The pan-genome and local adaptation of Arabidopsis thaliana. Kang, M., Wu, H., Liu, H., Liu, W., Zhu, M., Han, Y., Liu, W., Chen, C., Song, Y., Tan, L., Yin, K., Zhao, Y., Yan, Z., Lou, S., Zan, Y., & Liu, J. Nature Communications, 14(1):6259, Nature Publishing Group, October, 2023. ![The pan-genome and local adaptation of Arabidopsis thaliana [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 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.
@article{kang_pan-genome_2023,
title = {The pan-genome and local adaptation of {Arabidopsis} thaliana},
volume = {14},
copyright = {2023 The Author(s)},
issn = {2041-1723},
url = {https://www.nature.com/articles/s41467-023-42029-4},
doi = {10.1038/s41467-023-42029-4},
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.},
language = {en},
number = {1},
urldate = {2026-05-19},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
author = {Kang, Minghui and Wu, Haolin and Liu, Huanhuan and Liu, Wenyu and Zhu, Mingjia and Han, Yu and Liu, Wei and Chen, Chunlin and Song, Yan and Tan, Luna and Yin, Kangqun and Zhao, Yusen and Yan, Zhen and Lou, Shangling and Zan, Yanjun and Liu, Jianquan},
month = oct,
year = {2023},
keywords = {Evolutionary biology, Natural variation in plants, Plant evolution, Structural variation},
pages = {6259},
}
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