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

Area of Science:

• Genomics
• Evolutionary Biology
• Population Genetics

Background:

• Copy number variation (CNV) is a key source of genomic diversity influencing gene family evolution and ecological adaptation.
• The genome-wide ecological relevance of CNV remains largely unexplored.

Purpose of the Study:

• To investigate CNV across four Brassicaceae species to identify rapidly evolving gene families.
• To characterize CNV patterns within populations of Arabidopsis thaliana and A. lyrata.
• To explore the relationship between CNV, geography, and environmental factors.

Main Methods:

• Comparative genomic analysis of CNV across four Brassicaceae species.
• Application of a birth-death model to identify rapidly evolving gene families.
• Population-scale long-read sequencing for CNV characterization in A. thaliana and A. lyrata.
• Geographic structuring and environmental association analyses of CNV.

Main Results:

• Identified 231 rapidly evolving gene families.
• Observed significant CNV heterogeneity across species, with A. thaliana retaining duplicates and A. lyrata showing higher turnover.
• CNV profiles were geographically structured, mirroring demographic patterns.
• CNV in A. thaliana associated diffusely with climate, while A. lyrata showed stronger coupling with population structure.
• Environmentally associated CNVs were enriched in defense and stress-related functions.

Conclusions:

• CNV-environment relationships are network-level phenomena influenced by genomic architecture and evolutionary history.
• CNV acts as a context-dependent driver of genome evolution and ecological differentiation.
• CNV plays a significant role in shaping species adaptation to diverse environments.