title: Full-genome analyses of a Potato Virus Y (PVY) isolate infecting pepper (Capsicum annuum L.) in the Republic of South Africa.
abstract: Potato Virus Y (PVY) is a pathogen of economic importance in pepper and other major crop species in the family Solanaceae. Three major PVY strain groups: O, C, and N, have been distinguished on the basis of genome sequencing. In this study, the first full-genome sequence of a PVY isolate (JVW-186) infecting pepper from the province of KwaZulu-Natal, Republic of South Africa is reported. The complete genome sequence of JVW-186 was assembled from overlapping RT-PCR clones using MEGA 5 software. Two ORFs were identified at position 186 and 2915 of the sequence encoding the viral polyprotein and the frameshift translated protein P3N-PIPO, respectively. RDP4 software confirmed three recombination breakpoints at position 343, 1365, and 9308 of the sequence. At each recombination event, a 1,021-bp fragment at the 5' end in the region of the P1/HC-Pro protein and a 392-bp fragment in the region of the coat protein shared a high sequence similarity of 91.8 and 98.89 % to the potato borne PVY(C) isolate PRI-509 and the PVY(O) isolate SASA-110, respectively. The non-recombinant fragment 1 (342-bp) clustered within the C clade of PVY isolates; however, the large 7,942-bp fragment 3 did not cluster within any of the clades. This suggests the possibility of a PVY isolate that has evolved due to the dynamics of selection pressure or the likelihood of an ancestral PVY strain.
authors.affiliation: Discipline of Plant Pathology, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa.
authors.forename: Vaneson
authors.initials: V
authors.lastname: Moodley
authors.forename: Jacques D
authors.initials: JD
authors.lastname: Ibaba
authors.forename: Roobavathie
authors.initials: R
authors.lastname: Naidoo
authors.forename: Augustine
authors.initials: A
authors.lastname: Gubba
mesh_terms: D002212:Capsicum / Q000821:virology*; D016000:Cluster Analysis; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D020815:Polyproteins / Q000235:genetics; D017800:Potyvirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012367:RNA, Viral / Q000235:genetics*; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D013019:South Africa; D014764:Viral Proteins / Q000235:genetics
chemical_list: D020815:Polyproteins; D012367:RNA, Viral; D014764:Viral Proteins