Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval
Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval
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DOI：
10.1111/nph.15357
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发表时间：
2019-01-01
期刊：
影响因子：
9.4
通讯作者：
Davis, Charles C.
中科院分区：
文献类型：
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作者：
Cai, Liming;Xi, Zhenxiang;Davis, Charles C.
全基因组复制（WGD）在维管植物中广泛存在，并且经常与全球和气候剧变的主要事件相吻合，包括在第三纪边界的大规模灭绝（c。65 Ma）和更近的中新世全球干旱化时期（c. 10-5 Ma）。在这里，我们探讨WGD在不同的开花植物分支Malpighiales。使用来自42个物种的转录组和完整基因组，我们应用多管齐下的基因组管道来识别，定位，并确定年龄的WGD在Malpighiales使用三种手段的推断：分布的同义替换每个同义位点（KS）之间的旁系同源物，基因组（基因树）和解，和基于可能性的基因计数方法。我们保守地确定了22个古老的WGD，广泛分布在Malpighiales亚支。重要的是，这些事件集中在始新世-古新世过渡时期（c。54 Ma），在此期间，地球比新生代的任何时期都温暖和潮湿。这些结果表明，始新世气候最适期可能代表了一个以前未被认识到的植物多产WGD的时期，并进一步支持了多倍体化促进适应和提高植物生存在全球变化的假设，特别是对于热带生物，如Malpighiales，具有严格的耐热性。
Whole-genome duplications (WGDs) are widespread and prevalent in vascular plants and frequently coincide with major episodes of global and climatic upheaval, including the mass extinction at the Cretaceous-Tertiary boundary (c. 65 Ma) and during more recent periods of global aridification in the Miocene (c. 10-5 Ma). Here, we explore WGDs in the diverse flowering plant clade Malpighiales. Using transcriptomes and complete genomes from 42 species, we applied a multipronged phylogenomic pipeline to identify, locate, and determine the age of WGDs in Malpighiales using three means of inference: distributions of synonymous substitutions per synonymous site (K-s) among paralogs, phylogenomic (gene tree) reconciliation, and a likelihood-based gene-count method. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Importantly, these events are clustered around the Eocene-Paleocene transition (c. 54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climatic Optimum likely represents a previously unrecognized period of prolific WGDs in plants, and lends further support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during episodes of global change, especially for tropical organisms like Malpighiales, which have tight thermal tolerances.