copy-number-variation
Copy-number variation (CNV) refers to differences between individuals in the number of times particular DNA segments are duplicated or deleted within the genome. In plants, CNVs contribute to genetic diversity, adaptation to environmental stresses, and differences in traits like disease resistance, yield, and tolerance to drought or pathogens. Understanding CNV helps researchers uncover the structural genomic changes that drive plant evolution and can inform breeding programs aimed at developing more resilient crops.
open_in_new WikipediaPubMed · 2026-04-22
Standard genome sequencing tools have been systematically misreading the gene-duplication clusters that give plants their disease resistance, collapsing multiple distinct genes into one blurry copy. New long-read pangenome technology can finally reconstruct these regions accurately, revealing hidden genetic variation that matters for crop breeding.
Short-read sequencing routinely collapses multi-gene tandem arrays into a single consensus sequence, causing systematic undercounting of disease-resistance and specialized metabolism genes
Annotation pipelines compound sequencing errors by either fusing distinct array members into one oversized gene model or dropping array members entirely, even when the underlying assembly preserved them
Graph pangenomes built from long-read, haplotype-resolved assemblies restore individual array members with distinct coordinates, enabling accurate copy-number variant genotyping and per-gene expression analysis