URMITE, Centre National de la Recherche Scientifique UMR IRD 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France.
PLoS One. 2010 Dec 2;5(12):e15530. doi: 10.1371/journal.pone.0015530.
The discovery of Mimivirus, with its very large genome content, made it possible to identify genes common to the three domains of life (Eukarya, Bacteria and Archaea) and to generate controversial phylogenomic trees congruent with that of ribosomal genes, branching Mimivirus at its root. Here we used sequences from metagenomic databases, Marseillevirus and three new viruses extending the Mimiviridae family to generate the phylogenetic trees of eight proteins involved in different steps of DNA processing. Compared to the three ribosomal defined domains, we report a single common origin for Nucleocytoplasmic Large DNA Viruses (NCLDV), DNA processing genes rooted between Archaea and Eukarya, with a topology congruent with that of the ribosomal tree. As for translation, we found in our new viruses, together with Mimivirus, five proteins rooted deeply in the eukaryotic clade. In addition, comparison of informational genes repertoire based on phyletic pattern analysis supports existence of a clade containing NCLDVs clearly distinct from that of Eukarya, Bacteria and Archaea. We hypothesize that the core genome of NCLDV is as ancient as the three currently accepted domains of life.
巨型病毒的发现，其基因组内容非常庞大，使得鉴定出普遍存在于生命三个域（真核生物、细菌和古菌）的基因成为可能，并生成了与核糖体基因一致的具有争议的系统发育树，将巨型病毒分支在其根部。在这里，我们使用来自宏基因组数据库、马赛病毒和三个新病毒的序列，扩展了 Mimiviridae 科，以生成涉及 DNA 处理不同步骤的 8 种蛋白质的系统发育树。与三个核糖体定义的域相比，我们报告了核质大 DNA 病毒（NCLDV）的单一共同起源，DNA 处理基因在古菌和真核生物之间扎根，其拓扑结构与核糖体树一致。至于翻译，我们在我们的新病毒中发现，与 Mimivirus 一起，有五个蛋白质在真核生物进化枝中深深地扎根。此外，基于系统发育模式分析的信息基因库比较支持存在一个包含 NCLDV 的进化枝，与真核生物、细菌和古菌明显不同。我们假设 NCLDV 的核心基因组与目前公认的生命三个域一样古老。
