The pan-genome and local adaptation of Arabidopsis thaliana

Minghui Kang, Haolin Wu, Huanhuan Liu, Wenyu Liu, Mingjia Zhu, Yu Han, Wei Liu, Chunlin Chen, Yan Song, Luna Tan, Kangqun Yin, Yusen Zhao, Zhen Yan, Shangling Lou (), Yanjun Zan () and Jianquan Liu ()
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Minghui Kang: Lanzhou University
Haolin Wu: Sichuan University
Huanhuan Liu: Sichuan University
Wenyu Liu: Lanzhou University
Mingjia Zhu: Lanzhou University
Yu Han: Sichuan University
Wei Liu: Sichuan University
Chunlin Chen: Sichuan University
Yan Song: Sichuan University
Luna Tan: Sichuan University
Kangqun Yin: Sichuan University
Yusen Zhao: Sichuan University
Zhen Yan: Sichuan University
Shangling Lou: Lanzhou University
Yanjun Zan: Chinese Academy of Agricultural Sciences
Jianquan Liu: Lanzhou University

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: Abstract Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.

Date: 2023
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DOI: 10.1038/s41467-023-42029-4

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