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

Shaoqin Shen, Nan Li, Yujie Wang, Rong Zhou, Pengchuan Sun, Hao Lin, Wei Chen, Tong Yu, Zhuo Liu, Zhiyuan Wang, Xiao Tan, Changping Zhu, Shuyan Feng , Yu Zhang, Xiaoming Song*

*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

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.

Original languageEnglish
JournalPlant Biotechnology Journal
Volume20
Issue11
Pages (from-to)2107-2122
Number of pages16
ISSN1467-7644
DOIs
Publication statusPublished - Nov 2022

Keywords

  • crassulacean acid metabolism
  • expression pattern
  • genome assembly, functional annotation
  • genome evolution
  • ice plant

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