Chromosome VCF files and 1Mb recombination rate estimations for: Fine-scale recombination rate variation and association with genomic features in a butterfly

Genetic recombination is a key molecular mechanism that has profound
implications on both micro- and macro-evolutionary processes. However, the
determinants of recombination rate variation in holocentric organisms are
poorly understood, in particular in Lepidoptera (moths and butterflies).
The wood white butterfly (Leptidea sinapis) shows considerable
intraspecific variation in chromosome numbers and is a suitable system for
studying regional recombination rate variation and its potential molecular
underpinnings. Here, we developed a large whole-genome resequencing data
set from a population of wood whites to obtain high-resolution
recombination maps using linkage disequilibrium information. The analyses
revealed that larger chromosomes had a bimodal recombination landscape,
potentially due to interference between simultaneous chiasmata. The
recombination rate was significantly lower in subtelomeric regions, with
exceptions associated with segregating chromosome rearrangements, showing
that fissions and fusions can have considerable effects on the
recombination landscape. There was no association between the inferred
recombination rate and base composition, supporting a negligible influence
of GC-biased gene conversion in butterflies. We found significant but
variable associations between the recombination rate and the density of
different classes of transposable elements (TEs), most notably a
significant enrichment of SINEs in genomic regions with higher
recombination rate. Finally, the analyses unveiled significant enrichment
of genes involved in farnesyltranstransferase activity in recombination
cold-spots, potentially indicating that expression of transferases can
inhibit formation of chiasmata during meiotic division. Our results
provide novel information about recombination rate variation in
holocentric organisms and has particular implications for forthcoming
research in population genetics, molecular/genome evolution and
speciation.