DeBarry Jeremy D, Kissinger Jessica C
Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America; Department of Genetics, University of Georgia, Athens, Georgia, United States of America.
Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America; Department of Genetics, University of Georgia, Athens, Georgia, United States of America; Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America.
PLoS One. 2014 Jun 11;9(6):e99213. doi: 10.1371/journal.pone.0099213. eCollection 2014.
We characterize the prevalence, distribution, divergence, and putative functions of detectable two-copy paralogs and segmental duplications in the Apicomplexa, a phylum of parasitic protists. Apicomplexans are mostly obligate intracellular parasites responsible for human and animal diseases (e.g. malaria and toxoplasmosis). Gene loss is a major force in the phylum. Genomes are small and protein-encoding gene repertoires are reduced. Despite this genomic streamlining, duplications and gene family amplifications are present. The potential for innovation introduced by duplications is of particular interest. We compared genomes of twelve apicomplexans across four lineages and used orthology and genome cartography to map distributions of duplications against genome architectures. Segmental duplications appear limited to five species. Where present, they correspond to regions enriched for multi-copy and species-specific genes, pointing toward roles in adaptation and innovation. We found a phylum-wide association of duplications with dynamic chromosome regions and syntenic breakpoints. Trends in the distribution of duplicated genes indicate that recent, species-specific duplicates are often tandem while most others have been dispersed by genome rearrangements. These trends show a relationship between genome architecture and gene duplication. Functional analysis reveals: proteases, which are vital to a parasitic lifecycle, to be prominent in putative recent duplications; a pair of paralogous genes in Toxoplasma gondii previously shown to produce the rate-limiting step in dopamine synthesis in mammalian cells, a possible link to the modification of host behavior; and phylum-wide differences in expression and subcellular localization, indicative of modes of divergence. We have uncovered trends in multiple modes of duplicate divergence including sequence, intron content, expression, subcellular localization, and functions of putative recent duplicates that highlight the role of duplications in the continuum of forces that have shaped these genomes.
我们对顶复门（一类寄生原生生物）中可检测到的双拷贝旁系同源基因和片段重复的流行程度、分布、差异及假定功能进行了表征。顶复门生物大多是专性细胞内寄生虫，可引发人类和动物疾病（如疟疾和弓形虫病）。基因丢失是该门中的一股主要力量。其基因组较小，蛋白质编码基因库减少。尽管基因组进行了精简，但仍存在重复和基因家族扩增现象。重复所带来的创新潜力尤其令人关注。我们比较了四个谱系中12种顶复门生物的基因组，并利用直系同源关系和基因组图谱来绘制重复序列相对于基因组结构的分布。片段重复似乎仅限于5个物种。在存在片段重复的地方，它们对应于富含多拷贝和物种特异性基因的区域，表明其在适应和创新中发挥作用。我们发现全门范围内重复与动态染色体区域和同线断点存在关联。重复基因的分布趋势表明，近期的物种特异性重复通常是串联的，而大多数其他重复则因基因组重排而分散。这些趋势显示了基因组结构与基因重复之间的关系。功能分析揭示：对寄生生命周期至关重要的蛋白酶在假定的近期重复中较为突出；弓形虫中的一对旁系同源基因先前已证明在哺乳动物细胞多巴胺合成中产生限速步骤，这可能与宿主行为的改变有关；以及全门范围内在表达和亚细胞定位上的差异，表明了分化模式。我们发现了多种重复分化模式的趋势，包括序列、内含子含量、表达、亚细胞定位以及假定近期重复的功能，这些趋势突出了重复在塑造这些基因组的连续力量中的作用。
