The Role of a Large Genomic Inversion in Shaping DNA Methylation in Betula pendula: A Comparative Analysis Across Inversion Genotypes

Structural variations, particularly chromosomal inversions, are powerful drivers of plant genomic diversity because they can rearrange gene order, suppress recombination, and reconfigure regulatory landscapes. However, their impact on epigenetic mechanisms such as DNA methylation remains poorly understood, even beyond the specific context of forest trees. Here, I investigated the relationship between large-scale structural variation and DNA methylation in silver birch (Betula pendula), an ecologically and economically important species with a well-annotated reference genome. Using PacBio HiFi sequencing combined with sequence alignment, variant calling, and long-read methylation profiling, I identified a ~9 Mb chromosomal inversion on chromosome 1 in one of the haplotypes of the reference individual (V5834). This inversion was then used as a reference feature to survey its presence and orientation across additional B. pendula haplotypes. Principal component analysis of structural variant genotypes revealed distinct clustering of individuals carrying the alternative haplotype, indicating that the inversion contains polymorphisms that segregate within the population. Genome-wide methylation profiling detected numerous differentially methylated regions (DMRs) between individuals of different genotypes, disproportionately enriched within the inversion and frequently overlapping annotated genes and transposable elements. This suggests that structural rearrangement reshapes local chromatin states and regulatory potential. I also detected a heterozygous inversion on chromosome 8, further extending evidence of structural diversity in this species. By integrating long-read structural variant detection with methylation analysis, my study provides the first comprehensive view of how large chromosomal inversions in B. pendula are associated with distinctive DNA methylation signatures, likely mediated by transposable element activity, and highlights a possible process through which structural variation can influence epigenetic regulation, genome stability, and adaptive diversity in forest trees.