Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA.
Genome Res. 2010 Aug;20(8):1084-96. doi: 10.1101/gr.103713.109. Epub 2010 Jul 2.
During evolution, gene repatterning across eukaryotic genomes is not uniform. Some genomic regions exhibit a gene organization conserved phylogenetically, while others are recurrently involved in chromosomal rearrangement, resulting in breakpoint reuse. Both gene order conservation and breakpoint reuse can result from the existence of functional constraints on where chromosomal breakpoints occur or from the existence of regions that are susceptible to breakage. The balance between these two mechanisms is still poorly understood. Drosophila species have very dynamic genomes and, therefore, can be very informative. We compared the gene organization of the main five chromosomal elements (Muller's elements A-E) of nine Drosophila species. Under a parsimonious evolutionary scenario, we estimate that 6116 breakpoints differentiate the gene orders of the species and that breakpoint reuse is associated with approximately 80% of the orthologous landmarks. The comparison of the observed patterns of change in gene organization with those predicted under different simulated modes of evolution shows that fragile regions alone can explain the observed key patterns of Muller's element A (X chromosome) more often than for any other Muller's element. High levels of fragility plus constraints operating on approximately 15% of the genome are sufficient to explain the observed patterns of change and conservation across species. The orthologous landmarks more likely to be under constraint exhibit both a remarkable internal functional heterogeneity and a lack of common functional themes with the exception of the presence of highly conserved noncoding elements. Fragile regions rather than functional constraints have been the main determinant of the evolution of the Drosophila chromosomes.
在进化过程中，真核生物基因组中的基因重排并不均匀。一些基因组区域表现出系统发育上保守的基因组织，而另一些区域则经常涉及染色体重排，导致断点重复使用。基因顺序的保守性和断点的重复使用都可能是由于染色体断点发生的功能限制的存在，也可能是由于存在易断裂的区域。这两种机制之间的平衡仍未得到很好的理解。果蝇物种的基因组非常活跃，因此可以提供很多信息。我们比较了九个果蝇物种的主要五个染色体元件（Muller 的元素 A-E）的基因组织。在一个简约的进化情景下，我们估计有 6116 个断点区分了物种的基因顺序，并且断点的重复使用与大约 80%的同源标志有关。观察到的基因组织变化模式与不同模拟进化模式下预测的模式的比较表明，只有脆弱区域就可以比任何其他 Muller 元素更频繁地解释观察到的 Muller 元素 A（X 染色体）的关键模式。脆弱区域加上在大约 15%的基因组上起作用的约束可以解释观察到的种间变化和保守模式。受约束的同源标志更有可能表现出显著的内部功能异质性，并且缺乏共同的功能主题，除了存在高度保守的非编码元件。脆弱区域而不是功能限制是果蝇染色体进化的主要决定因素。
