Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes
Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes
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DOI：
10.1128/jb.01801-12
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发表时间：
2013-03-01
影响因子：
3.2
通讯作者：
Koonin, Eugene V.
中科院分区：
文献类型：
--
作者：
Kristensen, David M.;Waller, Alison S.;Koonin, Eugene V.
病毒是地球上最丰富的生物实体，包含大量的遗传多样性。最近，已测序的病毒基因组数量的快速增加为获得对病毒圈的结构和进化的新见解创造了前所未有的机会。在这里，我们介绍了噬菌体直系同源群 (POG) 的更新，这是来自噬菌体的 4,542 个直系同源基因簇的集合，现在还包括感染古细菌的病毒，并包含 1,000 多个不同的病毒基因组。对这一扩展数据集的分析表明，POG 的数量持续增长且未饱和，并且绝大多数 POG 仍对病毒具有特异性，在已知原病毒之外的原核细胞中缺乏同源物。因此，绝大多数病毒基因显然仍有待发现。一个补充性的观察结果是，许多病毒基因组仍然很少被 POG 覆盖（如果有的话）。随着更多基因组的测序，POG 的基因组覆盖范围预计会增加。在 57 个分类单元（具有来自至少 3 种不同病毒的基因组）中的三分之二中，鉴定出了在检测到的原病毒之外的原核基因组中未观察到的分类单元特异性单拷贝特征基因，其中一半存在于相应分类单元的所有成员中。这些特征可用于专门识别宏基因组样本中特定分类群中病毒的存在和量化丰度，从而获得对病毒与其宿主相关的生态和进化的新见解。
Viruses are the most abundant biological entities on earth and encompass a vast amount of genetic diversity. The recent rapid increase in the number of sequenced viral genomes has created unprecedented opportunities for gaining new insight into the structure and evolution of the virosphere. Here, we present an update of the phage orthologous groups (POGs), a collection of 4,542 clusters of orthologous genes from bacteriophages that now also includes viruses infecting archaea and encompasses more than 1,000 distinct virus genomes. Analysis of this expanded data set shows that the number of POGs keeps growing without saturation and that a substantial majority of the POGs remain specific to viruses, lacking homologues in prokaryotic cells, outside known proviruses. Thus, the great majority of virus genes apparently remains to be discovered. A complementary observation is that numerous viral genomes remain poorly, if at all, covered by POGs. The genome coverage by POGs is expected to increase as more genomes are sequenced. Taxon-specific, single-copy signature genes that are not observed in prokaryotic genomes outside detected proviruses were identified for two-thirds of the 57 taxa (those with genomes available from at least 3 distinct viruses), with half of these present in all members of the respective taxon. These signatures can be used to specifically identify the presence and quantify the abundance of viruses from particular taxa in metagenomic samples and thus gain new insights into the ecology and evolution of viruses in relation to their hosts.