Genomic Analyses Reveal Evidence of Independent Evolution, Demographic History, and Extreme Environment Adaptation of Tibetan Plateau Agaricus bisporus
Genomic Analyses Reveal Evidence of Independent Evolution, Demographic History, and Extreme Environment Adaptation of Tibetan Plateau Agaricus bisporus
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DOI：
10.3389/fmicb.2019.01786
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发表时间：
2019-08
影响因子：
5.2
通讯作者：
Lei Sun;Yuhua Fu;Yang Yang-Yang;Xinxin Wang;Weijie Cui;Dan Li;Xiaohui Yuan;Zhiwu Zhang;Yongping Fu;Yu Li
中科院分区：
文献类型：
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作者：
Lei Sun;Yuhua Fu;Yang Yang-Yang;Xinxin Wang;Weijie Cui;Dan Li;Xiaohui Yuan;Zhiwu Zhang;Yongping Fu;Yu Li
分布于我国青藏高原的双孢蘑菇具有很强的抗逆性，具有育种改良价值。然而，它的进化历史，专业化，并适应极端的青藏高原环境在很大程度上是未知的。本研究对青藏高原典型野生株ABM进行了全基因组测序，并与欧洲株H97和H39进行了比较基因组分析。组装的ABM基因组大小为30.4 Mb，包含8，562个蛋白质编码基因。ABM基因组与H97和H39具有高度保守的同线区和少量倒位。利用9种真菌的1,276个单拷贝正向同源基因构建的系统发育树表明，青藏高原和欧洲A.双孢菌在2550万年前分化。对29个菌株的基因组重测序分析表明，青藏高原种群经历了与欧美种群的显著分化并独立进化，全球气候变化对青藏高原种群的人口历史产生了重要影响。此外，我们还鉴定了与细胞壁和膜系统以及发育和防御系统相关的关键基因。双孢蘑菇适应青藏高原的恶劣环境。这些发现强调了基因组数据在评估蘑菇进化和适应方面的价值，并将促进A.双孢菌。
Agaricus bisporus distributed in the Tibetan Plateau of China has high-stress resistance that is valuable for breeding improvements. However, its evolutionary history, specialization, and adaptation to the extreme Tibetan Plateau environment are largely unknown. Here, we performed de novo genome sequencing of a representative Tibetan Plateau wild strain ABM and comparative genomic analysis with the reported European strain H97 and H39. The assembled ABM genome was 30.4 Mb in size, and comprised 8,562 protein-coding genes. The ABM genome shared highly conserved syntenic blocks and a few inversions with H97 and H39. The phylogenetic tree constructed by 1,276 single-copy orthologous genes in nine fungal species showed that the Tibetan Plateau and European A. bisporus diverged ∼5.5 million years ago. Population genomic analysis using genome resequencing of 29 strains revealed that the Tibetan Plateau population underwent significant differentiation from the European and American populations and evolved independently, and the global climate changes critically shaped the demographic history of the Tibetan Plateau population. Moreover, we identified key genes that are related to the cell wall and membrane system, and the development and defense systems regulated A. bisporus adapting to the harsh Tibetan Plateau environment. These findings highlight the value of genomic data in assessing the evolution and adaptation of mushrooms and will enhance future genetic improvements of A. bisporus.