Copy Number Variation: A Substrate for Plant Adaptation and Stress Response in Arabidopsis

Abstract

Copy number variation (CNV) is a major source of genomic diversity that shapes gene family evolution and may contribute to ecological differentiation, yet its genome-wide ecological relevance remains poorly understood. Here, we analyzed CNV across four Brassicaceae species (Arabidopsis thaliana, A. lyrata, A. halleri, and Arabis alpina) to identify gene families undergoing rapid expansion or contraction. Using a birth-death model, we identified 231 rapidly evolving gene families spanning diverse functional categories. We then characterized CNV within populations of A. thaliana and A. lyrata using population-scale long-read assemblies. CNV exhibited strong heterogeneity across gene families and species, with contrasting evolutionary outcomes: A. thaliana showed greater retention of duplicated copies, whereas A. lyrata exhibited higher pseudogenization and turnover. CNV profiles were strongly structured geographically, reflecting known demographic and phylogeographic patterns in both species. Environmental association analyses revealed species-specific architectures: CNV in A. thaliana showed a diffuse, polygenic association with climate, whereas in A. lyrata associations were more strongly coupled to population structure. Despite the functional diversity of rapidly evolving families, environmentally associated CNVs were significantly enriched in defense- and stress-related functions. These results demonstrate that CNV-environment relationships emerge at the level of gene family networks and are shaped by genomic architecture and lineage history, highlighting CNV as a context-dependent driver of genome evolution and ecological differentiation. SummaryGene copy number variation--where individuals carry different numbers of copies of the same gene--is a potentially important but poorly understood source of genetic diversity. The authors studied how copy numbers evolve across four mustard family plant species and whether this variation helps plants adapt to different environments. They found that gene families involved in disease resistance and stress responses were especially prone to rapid copy number changes. These changes tracked geography and local climate, but in ways that differed between species depending on their evolutionary history. The findings highlight gene copy number variation as a key, underappreciated contributor to how plants adapt to their environments.