Song Jie, Xu Qikai, Olsen Rolf, Loomis William F, Shaulsky Gad, Kuspa Adam, Sucgang Richard
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.
PLoS Comput Biol. 2005 Dec;1(7):e71. doi: 10.1371/journal.pcbi.0010071. Epub 2005 Dec 16.
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.
变形虫门是真菌和动物的姐妹进化枝，但在全基因组测序方面样本稀少。社会性变形虫盘基网柄菌和无线粒体病原体溶组织内阿米巴是首批全基因组测序的变形虫门生物。这两种生物都归类于锥虫亚门。为了鉴定变形虫门特有的基因组元件，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了比较。基于23种真核生物完整预测蛋白质组构建的扩展系统发育树将这两种变形虫置于同一谱系中，尽管估计它们的分歧大于动物和真菌之间的分歧，而且可能发生在变形虫门从后鞭毛生物谱系中分化出来后不久。这两种变形虫共有的1500个直系同源基因家族中的大多数也与植物、动物和真菌基因组共有。我们发现只有42个基因家族是变形虫谱系特有的；其中有大量包含FNIP结构域重复序列的蛋白质，以及盘基网柄菌中细胞类型正确分化所必需的一个假定转录因子。这些变形虫门特有的基因可能有助于设计针对变形虫病的新型诊断方法和治疗方法。
