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

Plant Journal - Tập 112 Số 5 - Trang 1316-1330 - 2022
Shengfu Zhong1,2,3, Bin Li4, Wei Chen2, Lili Wang5, Ju Guan2, Qiang Wang1, Zujun Yang6, Hao Yang2, Xianshu Wang2, Xiaojiao Yu2, Fu Peng2, Hongchang Liu7, Chen Chen2, Feiquan Tan1,2, Tianheng Ren2, Jinliang Shen8, Peigao Luo2,3
1Institute of Ecological Agriculture Sichuan Agricultural University 211 Huimin Road in Wenjiang District 611130 Chengdu Sichuan Province China
2Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province Sichuan Agricultural University 211 Huimin Road in Wenjiang District 611130 Chengdu Sichuan Province China
3State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant Protection, Chinese Academy of Agricultural Sciences 2 Yuanmingyuan West Road in Haidian District 100193 Beijing China
4State Key Laboratory of Tree Breeding and Forest Genetics Research Institute of Forestry, Chinese Academy of Forestry 1 Dongxiaofu Xiangshan Road in Haidian District 100091 Beijing China
5Biomarker Technologies Co., Ltd 12 Fuqian Street in Shunyi District 101300 Beijing China
6Center for Information in Biology, School of Life Science and Technology University of Electronic Science and Technology of China 2006 Xiyuan Avenue in West Hi-Tech Zone 611731 Chengdu Sichuan Province China
7Guizhou Key Laboratory for Propagation and Cultivation of Medicinal Plants Guizhou University 2708 Huaxi South Avenue in Huaxi District 550025 Guiyang Guizhou province China
8College of Forestry Sichuan Agricultural University 211 Huimin Road in Wenjiang District 611130 Chengdu Sichuan Province China

Tóm tắt

SUMMARYThe 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 (KS) 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. 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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Plant Journal

Tập 112 Số 5

1316-1330

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