DOI: 10.7272/q6hh6h9d
title: Data from: High-resolution estimates of crossover and noncrossover recombination from a captive baboon colony

description: Homologous recombination has been extensively studied in humans and a
 handful of model organisms. Much less is known about recombination in
 other species, including non-human primates. Here we present a study of
 crossovers and non-crossover (NCO) recombination in olive baboons (Papio
 anubis) from two pedigrees containing a total of 20 paternal and 17
 maternal meioses, and compare these results to linkage disequlibrium (LD)
 based recombination estimates from 36 unrelated olive baboons. We
 demonstrate how crossovers, combined with LD-based recombination
 estimates, can be used to identify genome assembly errors. We also
 quantify sex-specific differences in recombination rates, including
 elevated male crossover and reduced female crossover rates near telomeres.
 Finally, we add to the increasing body of evidence suggesting that while
 most NCO recombination tracts in mammals are short (e.g., &lt; 500
 bp), there are a non-negligible fraction of longer (e.g., &gt; 1 Kbp)
 NCO tracts. For NCO tracts shorter than 10 Kbp, we fit a mixture of two
 (truncated) geometric distributions model to the NCO tract length
 distribution and estimate that &gt;99% of all NCO tracts are very
 short (mean 24 bp), but the remaining tracts can be quite long (mean 4.3
 Kbp). A single geometric distribution model for NCO tract lengths is
 incompatible with the data, suggesting that LD-based methods for
 estimating NCO recombination rates that make this assumption may need to
 be modified.
description: <strong>VCF files</strong> VCF
 files contain raw unfiltered genotypes from 66 olive baboons
 (<em>Papio anubis</em>) from the Southwest National Primate
 Research Center (SNPRC). Genomes are aligned to the Panubis1.0 reference
 genome (GCA_008728515.1, Batra et al., 2020 (https://doi.org/10.1093/gigascience/giaa134)). Sequencing was performed with HiSeq 4000 and X machines (450 bp mean insert size, 150 bp x 150 bp paired-end sequencing) using DNA extracted from blood samples. Sequences generated for this study (n=23) were combined with previously generated sequence data from Robinson et al., 2019 (https://doi.org/10.1101/gr.247122.118) and Wu et al., 2020 (https://doi.org/10.1371/journal.pbio.3000838). All raw sequence data are available from the Sequence Read Archive under BioProject PRJNA433868. Median depth of coverage across samples is 35.6X. Briefly, reads were trimmed with TrimGalore v0.6.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) using the following options: -q 20 --stringency 1 --length 50, then aligned with BWA MEM v0.7.17 (Li, 2013 (https://arxiv.org/abs/1303.3997)) before marking duplicate reads with Picard v2.21.3 (https://broadinstitute.github.io/picard) and genotyping with GATK HaplotypeCaller v3.8-1-0-gf15c1c3ef (McKenna et al., 2010 (https://doi.org/10.1101/gr.107524.110)). Genotypes from each individual were merged into a joint call set using GATK GenotypeGVCFs, followed by GATK LeftAlignAndTrimVariants. VCF files compressed with bgzip (Bonfield et al., 2021 (https://doi.org/10.1093/gigascience/giab007)).   <strong>Panubis1.0_mask.bed.gz</strong> Bed file contains the coordinates of soft-masked bases in the Panubis1.0 genome assembly, which represent regions identified as repetitive by NCBI using WindowMasker (Morgulis et al., 2006, https://doi.org/10.1093/bioinformatics/bti774). Columns are: Chromosome, Start, End. File compressed with gzip.   <strong>baboon_pyrho_chr1-20.rmap.bed.gz</strong> Recombination map generated with pyrho v0.1.5 (Spence and Song, 2019, https://doi.org/10.1126/sciadv.aaw9206) using genotypes from 36 putatively unrelated baboons. Only the autosomes (Chromsomes 1-20) are included. Raw rates generated by pyrho were multiplied by 5.577 to match the total map length we estimated from crossovers (2,293 cM). Columns are: Chromosome, Start, End, Recombination rate (per bp). File compressed with gzip.