat environmental adaptation and molecular improvement of G. tsugae; genetic basis underlying those important biological processes. The molecular markers and genetic diversity analysis of G. tsugae germplasm resources are rarely reported before

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