Copy number variation: a substrate for plant adaptation and stress response in Arabidopsis
Abstract
Copy number variation 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 copy number variation 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 copy number variation within populations of A. thaliana and A. lyrata using population-scale long-read assemblies. Copy number variation 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. Copy number variation profiles were strongly structured geographically, reflecting known demographic and phylogeographic patterns in both species. Environmental association analyses revealed species-specific architectures: copy number variation 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 copy number variations were significantly enriched in defense- and stress-related functions. These results demonstrate that copy number variation–environment relationships emerge at the level of gene family networks and are shaped by genomic architecture and lineage history, highlighting copy number variation as a context-dependent driver of genome evolution and ecological differentiation.
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BibTeX
@article{karunarathne2026copy,
title = {{Copy number variation: a substrate for plant adaptation and stress response in Arabidopsis}},
author = {Piyal Karunarathne and Yannick Schäfer and Anna Glushkevich and Alison D Scott and Leen Abraham and Juliette de Meaux and Polina Yu Novikova and Thomas Wiehe and Laura E Rose},
journal = {G3: Genes | Genomes | Genetics},
year = {2026},
month = jul,
doi = {10.1093/g3journal/jkag183},
url = {https://doi.org/10.1093/g3journal/jkag183},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Copy number variation: a substrate for plant adaptation and stress response in Arabidopsis
AU - Piyal Karunarathne
AU - Yannick Schäfer
AU - Anna Glushkevich
AU - Alison D Scott
AU - Leen Abraham
AU - Juliette de Meaux
AU - Polina Yu Novikova
AU - Thomas Wiehe
AU - Laura E Rose
PY - 2026
DA - 2026/07/04
JO - G3: Genes | Genomes | Genetics
DO - 10.1093/g3journal/jkag183
UR - https://doi.org/10.1093/g3journal/jkag183
AB - Copy number variation 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 copy number variation 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 copy number variation within populations of A. thaliana and A. lyrata using population-scale long-read assemblies. Copy number variation 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. Copy number variation profiles were strongly structured geographically, reflecting known demographic and phylogeographic patterns in both species. Environmental association analyses revealed species-specific architectures: copy number variation 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 copy number variations were significantly enriched in defense- and stress-related functions. These results demonstrate that copy number variation–environment relationships emerge at the level of gene family networks and are shaped by genomic architecture and lineage history, highlighting copy number variation as a context-dependent driver of genome evolution and ecological differentiation.
SN - 2160-1836
ER -