Abstract
BackgroundMeiotic recombination has traditionally been explained based on the structural requirement to stabilize homologous chromosome pairs to ensure their proper meiotic segregation. Competing hypotheses seek to explain the emerging findings of significant heterogeneity in recombination rates within and between genomes, but intraspecific comparisons of genome-wide recombination patterns are rare. The honey bee (Apis mellifera) exhibits the highest rate of genomic recombination among multicellular animals with about five cross-over events per chromatid.ResultsHere, we present a comparative analysis of recombination rates across eight genetic linkage maps of the honey bee genome to investigate which genomic sequence features are correlated with recombination rate and with its variation across the eight data sets, ranging in average marker spacing ranging from 1 Mbp to 120 kbp. Overall, we found that GC content explained best the variation in local recombination rate along chromosomes at the analyzed 100 kbp scale. In contrast, variation among the different maps was correlated to the abundance of microsatellites and several specific tri- and tetra-nucleotides.ConclusionsThe combined evidence from eight medium-scale recombination maps of the honey bee genome suggests that recombination rate variation in this highly recombining genome might be due to the DNA configuration instead of distinct sequence motifs. However, more fine-scale analyses are needed. The empirical basis of eight differing genetic maps allowed for robust conclusions about the correlates of the local recombination rates and enabled the study of the relation between DNA features and variability in local recombination rates, which is particularly relevant in the honey bee genome with its exceptionally high recombination rate.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1281-2) contains supplementary material, which is available to authorized users.
Highlights
Meiotic recombination has traditionally been explained based on the structural requirement to stabilize homologous chromosome pairs to ensure their proper meiotic segregation
We found that the local recombination rate was correlated to a large number of sequence features, which can best be explained by these features’ relation to GC content
Based on eight medium-density linkage maps, we studied the relation between genome sequence features and local recombination rates
Summary
Meiotic recombination has traditionally been explained based on the structural requirement to stabilize homologous chromosome pairs to ensure their proper meiotic segregation. The honey bee (Apis mellifera) exhibits the highest rate of genomic recombination among multicellular animals with about five cross-over events per chromatid. The western honey bee (Apis mellifera) exhibits an exceptional recombination rate and presumably presents the most notable deviation from the general rule that explains genome wide recombination rates in many other Eukaryotes. With twenty centi-Morgans per million base-pairs (20 cM/Mb), honey bees have the highest rate of recombination among Metazoans [9]. This high rate may be a genus-wide phenomenon [10]. Various explanations have been proposed, mostly accounting for the observation that other social species in the order Hymenoptera seem to exhibit an elevated genomic recombination rate [9,12,13]
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