title: Comprehensive annotation of Glossina pallidipes salivary gland hypertrophy virus from Ethiopian tsetse flies: a proteogenomics approach.
abstract: Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; family Hytrosaviridae) can establish asymptomatic and symptomatic infection in its tsetse fly host. Here, we present a comprehensive annotation of the genome of an Ethiopian GpSGHV isolate (GpSGHV-Eth) compared with the reference Ugandan GpSGHV isolate (GpSGHV-Uga; GenBank accession number EF568108). GpSGHV-Eth has higher salivary gland hypertrophy syndrome prevalence than GpSGHV-Uga. We show that the GpSGHV-Eth genome has 190 291 nt, a low G+C content (27.9 %) and encodes 174 putative ORFs. Using proteogenomic and transcriptome mapping, 141 and 86 ORFs were mapped by transcripts and peptides, respectively. Furthermore, of the 174 ORFs, 132 had putative transcriptional signals [TATA-like box and poly(A) signals]. Sixty ORFs had both TATA-like box promoter and poly(A) signals, and mapped by both transcripts and peptides, implying that these ORFs encode functional proteins. Of the 60 ORFs, 10 ORFs are homologues to baculovirus and nudivirus core genes, including three per os infectivity factors and four RNA polymerase subunits (LEF4, 5, 8 and 9). Whereas GpSGHV-Eth and GpSGHV-Uga are 98.1 % similar at the nucleotide level, 37 ORFs in the GpSGHV-Eth genome had nucleotide insertions (n = 17) and deletions (n = 20) compared with their homologues in GpSGHV-Uga. Furthermore, compared with the GpSGHV-Uga genome, 11 and 24 GpSGHV ORFs were deleted and novel, respectively. Further, 13 GpSGHV-Eth ORFs were non-canonical; they had either CTG or TTG start codons instead of ATG. Taken together, these data suggest that GpSGHV-Eth and GpSGHV-Uga represent two different lineages of the same virus. Genetic differences combined with host and environmental factors possibly explain the differential GpSGHV pathogenesis observed in different G. pallidipes colonies.
authors.affiliation: Insect Pest Control Laboratories, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria.
authors.forename: Adly M M
authors.initials: AMM
authors.lastname: Abd-Alla
authors.affiliation: Insect Pest Control Laboratories, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria.|Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, PO Box 57811, Loresho, Nairobi, Kenya.|Laboratory of Virology, Wageningen University, 6708 PB, Wageningen, The Netherlands.
authors.forename: Henry M
authors.initials: HM
authors.lastname: Kariithi
authors.affiliation: Laboratoire de Pathologie Comparée, Faculté des Sciences, Université de Montpellier, 34095 Montpellier, France.
authors.forename: François
authors.initials: F
authors.lastname: Cousserans
authors.affiliation: 10 Lockhart Close, Kenilworth, Warwickshire CV8 1RB, UK.
authors.forename: Nicolas J
authors.initials: NJ
authors.lastname: Parker
authors.affiliation: Department of Medical Microbiology, School of Medicine, Acibadem University, 34752 Atas¸ehir, Istanbul, Turkey.
authors.forename: İkbal Agah
authors.initials: İA
authors.lastname: İnce
authors.affiliation: Grain, Forage and Bioenergy Research Unit, USDA-ARS, University of Nebraska East Campus, Lincoln, NE 68583, USA.
authors.forename: Erin D
authors.initials: ED
authors.lastname: Scully
authors.affiliation: Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands.
authors.forename: Sjef
authors.initials: S
authors.lastname: Boeren
authors.affiliation: Tropical Crop and Commodity Protection Research Unit, USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Centre, Hilo, HI 96720, USA.
authors.forename: Scott M
authors.initials: SM
authors.lastname: Geib
authors.affiliation: National Institute for Control and Eradication of Tsetse and Trypanosomosis (NICETT), Addis Ababa, Ethiopia.
authors.forename: Solomon
authors.initials: S
authors.lastname: Mekonnen
authors.affiliation: Laboratory of Virology, Wageningen University, 6708 PB, Wageningen, The Netherlands.
authors.forename: Just M
authors.initials: JM
authors.lastname: Vlak
authors.affiliation: Insect Pest Control Laboratories, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Parker
authors.affiliation: Insect Pest Control Laboratories, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria.
authors.forename: Marc J B
authors.initials: MJB
authors.lastname: Vreysen
authors.affiliation: Laboratoire de Pathologie Comparée, Faculté des Sciences, Université de Montpellier, 34095 Montpellier, France.
authors.forename: Max
authors.initials: M
authors.lastname: Bergoin
mesh_terms: D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D002874:Chromosome Mapping; D004267:DNA Viruses / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D004279:DNA, Viral / Q000235:genetics*; D059646:Genome Size; D016679:Genome, Viral; D007304:Insect Viruses / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D040901:Proteomics / Q000379:methods; D012469:Salivary Glands / Q000821:virology; D059467:Transcriptome; D014370:Tsetse Flies / Q000821:virology*; D014758:Viral Core Proteins; D037521:Virulence Factors
chemical_list: D004279:DNA, Viral; D014758:Viral Core Proteins; D037521:Virulence Factors