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 ...,
DNA extraction
DNA was extracted following two different protocols. In both cases, the dissected tissue was digested overnight in Laird’s buffer and homogenized with 20μl of proteinase K (20mg/ml, >600 mAU/ml), followed by incubation with RNase A at 37°C for 30 minutes. DNA was extracted from thoraces using salt extraction; 300 of NaCl (5M) was added, followed by centrifugation for 15 minutes at 13,000 revolutions per minute (rpm). Three washing steps were completed with one volume of 70% ethanol and centrifuging for five minutes at maximum speed. The remaining pellet was air-dried and then resuspended in 30 μl of MilliQ H2O. For the abdomens, a phenol-chloroform extraction protocol was used. Two cycles of phenol:chloroform:isoamyl alcohol (25:24:1) addition and centrifugation for five minutes at 13,000 rpm were completed, plus a third cleaning cycle using only chloroform. Precipitation of DNA was achieved by adding 2x volumes isopropanol + 0.1x 3M NaAc, incubating at -18°C overnigh..., The files can be opened in any editor software, both with GUI (such as BBEdit) and in the command line (such as nano).