Institut für Populationsgenetik, Vetmeduni Vienna, Austria.
Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Austria.
Genome Biol Evol. 2019 Apr 1;11(4):1345-1357. doi: 10.1093/gbe/evz082.
Meiotic recombination is crucial for chromosomal segregation and facilitates the spread of beneficial and removal of deleterious mutations. Recombination rates frequently vary along chromosomes and Drosophila melanogaster exhibits a remarkable pattern. Recombination rates gradually decrease toward centromeres and telomeres, with a dramatic impact on levels of variation in natural populations. Two close sister species, Drosophila simulans and Drosophila mauritiana do not only have higher recombination rates but also exhibit a much more homogeneous recombination rate that only drops sharply very close to centromeres and telomeres. Because certain sequence motifs are associated with recombination rate variation in D. melanogaster, we tested whether the difference in recombination landscape between D. melanogaster and D. simulans can be explained by the genomic distribution of recombination rate-associated sequence motifs. We constructed the first high-resolution recombination map for D. simulans based on 189 haplotypes from a natural D. simulans population and searched for short sequence motifs linked with higher than average recombination in both sister species. We identified five consensus motifs significantly associated with higher than average chromosome-wide recombination rates in at least one species and present in both. Testing fine resolution associations between motif density and recombination, we found strong and positive associations genome-wide over a range of scales in D. melanogaster, while the results were equivocal in D. simulans. Despite the strong association in D. melanogaster, we did not find a decreasing density of these short-repeat motifs toward centromeres and telomeres. We conclude that the density of recombination-associated repeat motifs cannot explain the large-scale recombination landscape in D. melanogaster, nor the differences to D. simulans. The strong association seen for the sequence motifs in D. melanogaster likely reflects their impact influencing local differences in recombination rates along the genome.
减数分裂重组对于染色体分离至关重要，并促进有益突变的传播和有害突变的消除。重组率经常沿着染色体变化，而黑腹果蝇则表现出显著的模式。重组率逐渐向着丝粒和端粒降低，对自然种群中变异水平有重大影响。两个近缘姐妹种，Drosophila simulans 和 Drosophila mauritiana 不仅具有更高的重组率，而且还表现出更为均匀的重组率，仅在非常靠近着丝粒和端粒的地方急剧下降。由于某些序列基序与黑腹果蝇的重组率变异有关，我们测试了 D. melanogaster 和 D. simulans 之间重组景观的差异是否可以用与重组率相关的序列基序的基因组分布来解释。我们根据来自自然 D. simulans 种群的 189 个单倍型构建了第一个 D. simulans 的高分辨率重组图谱，并在两个姐妹种中搜索与高于平均水平的重组相关的短序列基序。我们鉴定了五个显著与至少一种物种中高于平均水平的染色体范围重组率相关的一致基序，并且这些基序在两个物种中都存在。测试基序密度与重组之间的精细分辨率关联，我们在黑腹果蝇中发现了在多个尺度上具有强烈正相关的全基因组关联，而在 D. simulans 中的结果则不确定。尽管在黑腹果蝇中存在强烈关联，但我们没有发现这些短重复基序密度朝着着丝粒和端粒降低。我们得出结论，重组相关重复基序的密度不能解释黑腹果蝇的大规模重组景观，也不能解释与 D. simulans 的差异。在黑腹果蝇中，这些序列基序的强烈关联可能反映了它们影响基因组上局部重组率差异的影响。
