National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
J Bacteriol. 2013 Mar;195(5):941-50. doi: 10.1128/JB.01801-12. Epub 2012 Dec 7.
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.
病毒是地球上最丰富的生物实体，包含大量的遗传多样性。最近测序的病毒基因组数量迅速增加，为深入了解病毒圈的结构和进化提供了前所未有的机会。在这里，我们介绍了噬菌体直系同源群 (POG) 的更新，这是一组来自噬菌体的 4542 个直系同源基因簇，现在还包括感染古菌的病毒，并包含了 1000 多个不同的病毒基因组。对这个扩展数据集的分析表明，POG 的数量在不断增加，而且没有达到饱和，而且大多数 POG 仍然是病毒特有的，在原核细胞中没有同源物，也不在已知的前病毒之外。因此，显然还有大量的病毒基因有待发现。一个补充的观察结果是，许多病毒基因组仍然没有被 POG 很好地覆盖，如果有的话。随着更多基因组被测序，POG 对基因组的覆盖预计将会增加。对于三分之二的 57 个分类群（那些具有至少 3 个不同病毒基因组的分类群），我们确定了在原核细胞基因组中没有观察到的、特定于分类群的单拷贝特征基因，其中一半存在于各自分类群的所有成员中。这些特征基因可用于在宏基因组样本中特异性地识别特定分类群的病毒的存在并定量其丰度，从而深入了解病毒与其宿主之间的生态和进化。
