Gene content phylogeny of herpesviruses
Gene content phylogeny of herpesviruses
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DOI：
10.1073/pnas.97.10.5334
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发表时间：
2000-05-09
影响因子：
11.1
通讯作者：
Hutchison, CA
中科院分区：
文献类型：
--
作者：
Montague, MG;Hutchison, CA
邻位簇群[COG; Tatusov，R. L.，库宁，E. V. & Lipman，D. J.（1997）Science 278，631-637]鉴定了一组13种完全测序的疱疹病毒。每个COG代表了在几个疱疹基因组中保守的基因产物家族。这些家庭的定义，而不使用基于序列相似性的任意阈值标准。修改了COG技术，使得COG构建中的可变严格性成为可能。高严格性鉴定高度保守基因的核心集合。不同的COG严格性揭示了基因功能类别之间保守程度的差异。COG数据用于构建基于基因含量的全基因组系统发育树。这些树同意以及基于其他方法的树，并通过自举分析测试时是强大的。COG数据也被用来构建一个互反树，聚类具有相似系统发育谱的基因。这种聚类可能会给相关功能的基因或与疱疹病毒进化过程中获得和损失的相关历史提供线索。
Clusters of orthologous groups [COGs; Tatusov, R. L., Koonin, E. V. & Lipman, D. J. (1997) Science 278, 631-637] were identified for a set of 13 completely sequenced herpesviruses. Each COG represented a family of gene products conserved across several herpes genomes. These families were defined without using an arbitrary threshold criterion based on sequence similarity. The COG technique was modified so that variable stringency in COG construction was possible. High stringencies identify a core set of highly conserved genes. Varying COG stringency reveals differences in the degree of conservation between functional classes of genes. The COG data were used to construct whole-genome phylogenetic trees based on gene content. These trees agree well with trees based on other methods and are robust when tested by bootstrap analysis. The COG data also were used to construct a reciprocal tree that clustered genes with similar phylogenetic profiles. This clustering may give clues to genes with related functions or with related histories of acquisition and loss during herpesvirus evolution.