DOI: 10.5061/dryad.qrfj6q5m7
title: Chromosome VCF files and 1Mb recombination rate estimations for: Fine-scale recombination rate variation and association with genomic features in a butterfly

description: 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.
description: 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, &gt;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
 H<sub>2</sub>O. 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 overnight and centrifuging for 15 minutes at
 13,000 rpm. The final pellet was resuspended with 30 μl of MilliQ
 H<sub>2</sub>O. DNA purity was assessed with NanoDrop, and
 concentration measured with Qubit DNA Broad Range.
 Sequencing To capture
 the genetic variation in the population in Sweden, 84 individuals from
 different geographic regions and the highest DNA quality were selected for
 analysis. Library preparation for all 84 samples using the TruSeq PCR-free
 kit followed by multiplexing, and sequencing on two NovaSeq 6000 S4 lanes
 with 2×150 bp reads, were performed at the National Genomics
 Infrastructure (NGI), Stockholm. Read trimming Illumina sequencing adapters were trimmed by
 eliminating the first fifteen base pairs (bp) on each end of the raw reads
 with CutAdapt 1.9.1 (Martin 2011), filtered on Q-score &lt; 30 and a minimum length of 30 bp. Read quality after cleaning was assessed with FastQC (Andrews 2010). Before filtering, an average of 4.3 million reads per sample were obtained, and 2.5% were filtered out. Mapping and filtering For each individual, paired-end reads were mapped to the reference genome with bwa v0.7.17 (Li and Durbin 2009). Samtools v1.10 (Li et al. 2009) was used to select reads with paired information. MarkDuplicatesSpark as implemented in GATK v4.1.4.1 (McKenna et al. 2010) was used to eliminate duplicated regions with the –remove-sequencing-duplicates option. Recombination rate estimation Recombination rate was estimated with pyrho, and averaged over 1Mb intervals to assess the association of regional recombination rate with several genomic features.
description: The files can be opened in any editor software, both with GUI
 (such as BBEdit) and in the command line (such as nano).