Expanding networks of RNA virus evolution

See research article: http://www.biomedcentral.com/1471-2148/12/91 webciteViruses are the most abundant and genetically diverse biological entities on earth as demonstrated by recent metagenomic studies [1]. Unlike cellular life forms that all possess the same basic mechanism of genome replication and expression based upon double-stranded (ds)DNA genome and positive-strand messenger (plus) RNA, viruses use all forms of genetic material (positive-strand, negative-strand and dsRNA, single-stranded (ss)DNA, dsDNA) and execute virtually all conceivable genomic strategies (RNA or DNA replication and transcription, as well as reverse transcription of RNA to DNA). In particular, viruses with RNA genomes that do not go through a DNA stage in their reproduction are the simplest genetic elements, reminiscent of the putative primordial RNA world.Owing to their (relatively) small genomes and often rapid reproduction, diverse viral genomes were characterized in the early days of genomics, and many unexpected evolutionary relationships have been revealed between viruses with different genomic strategies that infect widely different hosts. A small set of virus hallmark genes encoding proteins essential for virus replication and morphogenesis form different combinations in diverse viruses but are absent from cellular genomes [2]. Along with lineage-specific genes present in subsets of viruses, the hallmark genes account for a rich network of evolutionary connections against the background of the extreme diversity of viruses. In the last few years, new technologies, in particular the rapid progress of metagenomics (indiscriminate sequencing of environmental DNA samples), have revealed many surprising novelties in the virus world. Perhaps the prime example is the discovery of giant viruses and their parasites, the virophages [3]. However, unexpected findings with substantial implications are also being reported for the much smaller and simpler RNA viruses.In a recent BMC Evolutionary