Biology
Document Type
Article
Abstract
Introduction: Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi. Objectives: This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution. Methods: We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution. Results: We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation. Conclusion: Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.
Publication Title
Journal of Advanced Research
Publication Date
5-2022
Volume
38
First Page
91
Last Page
106
ISSN
2090-1232
DOI
10.1016/j.jare.2021.09.008
Keywords
adaptation, genetic divergence, GWAS, phenotypic differentiation, population genomics, shiitake
Repository Citation
Zhang, Jingcheng; Shen, Nan; Li, Chuang; Xiang, Xingjie; Liu, Gaolei; Gui, Ying; Patev, Sean; Hibbett, David S.; Barry, Kerrie; Andreopoulos, William; Lipzen, Anna; Riley, Robert; He, Guifen; Yan, Mi; Grigoriev, Igor V.; Shan Kwan, Hoi; Kit Cheung, Man; Bian, Yinbing; and Xiao, Yang, "Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes" (2022). Biology. 165.
https://commons.clarku.edu/faculty_biology/165
Cross Post Location
Student Publications
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 4.0 International License.
Copyright Conditions
Zhang, J., Shen, N., Li, C., Xiang, X., Liu, G., Gui, Y., ... & Xiao, Y. (2022). Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes. Journal of Advanced Research, 38, 91-106. https://doi.org/10.1016/j.jare.2021.09.008
