Informative Regions In Viral Genomes

Abstract

Viruses, far from being just parasites affecting hosts fitness are major players in any microbial ecosystem. In spite of their broad abundance, viruses, in particular bacteriophages remain largely unknown since only about 20% of sequences obtained from viral community DNA surveys could be annotated by comparison to public databases. In order to shed some light into this genetic dark matter we expanded the search of orthologous groups as potential markers to viral taxonomy from bacteriophages and included eukaryotic viruses, establishing a set of 31,150 ViPhOGs. To this, we examine the non-redundant viral diversity stored in public databases, predict proteins in genomes lacking such information and all annotated and predicted proteins were used to identify potential protein domains. Clustering of domains and unannotated regions into orthologous groups was done using cogSoft. Finally, we employed a supervised classification method by using a Random Forest implementation to classify genomes into their taxonomy and found that the presence/absence of ViPhOGs is significantly associated with their taxonomy. Furthermore, we established a set of 1,457 ViPhOGs that given their importance for the classification could be considered as markers/signatures for the different taxonomic groups defined by the ICTV at the Order, Family, and Genus levels. Both, the ViPhOGs and informative ViPhOGs sets are available at the Open Science Framwork (OSF) under the ViPhOGs project (https://osf.io/2zd9r/).