The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana

Abstract

Knowledge of the exact distribution of meiotic crossovers (COs) and gene conversions (GCs) is essential for understanding many aspects of population genetics and evolution, from haplotype structure and long-distance genetic linkage to the generation of new allelic variants of genes. To this end, we resequenced the four products of 13 meiotic tetrads along with 10 doubled haploids derived from Arabidopsis thaliana hybrids. GC detection through short reads has previously been confounded by genomic rearrangements. Rigid filtering for misaligned reads allowed GC identification at high accuracy and revealed an ∼80-kb transposition, which undergoes copy-number changes mediated by meiotic recombination. Non-crossover associated GCs were extremely rare most likely due to their short average length of ∼25–50 bp, which is significantly shorter than the length of CO-associated GCs. Overall, recombination preferentially targeted non-methylated nucleosome-free regions at gene promoters, which showed significant enrichment of two sequence motifs.DOI: http://dx.doi.org/10.7554/eLife.01426.001

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

“…Using this approach, it was possible to generate genome wide recombination maps and to assess and compare the frequency of crossover and gene conversion events. We hypothesize that an inflated number of crossovers and gene conversions is caused by errors in the reference assembly, and after stringent filtering, the numbers of gene conversions and crossovers are similar to that reported by (Wijnker et al, 2013).…”

“…In human genomes, DSBs and recombination hot-spots exhibit specific sequence motifs or by sequences capable of forming non-B DNA structures (Chen et al, 2007). In A. thaliana, recombination hotspots seem to be biased towards a high AT content and away from methylated DNA, and carry at least two distinct sequence motifs (Wijnker et al, 2013).…”

“…Lastly, Agarwal et al sequenced transcripts of kabuli chickpea and aligned Illumina reads from kabuli, desi and wild populations with 454 transcripts (Wijnker et al, 2013). Using this method, they identified 1,986 SNPs between kabuli and desi, and 37,954 SNPs between kabuli and wild germplasm.…”

“…A follow-up study repeated the analysis, but under the assumption that genomic re-arrangements confound the mapping of short reads (Wijnker et al, 2013). The researchers removed all markers near putative duplicated regions to counter the errors introduced by mismapped reads.…”

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

“…Significant associations were found between hotspots and poly-A stretches (Choi et al 2013;Wijnker et al 2013;Shilo et al 2015) which are known to preferentially locate upstream of TSSs, resulting in reduced nucleosome occupancy that facilitates accessibility of the recombination machinery (Wu and Lichten 1994;Berchowitz et al 2009;Segal and Widom 2009;Pan et al 2011). Similarly, CCN-and CTT-repeat sequence motifs were also detected to be associated to recombination hotspots (Choi et al 2013;Shilo et al 2015;Wijnker et al 2013). These motifs are also located close to the TSSs and are similar to the motif targeted by the PRDM9 protein in humans and mouse, which may suggest a similar recognition by the recombination machinery.…”