The chromosome-level genome of Eucommia ulmoides provides insights into sex differentiation and α-linolenic acid biosynthesis

Qingxin Du; Qingxin Du; Qingxin Du; Zixian Wu; Panfeng Liu; Panfeng Liu; Panfeng Liu; Jun Qing; Jun Qing; Jun Qing; Feng He; Feng He; Feng He; Lanying Du; Lanying Du; Lanying Du; Zhiqiang Sun; Zhiqiang Sun; Zhiqiang Sun; Lili Zhu; Hongchu Zheng; Zongyi Sun; Long Yang; Lu Wang; Lu Wang; Lu Wang; Hongyan Du; Hongyan Du; Hongyan Du

doi:10.3389/fpls.2023.1118363

Frontiers in Plant Science (Mar 2023)

The chromosome-level genome of Eucommia ulmoides provides insights into sex differentiation and α-linolenic acid biosynthesis

Qingxin Du,
Qingxin Du,
Qingxin Du,
Zixian Wu,
Panfeng Liu,
Panfeng Liu,
Panfeng Liu,
Jun Qing,
Jun Qing,
Jun Qing,
Feng He,
Feng He,
Feng He,
Lanying Du,
Lanying Du,
Lanying Du,
Zhiqiang Sun,
Zhiqiang Sun,
Zhiqiang Sun,
Lili Zhu,
Hongchu Zheng,
Zongyi Sun,
Long Yang,
Lu Wang,
Lu Wang,
Lu Wang,
Hongyan Du,
Hongyan Du,
Hongyan Du

Affiliations

Qingxin Du: Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
Qingxin Du: Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
Qingxin Du: Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
Zixian Wu: Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
Panfeng Liu: Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
Panfeng Liu: Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
Panfeng Liu: Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
Jun Qing: Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
Jun Qing: Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
Jun Qing: Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
Feng He: Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
Feng He: Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
Feng He: Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
Lanying Du: Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
Lanying Du: Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
Lanying Du: Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
Zhiqiang Sun: Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
Zhiqiang Sun: Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
Zhiqiang Sun: Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
Lili Zhu: Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China
Hongchu Zheng: Product Department, Henan Jinduzhong Agricultural Science and Technology Co., Ltd., Yanling, China
Zongyi Sun: Operation Department, Grandomics Biosciences Co., Ltd., Wuhan, China
Long Yang: Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
Lu Wang: Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
Lu Wang: Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
Lu Wang: Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China
Hongyan Du: Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
Hongyan Du: Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Chinese Academy of Forestry, Zhengzhou, China
Hongyan Du: Engineering Research Center of Eucommia ulmoides, State Forestry and Grassland Administration, Zhengzhou, China

DOI: https://doi.org/10.3389/fpls.2023.1118363
Journal volume & issue: Vol. 14

Abstract

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Eucommia ulmoides Oliver is a typical dioecious plant endemic to China that has great medicinal and economic value. Here, we report a high-quality chromosome-level female genome of E. ulmoides obtained by PacBio and Hi-C technologies. The size of the female genome assembly was 1.01 Gb with 17 pseudochromosomes and 31,665 protein coding genes. In addition, Hi-C technology was used to reassemble the male genome released in 2018. The reassembled male genome was 1.24 Gb with the superscaffold N50 (48.30 Mb), which was increased 25.69 times, and the number of predicted genes increased by 11,266. Genome evolution analysis indicated that E. ulmoides has undergone two whole-genome duplication events before the divergence of female and male, including core eudicot γ whole-genome triplication event (γ-WGT) and a recent whole genome duplication (WGD) at approximately 27.3 million years ago (Mya). Based on transcriptome analysis, EuAP3 and EuAG may be the key genes involved in regulating the sex differentiation of E. ulmoides. Pathway analysis showed that the high expression of ω-3 fatty acid desaturase coding gene EU0103017 was an important reason for the high α-linolenic acid content in E. ulmoides. The genome of female and male E. ulmoides presented here is a valuable resource for the molecular biological study of sex differentiation of E. ulmoides and also will provide assistance for the breeding of superior varieties.

Published in Frontiers in Plant Science

ISSN: 1664-462X (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Agriculture: Plant culture
Website: https://www.frontiersin.org/journals/plant-science

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