Wang Nan, Baldi Pierre F, Gaut Brandon S
Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697-2525, USA.
Mol Phylogenet Evol. 2007 Jun;43(3):1066-75. doi: 10.1016/j.ympev.2006.11.019. Epub 2006 Nov 29.
We used complete sequence data from 30 complete Herpesviridae genomes to investigate phylogenetic relationships and patterns of genome evolution. The approach was to identify orthologous gene clusters among taxa and to generate a genomic matrix of gene content. We identified 17 genes with homologs in all 30 taxa and concatenated a subset of 10 of these genes for phylogenetic inference. We also constructed phylogenetic trees on the basis of gene content data. The amino acid and gene content phylogenies were largely concordant, but the amino acid data had much higher internal support. We mapped gene gain events onto the phylogenetic tree by assuming that genes were gained only once during the evolution of herpesviruses. Thirty genes were inferred to be present in the ancestor of all herpesvirus, a number smaller than previously hypothesized. Few genes of recent origin within herpesviruses could be identified as originating from transfer between virus and vertebrate hosts. Inferred rates of gene gain were heterogeneous, with both taxonomic and temporal biases. Nonetheless, the average rate of gene gain was approximately 3.5 x 10(-7) genes gained per year, which is an order of magnitude higher than the nucleotide mutation rate for these large DNA viruses.
我们使用来自30个完整疱疹病毒科基因组的完整序列数据来研究系统发育关系和基因组进化模式。方法是在分类群中识别直系同源基因簇，并生成基因内容的基因组矩阵。我们在所有30个分类群中鉴定出17个具有同源物的基因，并串联其中10个基因的一个子集用于系统发育推断。我们还基于基因内容数据构建了系统发育树。氨基酸和基因内容的系统发育在很大程度上是一致的，但氨基酸数据具有更高的内部支持度。我们通过假设基因在疱疹病毒进化过程中仅获得一次，将基因获得事件映射到系统发育树上。推断所有疱疹病毒的共同祖先中存在30个基因，这一数量比之前假设的要少。疱疹病毒中近期起源的基因很少能被确定为源自病毒与脊椎动物宿主之间的转移。推断的基因获得速率是异质的，存在分类学和时间上的偏差。尽管如此，基因获得的平均速率约为每年3.5×10⁻⁷个基因获得，这比这些大型DNA病毒的核苷酸突变率高一个数量级。
