Submitted to: Journal of Invertebrate Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/19/2011
Publication Date: 1/1/2012
Publication URL: http://handle.nal.usda.gov/10113/55413
Citation: Perera, O.P., Snodgrass, G.L., Allen, K.C., Jackson, R.E., Becnel, J.J., O'Leary, P.F., Luttrell, R.G. 2012. The complete genome sequence of a single-stranded RNA virus from the tarnished plant bug Lygus lineolaris (Palisot de Beauvois). Journal of Invertebrate Pathology. 109:11-19. Interpretive Summary: The genome of a positive-sense single-stranded RNA virus infecting the tarnished plant bug was characterized by nucleotide sequencing of polymerase chain reaction amplified genomic nucleic acid fragments. This small RNA virus, named LyLV-1, produced a single polypeptide of 2986 amino acids. The genomic polypeptide contained structural proteins such as capsid protein domains at the amino-terminal and non-structural proteins at the carboxy-terminal. This genomic organization was similar to the small RNA viruses of the genus Iflavirus (Picornavirales:Iflaviridae). In addition, the LyLV-1 genomic polypeptide showed high amino acid similarity (44%) to that of the sacbrood virus of the honey bee, a member of the genus Iflavirus. This novel virus is the first Iflavirus identified from the suborder Heteroptera and its potential as a biological control agent for the tarnished plant bug is discussed.
Technical Abstract: The complete genome sequence of a single-stranded RNA virus infecting the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), was identified by sequencing cDNA prepared from insects collected from the Mississippi Delta. The 9655 nucleotide positive sense single-stranded RNA genome of Lygus lineolaris single-stranded RNA virus (LyLV-1) contained a single open reading frame of 8958 nucleotides encoding a 2986 amino acid genome polypeptide. The open reading frame was flanked by untranslated regions of 603 and 69 nucleotides at the 5’- and 3’- ends of the genome, respectively. Database searches and homology based modeling was used to identify four capsid proteins (VP1-VP4), helicase/AAA-ATPase, cystiene protease (C3P), protease 2A, and the RNA-directed RNA polymerase (RdRp). In addition, a region with weak similarity to the eukaryotic structural maintenance of chromosome (SMC) domain was identified near the amino-terminal of the polyprotein and adjacent to the VP1 domain. The amino acid sequence of LyLV-1 was approximately 44.4% similar to that of sacbrood virus (SBV) of the honey bee. The genomic organization of both viruses showed remarkable similarity with the exception of highly divergent amino acid regions flanking fairly conserved structural and non-structural polypeptide regions. High similarity to the SBV genome and similarities in the genome organization and amino acid sequence with the viruses of the family Iflaviridae suggests that LyLV-1 is a novel member of this family. Although this virus may only cause covert infections under normal conditions, the potential for using this virus in biological control of L. lineolaris is discussed.