Do Viruses Exchange Genes across Superkingdoms of Life?

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

Viral proteins were scanned against a library of hidden Markov models (HMMs) (Gough et al., 2001; Gough and Chothia, 2002) maintained by the SUPERFAMILY database (ver. 1.75) (de Lima Morais et al., 2011) to detect SCOP FSFs using stringent Evalue cutoff of 10 −4 . Viral genomes with no hits were discarded from the analysis. This reduced the viral dataset to include a total of 3,460 viruses including 1,649 dsDNA, 534 ssDNA, 166 dsRNA, 991 ssRNA, and 120 retrotranscribing viruses. Virus host information was available for 3,440/3,460 viruses (Bao et al., 2004) and was used to identify 62 archaeoviruses, 1,223 bacterioviruses, and 2,155 eukaryoviruses (Table S1 ). In parallel, pre-calculated FSF assignments for ∼11 million proteins encoded by the completely-sequenced genomes of a total of 1,620 cellular organisms including 122 Archaea, 1,115 Bacteria, and 383 Eukarya were retrieved directly from the local installation of SUPERFAMILY MySQL database (July 2014). HMM assignments for viral proteomes can be downloaded from https://figshare. com/articles/Nasir_and_Caetano-Anolles_2015_zip/4833641.