Genome, genetic evolution, and environmental adaptation mechanisms of Schizophyllum commune in deep subseafloor coal-bearing sediments

Xuan Liu; Xin Huang; Chen Chu; Hui Xu; Long Wang; Yarong Xue; Zain Ul Arifeen Muhammad; Fumio Inagaki; Changhong Liu

doi:10.1016/j.isci.2022.104417

Genome, genetic evolution, and environmental adaptation mechanisms of Schizophyllum commune in deep subseafloor coal-bearing sediments

iScience. 2022 May 18;25(6):104417. doi: 10.1016/j.isci.2022.104417. eCollection 2022 Jun 17.

Authors

Xuan Liu¹, Xin Huang¹, Chen Chu¹, Hui Xu¹, Long Wang¹, Yarong Xue¹, Zain Ul Arifeen Muhammad¹, Fumio Inagaki^{2

3}, Changhong Liu¹

Affiliations

¹ State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China.
² Mantle Drilling Promotion Office, Institute for Marine-Earth Exploration and Engineering (MarE3), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama 236-0001, Japan.
³ Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai 980-8574, Japan.

Abstract

To understand the genomic evolution and adaptation strategies of fungi to subseafloor sedimentary environments, we de novo assembled the genome of Schizophyllum commune strain 20R-7-F01 isolated from ∼2.0 km-deep, ∼20-millionyearsago (Mya) coal-bearing sediments. Phylogenomics study revealed a differentiation time of 28-73 Mya between this strain and the terrestrial type-strain H4-8, in line with sediment age records. Comparative genome analyses showed that FunK1 protein kinase, NmrA family, and transposons in this strain are significantly expanded, possibly linking to the environmental adaptation and persistence in sediment for over millions of years. Re-sequencing study of 14 S. commune strains sampled from different habitats revealed that subseafloor strains have much lower nucleotide diversity, substitution rate, and homologous recombination rate than other strains, reflecting that the growth and/or reproduction of subseafloor strains are extremely slow. Our data provide new insights into the adaptation and long-term survival of the fungi in the subseafloor sedimentary biosphere.

Keywords: Geology; Mycology.