Division of Biological Sciences, The University of Montana, USA.
Genome Biol Evol. 2011;3:601-13. doi: 10.1093/gbe/evr060. Epub 2011 Jun 21.
Gene duplication may be an important mechanism for the evolution of new functions and for the adaptive modulation of gene expression via dosage effects. Here, we analyzed the fate of gene duplicates for two strains of a novel group of cyanobacteria (genus Acaryochloris) that produces the far-red light absorbing chlorophyll d as its main photosynthetic pigment. The genomes of both strains contain an unusually high number of gene duplicates for bacteria. As has been observed for eukaryotic genomes, we find that the demography of gene duplicates can be well modeled by a birth-death process. Most duplicated Acaryochloris genes are of comparatively recent origin, are strain-specific, and tend to be located on different genetic elements. Analyses of selection on duplicates of different divergence classes suggest that a minority of paralogs exhibit near neutral evolutionary dynamics immediately following duplication but that most duplicate pairs (including those which have been retained for long periods) are under strong purifying selection against amino acid change. The likelihood of duplicate retention varied among gene functional classes, and the pronounced differences between strains in the pool of retained recent duplicates likely reflects differences in the nutrient status and other characteristics of their respective environments. We conclude that most duplicates are quickly purged from Acaryochloris genomes and that those which are retained likely make important contributions to organism ecology by conferring fitness benefits via gene dosage effects. The mechanism of enhanced duplication may involve homologous recombination between genetic elements mediated by paralogous copies of recA.
基因复制可能是新功能进化和通过剂量效应调节基因表达的重要机制。在这里，我们分析了新型蓝细菌（Acaryochloris 属）两个菌株中基因副本的命运，这些蓝细菌产生远红光吸收叶绿素 d 作为其主要光合色素。这两个菌株的基因组都包含了异常数量的细菌基因副本。与真核基因组一样，我们发现基因副本的数量可以很好地用出生-死亡过程来模拟。大多数复制的 Acaryochloris 基因是相对较新的，是菌株特异性的，并且倾向于位于不同的遗传元件上。对不同分歧类别的重复序列的选择分析表明，少数的旁系同源基因在复制后立即表现出近中性进化动态，但大多数重复对（包括那些长期保留的）受到强烈的纯化选择，以防止氨基酸变化。重复保留的可能性因基因功能类别而异，而且在保留的最近重复序列的库中，菌株之间存在明显的差异，这可能反映了它们各自环境中营养状况和其他特征的差异。我们得出结论，大多数重复序列很快从 Acaryochloris 基因组中清除，而那些保留下来的重复序列可能通过基因剂量效应赋予适应性优势，从而对生物体的生态做出重要贡献。增强重复的机制可能涉及通过 recA 的旁系同源拷贝介导的遗传元件之间的同源重组。
