The chromosome-level genome of Akebia trifoliata as an important resource to study plant evolution and environmental adaptation in the Cretaceous

文献类型： 外文期刊

第一作者： Zhong, Shengfu

作者： Zhong, Shengfu;Chen, Wei;Guan, Ju;Yang, Hao;Wang, Xianshu;Yu, Xiaojiao;Fu, Peng;Chen, Chen;Tan, Feiquan;Ren, Tianheng;Luo, Peigao;Zhong, Shengfu;Luo, Peigao;Zhong, Shengfu;Tan, Feiquan;Li, Bin;Wang, Lili;Yang, Zujun;Liu, Hongchang;Shen, Jinliang

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关键词： Akebia trifoliata; whole genome duplication; integrated analysis; plant evolution; ancient environment

期刊名称：PLANT JOURNAL （ 影响因子：7.091； 五年影响因子：8.028 ）

ISSN： 0960-7412

年卷期： 2022 年 112 卷 5 期

页码：

收录情况： SCI

摘要： The environmental adaptation of eudicots is the most reasonable explanation for why they compose the largest clade of modern plants (> 70% of angiosperms), which indicates that the basal eudicots would be valuable and helpful to study their survival and ability to thrive throughout evolutionary processes. Here, we detected two whole-genome duplication (WGD) events in the high-quality assembled Akebia trifoliata genome (652.73 Mb) with 24 138 protein-coding genes based on the evidence of intragenomic and intergenomic collinearity, synonymous substitution rate (K-S) values and polyploidization and diploidization traces; these events putatively occurred at 85.15 and 146.43 million years ago (Mya). The integrated analysis of 16 species consisting of eight basal and eight core eudicots further revealed that there was a putative ancient WGD at the early stage of eudicots (temporarily designated theta) at 142.72 Mya, similar to the older WGD of Akebia trifoliata, and a putative core eudicot-specific WGD (temporarily designated omega). Functional enrichment analysis of retained duplicate genes following the theta event is suggestive of adaptation to the extreme environment change in both the carbon dioxide concentration and desiccation around the Jurassic-Cretaceous boundary, while the retained duplicate genes following the omega event is suggestive of adaptation to the extreme droughts, possibly leading to the rapid spread of eudicots in the mid-Cretaceous. Collectively, the A. trifoliata genome experienced two WGD events, and the older event may have occurred at the early stage of eudicots, which likely increased plant environmental adaptability and helped them survive in ancient extreme environments.

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