The many landscapes of recombination in Drosophila melanogaster.
The many landscapes of recombination in Drosophila melanogaster.
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DOI：
10.1371/journal.pgen.1002905
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Bailin S
中科院分区：
文献类型：
--
作者：
Comeron JM;Ratnappan R;Bailin S
重组是一个具有深刻进化意义的基本生物学过程。理论预测，重组提高了自然种群中选择的有效性。然而，由于缺乏基因组间和物种内重组率变异的详细特征，对这一预测的直接测试仅限于质量趋势。使用不精确的重组率也可能扭曲旨在评估跨基因组选择的存在和模式的群体遗传分析。在这里，我们首次报道了重组中基因组和群体变异的高分辨率描述，这也区分了减数分裂重组的两种结果：交换(CO)和基因转换(GC)。我们通过对总共1.39亿个信息性SNP进行基因分型来表征果蝇5860个雌性减数分裂的产物，并绘制了106964个重组事件的分辨率为2千碱基的图谱。这种方法使我们能够生成全基因组CO和GC图，以及对该物种个体间重组变异的详细描述。我们描述了重组率的许多水平的变化。在大范围内(100kb)，CO率沿染色体表现出极端和高度点状的变化，有热点和冷点。我们还显示，在我们的样本中，与低频率热点相关的CO景观存在广泛的种内差异。GC率在整个基因组中的分布比CO率更均匀，并且在CO减少或不存在的区域可以检测到。在局部尺度上，重组事件与许多序列基序相关，并倾向于发生在转录区内，因此表明染色质的可及性有利于双链断裂。为了获得重组率的相关估计，需要考虑基因组间和个体间重组过程中所有这些非独立的变异层，并应将其纳入新一代选择与连锁相互作用的群体遗传模型中。大多数有性真核生物需要同源染色体之间的重组，才能从二倍体生殖细胞形成单倍体配子。在进化上，重组提高了自然种群中选择的有效性，从而解释了重组和性别的普遍性。重组也是群体遗传学研究中的一个中心参数，旨在检测基因组中是否存在选择。然而，当前的进化分析因使用不精确的重组率而受到阻碍，这些重组率可能会影响结果并扭曲其解释。这一局限性与缺乏对基因组间和物种内重组的自然变异的详细描述有关。我们对黑腹果蝇的研究代表了对重组的第一次完整的、全基因组的描述，这种重组可以缓解任何有机体的这些缺陷。我们的结果和结论将有助于描述所观察到的基因组间重组变异的分子基础，并对选择的群体遗传学分析产生直接影响，为更好地捕捉重组及其后果的自然变异的新一代群体模型奠定基础。
Recombination is a fundamental biological process with profound evolutionary implications. Theory predicts that recombination increases the effectiveness of selection in natural populations. Yet, direct tests of this prediction have been restricted to qualitative trends due to the lack of detailed characterization of recombination rate variation across genomes and within species. The use of imprecise recombination rates can also skew population genetic analyses designed to assess the presence and mode of selection across genomes. Here we report the first integrated high-resolution description of genomic and population variation in recombination, which also distinguishes between the two outcomes of meiotic recombination: crossing over (CO) and gene conversion (GC). We characterized the products of 5,860 female meioses in Drosophila melanogaster by genotyping a total of 139 million informative SNPs and mapped 106,964 recombination events at a resolution down to 2 kilobases. This approach allowed us to generate whole-genome CO and GC maps as well as a detailed description of variation in recombination among individuals of this species. We describe many levels of variation in recombination rates. At a large-scale (100 kb), CO rates exhibit extreme and highly punctuated variation along chromosomes, with hot and coldspots. We also show extensive intra-specific variation in CO landscapes that is associated with hotspots at low frequency in our sample. GC rates are more uniformly distributed across the genome than CO rates and detectable in regions with reduced or absent CO. At a local scale, recombination events are associated with numerous sequence motifs and tend to occur within transcript regions, thus suggesting that chromatin accessibility favors double-strand breaks. All these non-independent layers of variation in recombination across genomes and among individuals need to be taken into account in order to obtain relevant estimates of recombination rates, and should be included in a new generation of population genetic models of the interaction between selection and linkage. Most sexual eukaryotes require recombination between homologous chromosomes for the proper formation of haploid gametes from diploid germ cells. Evolutionarily, recombination increases the effectiveness of selection in natural populations, thus explaining the pervasiveness of recombination and sex. Recombination is also a central parameter in population genetic studies designed to detect the presence of selection acting across genomes. Current evolutionary analyses are hindered, however, by the use of imprecise recombination rates that can influence the results and skew their interpretation. This limitation is associated with the lack of detailed characterization of natural variation in recombination across genomes and within species. Our study in Drosophila melanogaster represents the first integrated, whole-genome description of recombination that alleviates these deficiencies in any organism. Our results and conclusions will help to characterize the molecular basis of the observed variation in recombination across genomes and have an immediate impact on population genetic analyses of selection, laying the foundation for a new generation of population models that will better capture natural variation in recombination and its consequences.
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