Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.
PLoS Genet. 2010 Sep 9;6(9):e1001099. doi: 10.1371/journal.pgen.1001099.
Plasmodium parasites, the causal agents of malaria, result in more than 1 million deaths annually. Plasmodium are unicellular eukaryotes with small ∼23 Mb genomes encoding ∼5200 protein-coding genes. The protein-coding genes comprise about half of these genomes. Although evolutionary processes have a significant impact on malaria control, the selective pressures within Plasmodium genomes are poorly understood, particularly in the non-protein-coding portion of the genome. We use evolutionary methods to describe selective processes in both the coding and non-coding regions of these genomes. Based on genome alignments of seven Plasmodium species, we show that protein-coding, intergenic and intronic regions are all subject to purifying selection and we identify 670 conserved non-genic elements. We then use genome-wide polymorphism data from P. falciparum to describe short-term selective processes in this species and identify some candidate genes for balancing (diversifying) selection. Our analyses suggest that there are many functional elements in the non-genic regions of these genomes and that adaptive evolution has occurred more frequently in the protein-coding regions of the genome.
疟原虫寄生虫是疟疾的致病因子，每年导致超过 100 万人死亡。疟原虫是单细胞真核生物，其基因组大小约为 23Mb，编码约 5200 个蛋白质编码基因。这些基因编码了约一半的蛋白质编码基因。尽管进化过程对疟疾控制有重大影响，但疟原虫基因组内的选择压力知之甚少，特别是在基因组的非编码部分。我们使用进化方法描述了这些基因组中编码区和非编码区的选择过程。基于对七种疟原虫物种的基因组比对，我们表明蛋白质编码区、基因间区和内含子区都受到纯化选择的影响，我们鉴定了 670 个保守的非基因元件。然后，我们利用来自恶性疟原虫的全基因组多态性数据来描述该物种的短期选择过程，并鉴定了一些可能受到平衡（多样化）选择的候选基因。我们的分析表明，这些基因组的非编码区有许多功能元件，而且适应性进化在基因组的蛋白质编码区更为频繁。
