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Full-genome analyses of a Potato Virus Y (PVY) isolate infecting pepper (Capsicum annuum L.) in the Republic of South Africa

Virus Genes volume 49, pages 466–476 (2014)Cite this article

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 PVYC isolate PRI-509 and the PVYO 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.

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Acknowledgments

The authors would like to thank the National Research Foundation of South Africa for financial support of VM during the course of the study.

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  1. Discipline of Plant Pathology, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa

    Vaneson Moodley, Jacques D. Ibaba, Roobavathie Naidoo & Augustine Gubba

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  1. Vaneson Moodley
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  2. Jacques D. Ibaba
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  3. Roobavathie Naidoo
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  4. Augustine Gubba
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Correspondence to Augustine Gubba.

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Moodley, V., Ibaba, J.D., Naidoo, R. et al. Full-genome analyses of a Potato Virus Y (PVY) isolate infecting pepper (Capsicum annuum L.) in the Republic of South Africa. Virus Genes 49, 466–476 (2014). https://doi.org/10.1007/s11262-014-1121-5

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  • DOI: https://doi.org/10.1007/s11262-014-1121-5

Keywords

  • Potato Virus Y
  • Pepper
  • Full-genome sequencing
  • South Africa