Kuo Chih-Horng, Kissinger Jessica C
Department of Genetics, University of Georgia, Athens, GA 30602, USA.
BMC Evol Biol. 2008 Apr 11;8:108. doi: 10.1186/1471-2148-8-108.
Lineage-specific genes, the genes that are restricted to a limited subset of related organisms, may be important in adaptation. In parasitic organisms, lineage-specific gene products are possible targets for vaccine development or therapeutics when these genes are absent from the host genome.
In this study, we utilized comparative approaches based on a phylogenetic framework to characterize lineage-specific genes in the parasitic protozoan phylum Apicomplexa. Genes from species in two major apicomplexan genera, Plasmodium and Theileria, were categorized into six levels of lineage specificity based on a nine-species phylogeny. In both genera, lineage-specific genes tend to have a higher level of sequence divergence among sister species. In addition, species-specific genes possess a strong codon usage bias compared to other genes in the genome. We found that a large number of genus- or species-specific genes are putative surface antigens that may be involved in host-parasite interactions. Interestingly, the two parasite lineages exhibit several notable differences. In Plasmodium, the (G + C) content at the third codon position increases with lineage specificity while Theileria shows the opposite trend. Surface antigens in Plasmodium are species-specific and mainly located in sub-telomeric regions. In contrast, surface antigens in Theileria are conserved at the genus level and distributed across the entire lengths of chromosomes.
Our results provide further support for the model that gene duplication followed by rapid divergence is a major mechanism for generating lineage-specific genes. The result that many lineage-specific genes are putative surface antigens supports the hypothesis that lineage-specific genes could be important in parasite adaptation. The contrasting properties between the lineage-specific genes in two major apicomplexan genera indicate that the mechanisms of generating lineage-specific genes and the subsequent evolutionary fates can differ between related parasite lineages. Future studies that focus on improving functional annotation of parasite genomes and collection of genetic variation data at within- and between-species levels will be important in facilitating our understanding of parasite adaptation and natural selection.
谱系特异性基因，即局限于有限相关生物子集的基因，可能在适应性方面发挥重要作用。在寄生生物中，当这些基因在宿主基因组中不存在时，谱系特异性基因产物可能是疫苗开发或治疗的潜在靶点。
在本研究中，我们利用基于系统发育框架的比较方法来表征寄生原生动物门顶复门中的谱系特异性基因。基于九物种系统发育，来自两个主要顶复门属（疟原虫属和泰勒虫属）物种的基因被分类为六个谱系特异性水平。在这两个属中，谱系特异性基因在姐妹物种之间往往具有更高水平的序列差异。此外，与基因组中的其他基因相比，物种特异性基因具有强烈的密码子使用偏好。我们发现大量属或物种特异性基因是可能参与宿主 - 寄生虫相互作用的假定表面抗原。有趣的是，这两个寄生虫谱系表现出几个显著差异。在疟原虫属中，第三密码子位置的（G + C）含量随着谱系特异性增加，而泰勒虫属则呈现相反趋势。疟原虫属中的表面抗原是物种特异性的，主要位于亚端粒区域。相比之下，泰勒虫属中的表面抗原在属水平上保守，并分布在染色体的整个长度上。
我们的结果为基因复制后快速分化是产生谱系特异性基因的主要机制这一模型提供了进一步支持。许多谱系特异性基因是假定表面抗原的结果支持了谱系特异性基因在寄生虫适应性中可能很重要的假设。两个主要顶复门属中谱系特异性基因之间的对比特性表明，相关寄生虫谱系之间产生谱系特异性基因的机制和随后的进化命运可能不同。未来专注于改善寄生虫基因组功能注释以及物种内和物种间遗传变异数据收集的研究，对于促进我们对寄生虫适应性和自然选择的理解将很重要。
