High-quality ice plant reference genome analysis provides insights into genome evolution and allows exploration of genes involved in the transition from C3 to CAM pathways

Authors

Shaoqin Shen, North China University of Science and Technology
Nan Li, North China University of Science and Technology
Yujie Wang, North China University of Science and Technology
Rong Zhou, Aarhus University
Pengchuan Sun, Sichuan University
Hao Lin, University of Electronic Science and Technology of China
Wei Chen, North China University of Science and Technology, Chengdu University of Traditional Chinese Medicine
Tong Yu, North China University of Science and Technology
Zhuo Liu, North China University of Science and Technology
Zhiyuan Wang, North China University of Science and Technology
Xiao Tan, North China University of Science and Technology
Changping Zhu, North China University of Science and Technology
Shuyan Feng, North China University of Science and Technology
Yu Zhang, North China University of Science and Technology
Xiaoming Song, North China University of Science and Technology, University of Electronic Science and Technology of China, University of Nebraska-Lincoln

Document Type

Article

Date of this Version

7-10-2022

Citation

Plant Biotechnology Journal (2022) 20, pp. 2107–2122 doi: 10.1111/pbi.13892

Comments

Open access.

Abstract

Ice plant (Mesembryanthemum crystallinum), a member of the Aizoaceae family, is a typical halophyte crop and a model plant for studying the mechanism of transition from C3 photosynthesis to crassulacean acid metabolism (CAM). Here, we report a high-quality chromosome-level ice plant genome sequence. This 98.05% genome sequence is anchored to nine chromosomes, with a total length of 377.97 Mb and an N50 scaffold of 40.45 Mb. Almost half of the genome (48.04%) is composed of repetitive sequences, and 24 234 genes have been annotated. Subsequent to the ancient whole-genome triplication (WGT) that occurred in eudicots, there has been no recent whole-genome duplication (WGD) or WGT in ice plants. However, we detected a novel WGT event that occurred in the same order in Simmondsia chinensis, which was previously overlooked. Our findings revealed that ice plants have undergone chromosome rearrangements and gene removal during evolution. Combined with transcriptome and comparative genomic data and expression verification, we identified several key genes involved in the CAM pathway and constructed a comprehensive network. As the first genome of the Aizoaceae family to be released, this report will provide a rich data resource for comparative and functional genomic studies of Aizoaceae, especially for studies on salt tolerance and C3-to-CAM transitions to improve crop yield and resistance.