Great majority of recombination events in Arabidopsis are gene conversion events

Abstract

The evolutionary importance of meiosis may not solely be associated with allelic shuffling caused by crossing-over but also have to do with its more immediate effects such as gene conversion. Although estimates of the crossing-over rate are often well resolved, the gene conversion rate is much less clear. In Arabidopsis, for example, nextgeneration sequencing approaches suggest that the two rates are about the same, which contrasts with indirect measures, these suggesting an excess of gene conversion. Here, we provide analysis of this problem by sequencing 40 F 2 Arabidopsis plants and their parents. Small gene conversion tracts, with biased gene conversion content, represent over 90% (probably nearer 99%) of all recombination events. The rate of alteration of protein sequence caused by gene conversion is over 600 times that caused by mutation. Finally, our analysis reveals recombination hot spots and unexpectedly high recombination rates near centromeres. This may be responsible for the previously unexplained pattern of high genetic diversity near Arabidopsis centromeres.W hen considering the population genetic impact of recombination, classical theories predominantly concentrate on the impact of allelic shuffling, mediated by crossing-over, and the effect this has on linkage disequilibrium and, in turn, the effect the fate of one allele has on its genomic neighbors (1). However, when programmed double-strand breaks (DSBs) are introduced into chromosomes to initiate meiotic recombination, both crossover (CO) and noncrossover (non-CO) recombination events can occur.

Polarized gene conversion at the bz locus of maize

“…Lu et al (13) and Wijnker et al (12) sequenced the four products of, respectively, 2 and 13 pollen tetrads from a Columbia/Landsberg qrt1 F 1 and detected an average of only one to two NCO gene conversion events per meiosis, most of which included just a single marker. A subsequent reanalysis (44) of the Yang et al high-throughput sequencing data (43) led to the conclusion that many of the NCO gene conversions had arisen from misinterpretations of the short read sequence data and that the true number was much lower and consistent with other findings.…”

“…As discussed above, the degree of NCO gene conversion appears to be a function of the percent identity of the recombining sequences, so we can expect it to vary both at the gene level within a species and at the genome level between species. Another caveat in extrapolating genome-wide results from one species to another is that in some species, like Arabidopsis, most recombination events occur in intergenic regions (13,43,45), whereas in others, like maize, most recombination is intragenic (17,46). The latter observation is not surprising given the high degree of intergenic gross structural polymorphism in maize (36,47).…”

“…Yang et al (43) resequenced 40 F 2 progeny plants from a Columbia/ Landsberg F 1 hybrid and detected a large number of gene conversions, which were defined as short double switches (<10 kb) between the two parental sequences (conversion tracts). The authors estimated that small gene conversion tracts represented >90% of all recombination events in the Columbia/Landsberg hybrid.…”

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

“…thaliana (Yang et al, 2012), where they re-sequenced 40 F2 individuals from the A. thaliana lines Columbia and Landsberg erecta to compare the distribution of crossovers and gene conversions with the two parental individuals. This study identified more than 3000 gene conversions and 73 crossovers per plant.…”

“…The researchers removed all markers near putative duplicated regions to counter the errors introduced by mismapped reads. This way, they estimated 1-3 gene conversions and 10 crossovers per meiosis, a much smaller number than presented in (Yang et al, 2012). One of the limitations of most forms of genotyping, including RAD GBS, is that only a restricted set of the total SNPs are assayed across a population.…”