Principles of genome evolution in the Drosophila melanogaster species group.
Principles of genome evolution in the Drosophila melanogaster species group.
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DOI：
10.1371/journal.pbio.0050152
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发表时间：
2007-06
期刊：
影响因子：
9.8
通讯作者：
Bergman CM
中科院分区：
文献类型：
--
作者：
Ranz JM;Maurin D;Chan YS;von Grotthuss M;Hillier LW;Roote J;Ashburner M;Bergman CM
Sturtevant和Plunkett在1926年发现，密切相关的物种往往通过染色体倒置而不同。我们对这些倒置是如何产生的了解仍然非常有限，尽管一种流行的观点认为它们是由反向重复序列之间的异位重组事件促进的。相关物种基因组序列的可获得性现在使我们能够详细研究产生种间倒置的机制。我们分析了区分黑腹果蝇和两个近缘物种--拟果蝇和雅库巴果蝇染色体的29个倒位的断点区，并重建了它们起源的分子事件。实验和计算分析表明，59%(17/29)的反转断裂区与基因或其他非重复序列的反向复制有关。在只有两种情况下，我们在反转断点中找到了反向重复序列的证据。我们认为，与翻转断点区相关的反向复制的存在是交错断裂的结果，无论是同色单体还是染色单体，而不是反向重复序列之间的异位交换，这是黑腹蛇物种群中产生倒置的普遍机制。群外分析还揭示了断点回收广泛存在的证据。最后，我们发现黑腹夜蛾的表达结构域可能在雅库巴夜蛾中被破坏，这使人们对它们潜在的适应意义产生了疑问。基因在染色体上的组织会随着进化时间的推移而变化。在一些生物中，如果蝇和蚊子，染色体区域的倒置很普遍。这与适应环境压力和物种形成有关。然而，在分子水平上产生反转的机制还知之甚少。流行的观点涉及基因组中适度重复的序列之间的相互作用。在这里，我们使用分子和计算方法来研究29个倒位，这些倒位区分了三个密切相关的果蝇物种的染色体。我们发现，几乎没有支持重复序列在倒置起源中的因果作用，而是在许多倒置的断裂点区域检测到祖先特有序列(通常是蛋白质编码基因)的反向重复的存在。这导致我们提出了一个替代模型，在该模型中，反转的产生与侧翼序列的复制的产生相耦合。此外，我们还发现了容易断裂的基因组区域的证据，这些区域与现有物种祖先进化过程中独立产生的倒位有关。比较了三种近缘果蝇的染色体倒位断裂点。许多都与反向基因复制有关，这表明它们产生的普遍机制涉及交错断裂点。
That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. The availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. We have analyzed the breakpoint regions of the 29 inversions that differentiate the chromosomes of Drosophila melanogaster and two closely related species, D. simulans and D. yakuba, and reconstructed the molecular events that underlie their origin. Experimental and computational analysis revealed that the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences. In only two cases do we find evidence for inverted repetitive sequences in inversion breakpoints. We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group. Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance. The organization of genes on chromosomes changes over evolutionary time. In some organisms, such as fruit flies and mosquitoes, inversions of chromosome regions are widespread. This has been associated with adaptation to environmental pressures and speciation. However, the mechanisms by which inversions are generated at the molecular level are poorly understood. The prevailing view involves the interactions of sequences that are moderately repeated in the genome. Here, we use molecular and computational methods to study 29 inversions that differentiate the chromosomes of three closely related fruit fly species. We find little support for a causal role of repetitive sequences in the origin of inversions and, instead, detect the presence of inverted duplications of ancestrally unique sequences (generally protein-coding genes) in the breakpoint regions of many inversions. This leads us to propose an alternative model in which the generation of inversions is coupled with the generation of duplications of flanking sequences. Additionally, we find evidence for genomic regions that are prone to breakage, being associated with inversions generated independently during the evolution of the ancestors of existing species. Chromosomal inversion breakpoints were compared between three closely related Drosophila species. Many are associated with inverted gene duplications, suggesting that the prevalent mechanism for their generation involves staggered breakpoints.
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影响因子：
12.3
作者：
Bailey JA;Baertsch R;Kent WJ;Haussler D;Eichler EE
通讯作者：
Eichler EE
影响因子：
10.7
作者：
Casals, F;C치ceres, M;Ruiz, A
通讯作者：
Ruiz, A
影响因子：
3.1
作者：
Bridges, CB
通讯作者：
Bridges, CB
DOI：
10.1073/pnas.0502702102
发表时间：
2005-06-07
影响因子：
11.1
作者：
Belyakin, SN;Christophides, GK;Zhimulev, IF
通讯作者：
Zhimulev, IF
影响因子：
7
作者：
Coghlan, A;Wolfe, KH
通讯作者：
Wolfe, KH