VIGOR extended to annotate genomes for additional 12 different viruses

Wang, Shiliang; Sundaram, Jaideep P.; Stockwell, Timothy B.

Investigators from Microbial Sequencing Center (MSC, 2003) and Genome Sequencing Center for Infectious Diseases (GSCID, 2009) at J. Craig Venter Institute, sponsored by the National Institute of Allergy and Infectious Diseases, are sequencing various pathogenic genomes, including different viral genomes. Thousands of influenza genomes and hundreds of coronavirus genomes, rotavirus genomes and other viral genomes were sequenced by MSC. Viral genomes are relatively small (ranging from a few kb to 100 kb) compared with bacterial and eukaryotic genomes. However, the genome structure and gene features can be as complex as eukaryotic genomes. In addition to the normal splicing to generate mature messenger ribonucleicacid (mRNA) like the splicing in eukaryotic genome, a variety of complex gene features, such as alternative splicing, ribosomal slippage, ribonucleicacid (RNA) editing, stop codon leakage (stop codon read-through), ribosomal shunting (alternative translation initiation) and gene overlapping, can also be found in many viral genomes. A large number of viruses, such as rhinovirus and yellow fever virus, have only one open reading frame encoded in their small genomes. The single polyprotein of these viruses needs to be processed into mature peptides that will be incorporated into virus structure and be functional during virus replication. These complex gene features must be accurately defined in order to correctly understand these genomes.