Do Viruses Exchange Genes across Superkingdoms of Life?

Malik, Shahana S.; Azem-e-Zahra, Syeda; Kim, Kyung Mo; Caetano-Anollés, Gustavo; Nasir, Arshan

Proteome data used in this study was taken from Nasir and Caetano-Anollés (2015) . In brief, a total of 190,610 protein sequences corresponding to 3,966 completely-sequenced reference genomes of viruses that were available on the NCBI Viral Genomes Resource in June 2014 (Brister et al., 2015) were downloaded. Reference virus genomes are well-curated first genomes submitted for any virus species. Subsequent submissions of new genomes for that virus species are termed "genome neighbors." In our study, we only kept reference viral genomes, corresponding to any of the seven known viral replicon types (i.e., dsDNA, ssDNA, plus-ssRNA, minus-ssRNA, dsRNA, and retrotranscribing viruses) and excluding genomic neighbors, viruses that were listed as either "unclassified" or "unassigned" and deltaviruses.