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

被引:24
作者
Xiao, Yang [1 ,2 ]
Cheng, Xuanjin [2 ]
Liu, Jun [1 ]
Li, Chuang [1 ]
Nong, Wenyan [2 ]
Bian, Yinbing [1 ]
Cheung, Man Kit [2 ]
Kwan, Hoi Shan [2 ]
机构
[1] Huazhong Agr Univ, Inst Appl Mycol, Wuhan 430070, Hubei Province, Peoples R China
[2] Chinese Univ Hong Kong, Sch Life Sci, Shatin, Hong Kong, Peoples R China
来源
SCIENTIFIC REPORTS | 2016年 / 6卷
基金
中国国家自然科学基金;
关键词
GENETIC DIVERSITY; CULTIVATED STRAINS; LOCAL ADAPTATION; MATING-TYPE; GROWTH-RATE; YEAST; WILD; IDENTIFICATION; DOMESTICATION; MARKERS;
D O I
10.1038/srep36789
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
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页数:12
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共 57 条
  • [1] Alexa A., 2007, ENCY SYSTEMBIOL, V23, P193
  • [2] Fast model-based estimation of ancestry in unrelated individuals
    Alexander, David H.
    Novembre, John
    Lange, Kenneth
    [J]. GENOME RESEARCH, 2009, 19 (09) : 1655 - 1664
  • [3] A population genomics insight into the Mediterranean origins of wine yeast domestication
    Almeida, Pedro
    Barbosa, Raquel
    Zalar, Polona
    Imanishi, Yumi
    Shimizu, Kiminori
    Turchetti, Benedetta
    Legras, Jean-Luc
    Serra, Marta
    Dequin, Sylvie
    Couloux, Arnaud
    Guy, Julie
    Bensasson, Douda
    Goncalves, Paula
    Sampaio, Jose Paulo
    [J]. MOLECULAR ECOLOGY, 2015, 24 (21) : 5412 - 5427
  • [4] Fungi sensing environmental stress
    Alonso-Monge, R.
    Roman, E.
    Arana, D. M.
    Pla, J.
    Nombela, C.
    [J]. CLINICAL MICROBIOLOGY AND INFECTION, 2009, 15 : 17 - 19
  • [5] The Pbs2 MAP kinase kinase is essential for the oxidative-stress response in the fungal pathogen Candida albicans
    Arana, DM
    Nombela, C
    Alonso-Monge, R
    Pla, J
    [J]. MICROBIOLOGY-SGM, 2005, 151 : 1033 - 1049
  • [6] Sensing the environment: lessons from fungi
    Bahn, Yong-Sun
    Xue, Chaoyang
    Idnurm, Alexander
    Rutherford, Julian C.
    Heitman, Joseph
    Cardenas, Maria E.
    [J]. NATURE REVIEWS MICROBIOLOGY, 2007, 5 (01) : 57 - 69
  • [7] Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives
    Baute, Gregory J.
    Kane, Nolan C.
    Grassa, Christopher J.
    Lai, Zhao
    Rieseberg, Loren H.
    [J]. NEW PHYTOLOGIST, 2015, 206 (02) : 830 - 838
  • [8] Trimmomatic: a flexible trimmer for Illumina sequence data
    Bolger, Anthony M.
    Lohse, Marc
    Usadel, Bjoern
    [J]. BIOINFORMATICS, 2014, 30 (15) : 2114 - 2120
  • [9] Genetic isolation between two recently diverged populations of a symbiotic fungus
    Branco, Sara
    Gladieux, Pierre
    Ellison, Christopher E.
    Kuo, Alan
    LaButti, Kurt
    Lipzen, Anna
    Grigoriev, Igor V.
    Liao, Hui-Ling
    Vilgalys, Rytas
    Peay, Kabir G.
    Taylor, John W.
    Bruns, Thomas D.
    [J]. MOLECULAR ECOLOGY, 2015, 24 (11) : 2747 - 2758
  • [10] Stress adaptation in a pathogenic fungus
    Brown, Alistair J. P.
    Budge, Susan
    Kaloriti, Despoina
    Tillmann, Anna
    Jacobsen, Mette D.
    Yin, Zhikang
    Ene, Iuliana V.
    Bohovych, Iryna
    Sandai, Doblin
    Kastora, Stavroula
    Potrykus, Joanna
    Ballou, Elizabeth R.
    Childers, Delma S.
    Shahana, Shahida
    Leach, Michelle D.
    [J]. JOURNAL OF EXPERIMENTAL BIOLOGY, 2014, 217 (01) : 144 - 155