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

作者：Shengfu Zhong, Bin Li, Wei Chen, Lili Wang, Ju Guan, Qiang Wang, Zhenglin Yang, Hao Yang, Xianshu Wang, Xiaojiao Yu, Fu Peng, Hongchang Liu, Chen Chen, Feiquan Tan, Tianheng Ren, Jinliang Shen, Peigao Luo · 发表于：The Plant Journal · 年份：2022 · DOI：10.1111/tpj.16011 · 被引用次数：31 · 研究领域：Genomics and Phylogenetic Studies、Chromosomal and Genetic Variations、Plant Disease Resistance and Genetics

SUMMARY 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 θ) at 142.72 Mya, similar to the older WGD of Akebia trifoliata , and a putative core eudicot‐specific WGD (temporarily designated ω). Functional enrichment analysis of retained duplicate genes following the θ 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 ω event is suggestive of adaptation to the extreme droughts, possibly leading to the rapid spread of eudicots in the mid‐Cretaceous. Collectively, the A. trifoli...