Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China

The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the Chinese L. edodes population with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains of L. edodes in China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence of L. edodes in China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits of L. edodes cultivars in China.

Under stress conditions, effective signal transduction is a premise that passes environmental information into the inside of a fungal cell. There are several signaling pathways which have evolved in fungi to respond to environmental stresses, including MAPK (mitogen activated protein kinase), cAMP-PKA (cyclic AMP-protein kinase A), TOR (target-of-rapamycin), and Ca 2+ -calcineurin pathways 1,2 . Gene aug_scv1_leest_g2962 codes for a Pbs2-like MAPKK protein. In fungi, the Hog1-mediated MAPK pathway is widely involved in resistance to thermal shocks, osmotic stress, oxidative stress and heavy metals 1 . Pbs2 is responsible for activating Hog1 in the Hog1 pathway 3 . Recently, the Hog1 pathway has been reported to be involved in stress response in macro-basidiomycetes, Heterobasidion annosum 4 . Gene aug_scv1_leest_g2964, encoding a kinase similar to Saccharomyces cerevisiae Yak1. Yak1 phosphorylates and activates the transcription factors Hsf1 (heat-shock transcription factor) and Msn2, which play important roles in cellular homeostasis by activating gene expression during stress conditions, including heat shock, nutrient starvation and oxidative stress 5 . Yak1, along with phosphoprotein Pop2, functions as a part of a glucose-sensing system that controls the growth of yeast 6 . Hsf1 is conserved from yeast to humans and it is essential for the viability of an organism 7 and it is also a master regulator of HSP (heat-shock protein) expression 8 .
Fungal heat-shock proteins (HSP) also function as crucial regulators of stress response, and are involved in various biological pathways. Aug_scv1_leest_g6029 codes for a homolog of Hsp40, also called DnaJ. Hsp40 is a cofactor of the Hsp70 (DnaK) responsible for the initial folding of nascent polypeptide in biotic and abiotic stresses 9,10 . In bacteria, the DnaK/DnaJ/GrpE chaperone functions as a critical thermosensor detecting temperature variation by modulating conformational changes of GrpE 11 .
Characteristics of lipid in membrane is another factor that contributes to stress response 12 . In mushroom-forming fungi, membrane alteration is a stress signal that triggers the shift from vegetative growth to reproductive growth 13 . The homologs of several genes involved in lipid metabolism have been identified here.
Aug_scv1_leest_g3811 encodes a glycerol-3-phosphate o-acyltransferase. In bacteria, acyltransferases control the temperature-dependent remodeling of membrane lipid A under different environmental temperature conditions 14 . Aug_scv1_leest_g4530 codes for a C4-methyl sterol oxidase that participates in the fatty acid biosynthetic process. Ergosterol biosynthesis is the pathway responsible for the construction of ergosterol -an important component of fungal membrane -and it is required for maintaining the membrane stability and fluidity 15 . In Aspergillus fumigatus, the C4-methyl sterol oxidase is involved in maintaining canonical ergosterol biosynthesis and the stress response to the environment 16 .
Twelve other genes are related to stress response and fruiting body initiation and they are involved in the population differentiation of one or two groups ( Table 2). Aug_scv1_leest_g5779 and aug_scv1_leest_g8857, code for PKC-like kinase. Gene aug_scv1_leest_g6391 encodes tuberin and gene aug_scv1_leest_g7437 codes for guanine nucleotide-exchange factor 1 (GEF1). The homologs of these genes were reported to serve in stress-signaling pathways [17][18][19][20] . A homolog of BAG domain-containing protein encoding by aug_scv1_leest_g2961, which can interact with and regulate Hsp70 under stress conditions 21 .
Transcription factors (TFs) govern changes in gene expression in response to environmental stresses. PriB TF encoded by aug_scv1_leest_g8832, is related to fruiting body initiation in L. edodes 23 . A GATA transcription factor encoded by aug_scv1_leest_g9618, whose homolog acts as modulator of stress response 24 .
Aug_scv1_leest_g3008 codes for endoplasmic reticulum oxidoreductin 1, and aug_scv1_leest_g7483 encodes a SNF2 family DNA-dependent ATPase, whose homologs interact with Hsf1 and respond to temperature stress in 68 yeast 25,26 .
In addition, gene productions of aug_scv1_leest_g9807 and aug_scv1_leest_g12501 are DEAD box RNA helicases, which are key factors in the cold response in fungi 27 .