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
Affiliations
Xuan Liu
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
Xin Huang
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
Chen Chu
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
Hui Xu
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
Long Wang
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China; Corresponding author
Yarong Xue
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
Zain Ul Arifeen Muhammad
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
Fumio Inagaki
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; Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai 980-8574, Japan
Changhong Liu
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China; Corresponding author
Summary: 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.
