State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
Nat Commun. 2023 Oct 6;14(1):6259. doi: 10.1038/s41467-023-42029-4.
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.
拟南芥是研究植物生物学各个方面的模式物种。然而，基因组结构变异（SVs）及其相关基因对这种广泛分布的物种的局部适应的贡献仍不清楚。在这里，我们从头组装了 32 个拟南芥生态型的染色体水平基因组，确定了可变基因扩展了不同生态型的基因库，从而有助于局部适应。我们开发了基于图的泛基因组，并鉴定出 61332 个与 18883 个基因重叠的 SVs，其中一些基因高度参与了该物种的生态适应。例如，我们观察到西藏-0 生态型中 HPCA1 基因启动子区域的一个特定的 332bp 插入，该插入增强了基因表达，从而促进了对高山环境的适应。这些发现增加了我们对拟南芥在不同生境中局部适应的分子机制的理解。
