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

TL;DR

This study maps the distribution of meiotic crossovers and gene conversions in Arabidopsis thaliana, revealing their genomic locations, characteristics, and the influence of chromatin features on recombination events.

Contribution

It provides high-resolution identification of GCs and COs, uncovers a transposition event linked to recombination, and characterizes the genomic and sequence features associated with meiotic recombination.

Findings

GCs are extremely rare outside COs, with short average length (~25-50 bp).

Recombination preferentially occurs in non-methylated, nucleosome-free promoter regions.

Identified an ~80-kb transposition mediated by meiotic recombination.

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.