Bacterial proteins pinpoint a single eukaryotic root
Bacterial proteins pinpoint a single eukaryotic root
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DOI：
10.1073/pnas.1420657112
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发表时间：
2015-02-17
影响因子：
11.1
通讯作者：
Elias, Marek
中科院分区：
文献类型：
--
作者：
Derelle, Romain;Torruella, Guifre;Elias, Marek
真核基因和古细菌同源基因之间的系统发育距离很大，这阻碍了真核基因组学研究中真核根位置的确定。最近，已经提出了一种创新的方法来规避这个问题：作为系统发育标记的蛋白质，已从细菌供体来源转移到真核生物，出现后，从古细菌。使用这种方法，最近的两项独立研究已经建立了基于细菌序列的基因组数据集，导致对真核根的不同预测。利用jakobid Andalucia godoyi和两种已知马拉维单胞菌物种（Malawimonas jakobiformis和Malawimonas calforniana）的额外基因组序列，我们重新分析了这两个系统基因组数据集。我们发现，这两个数据集精确定位的真核生物的根是“Unikonta”和“Bikonta”之间的相同的系统发育位置，与malawimonad和collodictyonid血统的Unikonta一侧的根。我们的研究结果坚定地表明：（i）掘孔动物超群不是单系的;（ii）真核生物最后的共同祖先是双鞭毛生物。根据我们的研究结果，我们建议将两个主要的真核生物群Unikonta和Bikonta分别重新命名为Opimoda和Diphoda。
The large phylogenetic distance separating eukaryotic genes and their archaeal orthologs has prevented identification of the position of the eukaryotic root in phylogenomic studies. Recently, an innovative approach has been proposed to circumvent this issue: the use as phylogenetic markers of proteins that have been transferred from bacterial donor sources to eukaryotes, after their emergence from Archaea. Using this approach, two recent independent studies have built phylogenomic datasets based on bacterial sequences, leading to different predictions of the eukaryotic root. Taking advantage of additional genome sequences from the jakobid Andalucia godoyi and the two known malawimonad species (Malawimonas jakobiformis and Malawimonas californiana), we reanalyzed these two phylogenomic datasets. We show that both datasets pinpoint the same phylogenetic position of the eukaryotic root that is between "Unikonta" and "Bikonta," with malawimonad and collodictyonid lineages on the Unikonta side of the root. Our results firmly indicate that (i) the supergroup Excavata is not monophyletic and (ii) the last common ancestor of eukaryotes was a biflagellate organism. Based on our results, we propose to rename the two major eukaryotic groups Unikonta and Bikonta as Opimoda and Diphoda, respectively.