Jumbled genomes: missing Apicomplexan synteny.
Jumbled genomes: missing Apicomplexan synteny.
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DOI：
10.1093/molbev/msr103
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发表时间：
2011-10
影响因子：
10.7
通讯作者：
Kissinger JC
中科院分区：
文献类型：
--
作者：
DeBarry JD;Kissinger JC
全基因组比较通过了解基因库、基因增益/丢失和基因组组织来深入了解基因组进化。我们关于真核基因组进化的大部分知识都源自对多细胞模型生物的研究。真核门顶复门含有专性细胞内原生寄生虫，它们导致多种人类和兽医疾病（例如疟疾、弓形虫病和泰勒虫病）。我们开发了一种基于计算机蛋白质编码基因的管道，用于研究 6 个属 12 个 apicomplexan 物种的同线性。谱系之间的基因组重排是广泛的。同线性区域（保守的基因内容和顺序）在谱系之间很少见，并且在整个门中似乎完全不存在，在同一条染色体上没有发现任何三个基因组，并且在任何直系同源基因的上下游 25 kb 内具有相同的顺序。主要谱系之间的保守同线性仅限于疟原虫和泰勒虫/巴贝斯虫物种的小区域，并且在这些保守区域内，有许多推测针对细胞器的蛋白质。考虑到分歧时间以及所检查的任何物种内明显不存在转座元件（TE），观察到的总体缺乏同线性是令人惊讶的。 TE 在迄今为止研究的所有其他真核生物群体中普遍存在，并且已被证明参与基因组重排。相对于其他经过充分研究的单细胞和多细胞真核生物，顶端复合体内部的基因组进化似乎有不同的标准。
Whole-genome comparisons provide insight into genome evolution by informing on gene repertoires, gene gains/losses, and genome organization. Most of our knowledge about eukaryotic genome evolution is derived from studies of multicellular model organisms. The eukaryotic phylum Apicomplexa contains obligate intracellular protist parasites responsible for a wide range of human and veterinary diseases (e.g., malaria, toxoplasmosis, and theileriosis). We have developed an in silico protein-encoding gene based pipeline to investigate synteny across 12 apicomplexan species from six genera. Genome rearrangement between lineages is extensive. Syntenic regions (conserved gene content and order) are rare between lineages and appear to be totally absent across the phylum, with no group of three genes found on the same chromosome and in the same order within 25 kb up- and downstream of any orthologous genes. Conserved synteny between major lineages is limited to small regions in Plasmodium and Theileria/Babesia species, and within these conserved regions, there are a number of proteins putatively targeted to organelles. The observed overall lack of synteny is surprising considering the divergence times and the apparent absence of transposable elements (TEs) within any of the species examined. TEs are ubiquitous in all other groups of eukaryotes studied to date and have been shown to be involved in genomic rearrangements. It appears that there are different criteria governing genome evolution within the Apicomplexa relative to other well-studied unicellular and multicellular eukaryotes.
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影响因子：
64.8
作者：
Carlton, Jane M.;Adams, John H.;Silva, Joana C.;Bidwell, Shelby L.;Lorenzi, Hernan;Caler, Elisabet;Crabtree, Jonathan;Angiuoli, Samuel V.;Merino, Emilio F.;Amedeo, Paolo;Cheng, Qin;Coulson, Richard M. R.;Crabb, Brendan S.;del Portillo, Hernando A.;Essien, Kobby;Feldblyum, Tamara V.;Fernandez-Becerra, Carmen;Gilson, Paul R.;Gueye, Amy H.;Guo, Xiang;Kang'a, Simon;Kooij, Taco W. A.;Korsinczky, Michael;Meyer, Esmeralda V. -S.;Nene, Vish;Paulsen, Ian;White, Owen;Ralph, Stuart A.;Ren, Qinghu;Sargeant, Tobias J.;Salzberg, Steven L.;Stoeckert, Christian J.;Sullivan, Steven A.;Yamamoto, Marcio M.;Hoffman, Stephen L.;Wortman, Jennifer R.;Gardner, Malcolm J.;Galinski, Mary R.;Barnwell, John W.;Fraser-Liggett, Claire M.
通讯作者：
Fraser-Liggett, Claire M.
影响因子：
6.7
作者：
Chaal BK;Gupta AP;Wastuwidyaningtyas BD;Luah YH;Bozdech Z
通讯作者：
Bozdech Z
影响因子：
4.5
作者：
Fischer G;Rocha EP;Brunet F;Vergassola M;Dujon B
通讯作者：
Dujon B
影响因子：
4.4
作者：
Durand PM;Oelofse AJ;Coetzer TL
通讯作者：
Coetzer TL
影响因子：
1.5
作者：
Bender, A;van Dooren, GG;Schneider, G
通讯作者：
Schneider, G