Comparing the Dictyostelium and Entamoeba genomes reveals an ancient split in the Conosa lineage.
Comparing the Dictyostelium and Entamoeba genomes reveals an ancient split in the Conosa lineage.
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DOI：
10.1371/journal.pcbi.0010071
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发表时间：
2005-12
影响因子：
4.3
通讯作者：
Sucgang, Richard
中科院分区：
文献类型：
--
作者：
Song, Jie;Xu, Qikai;Olsen, Rolf;Loomis, William F;Shaulsky, Gad;Kuspa, Adam;Sucgang, Richard
阿米巴虫是真菌和动物的姐妹分支，但对于完全测序的基因组来说，样本很少。群居变形虫盘状盘骨变形虫和线粒体病原体溶组织内变形虫是第一个完成基因组测序的变形虫。这两种生物都被归入松果亚门。为了鉴定变形虫特有的基因组元素，我们将这两个基因组相互比较并与其他真核生物基因组进行比较。根据23种真核生物的完整预测蛋白质组构建的扩展的系统发育树将这两种变形虫放在同一个谱系中，尽管据估计这种差异比动物和真菌之间的差异更大，并且可能发生在变形虫从opisthokont谱系分裂后不久。在这两种变形虫共有的1500个同源基因家族中，大多数也与植物、动物和真菌基因组共享。我们发现只有42个基因家族与变形虫谱系不同；其中包括大量含有重复FNIP结构域的蛋白质，以及一种被认为是盘状豆科植物正确细胞类型分化所必需的转录因子。这些阿米巴原虫特异性基因可能有助于设计新的阿米巴原虫病理诊断和治疗方法。大多数单细胞真核生物被集中在一个单一的分类中，直到分子测序显示它们是一个非常多样化的群体，这说明了真核生物进化所采取的不同途径。比较一个有代表性的基因子集表明，有一个特别的群体，阿米巴虫，是动物和真菌的姐妹群体，甚至比植物更接近。尽管它们具有多样性，但很少有简单的真核生物成为完整基因组测序的主题。最近完成了两种阿米巴原虫的基因组，一种自由生活的社会性阿米巴原虫（Dictyostelium disideum）和一种致病性阿米巴原虫（Entamoeba olyhisttica）。作者将每种生物编码的预测蛋白质相互比较，并与其他具有代表性的真核生物进行比较，并使用不仅仅是几个具有代表性的基因，而是23种生物的整个基因组构建了一个系统发育树。结果树紧密地重建了从采样基因中预测的关系，包括加强变形虫与动物和真菌之间的密切关系。作者还发现很少有基因完全由变形虫遗传。由于一些阿米巴虫是重要的临床病原体，这些基因可能是不影响动物宿主的治疗剂的良好靶点。
The Amoebozoa are a sister clade to the fungi and the animals, but are poorly sampled for completely sequenced genomes. The social amoeba Dictyostelium discoideum and amitochondriate pathogen Entamoeba histolytica are the first Amoebozoa with genomes completely sequenced. Both organisms are classified under the Conosa subphylum. To identify Amoebozoa-specific genomic elements, we compared these two genomes to each other and to other eukaryotic genomes. An expanded phylogenetic tree built from the complete predicted proteomes of 23 eukaryotes places the two amoebae in the same lineage, although the divergence is estimated to be greater than that between animals and fungi, and probably happened shortly after the Amoebozoa split from the opisthokont lineage. Most of the 1,500 orthologous gene families shared between the two amoebae are also shared with plant, animal, and fungal genomes. We found that only 42 gene families are distinct to the amoeba lineage; among these are a large number of proteins that contain repeats of the FNIP domain, and a putative transcription factor essential for proper cell type differentiation in D. discoideum. These Amoebozoa-specific genes may be useful in the design of novel diagnostics and therapies for amoebal pathologies. Most single-celled eukaryotes were lumped together in a single catchall classification until molecular sequencing revealed that they are a very diverse group that illustrates the different paths eukaryotic evolution has taken. Comparing a representative subset of genes indicates that one group in particular, the Amoebozoa, are a sister group to the animals and fungi, even more closely related than the plants. Despite their diversity, few simple eukaryotes have been the subject of complete genome sequencing. The genomes of two amoebozoa, Dictyostelium discoideum (a free-living social amoeba) and Entamoeba histolytica (a pathogenic amoeba), were recently completed. The authors compared the predicted proteins encoded by each organism to each other, and to other representative eukaryotes, and built a phylogenetic tree using not just a few representative genes, but the entire genomes of 23 organisms. The resulting tree closely re-created the relationships predicted from the sampled genes, including reinforcing the close relationship between the amoebozoa and the animals and fungi. The authors also found very few genes that are exclusively inherited by amoebozoa. Since some amoebozoa are important clinical pathogens, these genes are likely good targets for therapeutic agents that will not affect the animal host.