title: Evolution of genome size and complexity in the rhabdoviridae.
abstract: RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3' to 5' direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae.
authors: CSIRO Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia.
authors: Peter J
authors: PJ
authors: Walker
authors: CSIRO Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia.
authors: Cadhla
authors: C
authors: Firth
authors: Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, United States of America.
authors: Steven G
authors: SG
authors: Widen
authors: CSIRO Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia.
authors: Kim R
authors: KR
authors: Blasdell
authors: Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, Center for Tropical Diseases, and Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, Texas, United States of America.
authors: Hilda
authors: H
authors: Guzman
authors: Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, United States of America.
authors: Thomas G
authors: TG
authors: Wood
authors: CSIRO Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia.
authors: Prasad N
authors: PN
authors: Paradkar
authors: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.
authors: Edward C
authors: EC
authors: Holmes
authors: Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, Center for Tropical Diseases, and Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, Texas, United States of America.
authors: Robert B
authors: RB
authors: Tesh
authors: Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, Center for Tropical Diseases, and Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, Texas, United States of America.
authors: Nikos
authors: N
authors: Vasilakis
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D016679:Genome, Viral / Q000502:physiology*; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000502:physiology*; D012367:RNA, Viral / Q000235:genetics*; D012209:Rhabdoviridae / Q000235:genetics*
chemical_list: D012367:RNA, Viral