Pleurotus eryngii Genomes Reveal Evolution and Adaptation to the Gobi Desert Environment
Pleurotus eryngii Genomes Reveal Evolution and Adaptation to the Gobi Desert Environment
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杏鲍菇基因组揭示了对戈壁沙漠环境的进化和适应
DOI：
10.3389/fmicb.2019.02024
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发表时间：
2019-09-03
影响因子：
5.2
通讯作者：
Li, Yu
中科院分区：
文献类型：
--
作者：
Dai, Yueting;Sun, Lei;Li, Yu
杏鲍菇(Pleurotus Eryngii)是世界上最珍贵的食用菌之一。在杏鲍菇种类繁多的变种中，杏鲍菇是杏鲍菇的变种。最常见的是杏鲍鱼，分布在世界各地，而杏鲍鱼是最常见的。阿魏科仅分布于欧洲和中国，特别适应于新疆自治区戈壁滩的中国。然而，对杏鲍鱼进化和适应不同环境的全基因组模式知之甚少。在这里，我们展示了杏鲍菇高质量的基因组序列。Eryngii菌株PEE81起源于欧洲，P.eryngii var.阿魏菌菌株PEF12起源于中国的戈壁沙漠。PEE81和PEF12的组装基因组大小分别为53.6和48.0Mbp，均大于已报道的侧耳属其他基因组。我们认为，长末端重复序列(LTR)反转录转座子的选择性扩增增加了侧耳属的基因组大小，并可能在推动其快速物种多样性方面发挥关键作用。平菇PEE81、PEF12、托里氏侧耳、平菇和侧耳的分子钟分析。弗洛里达纳斯表明，侧耳属在3800万年前(Mya)的时间尺度上的分歧估计在∼4到∼之间，而Pleurotus的∼81和PEF12在Mya 13Mya之间存在分歧。对33个不同地理位置的杏鲍菇菌株进行了全基因组重测序。Eryngii和var.然后进行阿魏化，并调查了这两个群体之间和群体内的基因组变异。对这两个种群的比较分析发现了几个与应激反应和DNA修复有关的候选基因，这些基因可能与戈壁沙漠环境的适应有关。这些发现为研究平菇属的基因组进化提供了新的思路，也为平菇育种提供了宝贵的基因组资源。
Pleurotus eryngii (King Oyster) is one of the most highly prized edible mushrooms. Among the diverse varieties within P. eryngii, P. eryngii var. eryngii is the commonest one, with a worldwide distribution, while P. eryngii var. ferulae is only distributed in Europe and China, and is especially adapted to the Gobi Desert in Xinjiang Autonomous Region of China. However, little is known about the genome-wide pattern of evolution and adaptation to the divergent environments of P. eryngii. Here, we present the high-quality genome sequences of P. eryngii var. eryngii strain PEE81 originating from Europe and P. eryngii var. ferulae strain PEF12 originating from the Gobi Desert of China. The assembled genome sizes of PEE81 and PEF12 were 53.6 and 48.0 Mbp, respectively, which are larger than other reported genomes in the genus Pleurotus. We propose that the selective amplification of long terminal repeat (LTR) retrotransposons increases the genome size of the genus Pleurotus, and may play a key role in driving their rapid species diversification. Molecular clock analyses of five Pleurotus species, namely PEE81, PEF12, P. tuoliensis, P. ostreatus and P. cf. floridanus suggest that the divergence estimates of the genus Pleurotus over time scales ranged from ∼4 to ∼38 million years ago (Mya), and PEE81 and PEF12 diverged at ∼13 Mya. The whole genome resequencing of 33 geographically diverse strains of P. eryngii var. eryngii and var. ferulae was then performed and the genome variation among and within these two populations were investigated. Comparative analyses of these two populations detected several candidate genes related to stress responses and DNA repair that are putatively involved in adaptation to the Gobi Desert environment. These findings offer insights into genome evolution of the genus Pleurotus and provide valuable genomic resources for King Oyster mushroom breeding.