Stuart G W, Moffett P K, Bozarth R F
Department of Life Sciences, Indiana State University, Terre Haute, Indiana 47809, USA.
Arch Virol. 2006 Jun;151(6):1159-77. doi: 10.1007/s00705-005-0692-9. Epub 2006 Jan 3.
Rigorous large-scale whole genome comparisons are capable of providing more comprehensive and potentially more accurate descriptions of viral relationships, allowing for the effective validation and modification of current taxonomy. Using a set of 5 togaviruses as an outgroup, a comprehensive phylogeny for 115 isometric positive ssRNA plant viruses was generated based on the simultaneous comparison of over 480 ORFs found within completely sequenced genomes. With the exception of a diverse group of viruses representing the family Comoviridae, the single tree generated contained well supported branches corresponding to well established groups of viruses, including Bromoviridae, Umbravirus, Sobemovirus, and Tymoviridae. In addition, evidence for specific relationships between groups were also observed, specifically Tombusviridae + Umbravirus, and Luteoviridae + Sobemovirus. Various well established subgroups of viruses were also well resolved within the tree. In addition, some recent proposals involving the creation of new genera or the inclusion of newly described viruses into established genera were supported, while others were not. The evidence for frequent gene sharing and the potential consequences to viral taxonomy are discussed.
严格的大规模全基因组比较能够提供更全面且可能更准确的病毒关系描述，从而有效验证和修订当前的分类法。以一组5种披膜病毒作为外类群，基于对完全测序基因组中发现的480多个开放阅读框的同时比较，构建了115种等轴对称正链单链RNA植物病毒的综合系统发育树。除了代表豇豆花叶病毒科的一组多样病毒外，生成的单一树包含了与已确立的病毒组相对应的、支持良好的分支，包括雀麦花叶病毒科、类病毒、南方菜豆花叶病毒和番茄病毒科。此外，还观察到了各病毒组之间特定关系的证据，特别是番茄丛矮病毒科+类病毒，以及黄症病毒科+南方菜豆花叶病毒。各种已确立的病毒亚组在树中也得到了很好的解析。此外，一些涉及创建新属或将新描述的病毒纳入已确立属的近期提议得到了支持，而其他提议则未得到支持。文中讨论了频繁基因共享的证据及其对病毒分类学的潜在影响。
