Castillo-Davis Cristian I, Bedford Trevor B C, Hartl Daniel L
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Masschusetts, USA.
Mol Biol Evol. 2004 Jul;21(7):1422-7. doi: 10.1093/molbev/msh143. Epub 2004 Apr 14.
Very little is known about molecular evolution in the human malaria parasite Plasmodium falciparum. Given the potentially important role that introns play in directing transcription and the posttranscriptional control of gene expression, we compare rates of intron/gain loss and intronic substitution in P. falciparum and the rodent malaria P. y. yoelii in both orthologous and duplicate genes. Specifically, we test the hypothesis that intron gain/loss and protein evolution is accelerated in duplicate genes versus orthologous genes in both parasites using the genome sequence of both species. We find that duplicate genes in both P. falciparum and P. y. yoelii exhibit a dramatic acceleration of both intron gain/loss and protein evolution in comparison with orthologs, suggesting increased directional and/or relaxed selection in duplicate genes. Further, we find that rates of intron gain/loss and protein evolution are weakly coupled in orthologs but not paralogs, supporting the hypothesis that selection acts on genes as functionally integrated units after speciation but not necessarily after gene duplication. In contrast, we find that rates of nucleotide substitution do not differ significantly between intronic sites and synonymous sites among duplicate genes, implying that a large fraction of intronic sites in Plasmodium evolve under little or no selective constraint.
对于人类疟原虫恶性疟原虫的分子进化，人们了解甚少。鉴于内含子在指导转录和基因表达的转录后控制中可能发挥的重要作用，我们比较了恶性疟原虫和啮齿类疟原虫约氏疟原虫直系同源基因和重复基因中的内含子获得/丢失率和内含子替换率。具体而言，我们利用这两个物种的基因组序列，检验了在这两种寄生虫中，重复基因相对于直系同源基因，内含子获得/丢失和蛋白质进化加速的假说。我们发现，与直系同源基因相比，恶性疟原虫和约氏疟原虫中的重复基因在内含子获得/丢失和蛋白质进化方面均表现出显著加速，这表明重复基因中的定向选择和/或松弛选择有所增加。此外，我们发现直系同源基因中内含子获得/丢失率与蛋白质进化率之间的耦合较弱，而旁系同源基因则不然，这支持了以下假说：物种形成后，选择作用于作为功能整合单元的基因，但基因复制后不一定如此。相比之下，我们发现重复基因中内含子位点和同义位点之间的核苷酸替换率没有显著差异，这意味着疟原虫中很大一部分内含子位点在很少或没有选择约束的情况下进化。
