A survey of innovation through duplication in the reduced genomes of twelve parasites.
A survey of innovation through duplication in the reduced genomes of twelve parasites.
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DOI：
10.1371/journal.pone.0099213
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Kissinger JC
中科院分区：
文献类型：
--
作者：
DeBarry JD;Kissinger JC
我们描述了寄生原生生物门 Apicomplexa 中可检测的双拷贝旁系同源物和节段重复的流行率、分布、分歧和推定功能。顶复门主要是导致人类和动物疾病（例如疟疾和弓形体病）的专性细胞内寄生虫。基因丢失是该门的主要力量。基因组很小，编码蛋白质的基因库也减少了。尽管基因组得到了精简，但重复和基因家族扩增仍然存在。重复带来的创新潜力尤其令人感兴趣。我们比较了四个谱系的十二个顶端复合体的基因组，并使用直系学和基因组制图来绘制针对基因组结构的重复分布。片段重复似乎仅限于五个物种。如果存在，它们对应于富含多拷贝和物种特异性基因的区域，指出在适应和创新中的作用。我们发现了全门重复与动态染色体区域和同线断点的关联。重复基因分布的趋势表明，最近的物种特异性重复基因通常是串联的，而大多数其他基因则通过基因组重排而分散。这些趋势显示了基因组结构和基因复制之间的关系。功能分析揭示：蛋白酶对寄生生命周期至关重要，在假定的最近重复中很突出；弓形虫中的一对旁系同源基因先前已被证明可在哺乳动物细胞中产生多巴胺合成的限速步骤，这可能与宿主行为的改变有关；表达和亚细胞定位的全门差异，表明分歧模式。我们发现了重复分歧的多种模式的趋势，包括序列、内含子内容、表达、亚细胞定位和假定的最近重复的功能，这些趋势强调了重复在塑造这些基因组的连续力量中的作用。
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.
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影响因子：
3.7
作者：
Behnke MS;Wootton JC;Lehmann MM;Radke JB;Lucas O;Nawas J;Sibley LD;White MW
通讯作者：
White MW
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
4.4
作者：
Durand PM;Oelofse AJ;Coetzer TL
通讯作者：
Coetzer TL
影响因子：
10.1
作者：
Luo, Y;Su, B;Field, CB
通讯作者：
Field, CB
DOI：
10.1098/rspb.2006.3537
发表时间：
2006-08-07
影响因子：
4.7
作者：
Berney, Cedric;Pawlowski, Jan
通讯作者：
Pawlowski, Jan