African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12487

Full Length Research Paper

Characterization of three full Iris yellow spot virus genes of a garlic-infecting isolate from Zimbabwe using next-generation sequencing technology

Charles Karavina
  • Charles Karavina
  • Department of Plant Pathology, School of Agriculture, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, South Africa.
  • Google Scholar
Jacques Davy Ibaba
  • Jacques Davy Ibaba
  • Department of Plant Pathology, School of Agriculture, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, South Africa.
  • Google Scholar
Augustine Gubba
  • Augustine Gubba
  • Department of Plant Pathology, School of Agriculture, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, South Africa.
  • Google Scholar


  •  Received: 28 December 2018
  •  Accepted: 29 January 2019
  •  Published: 31 October 2019

References

Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalinskiene M, Samuitiene M, Boonham N (2009). Next-generation sequencing and metagenomics analysis: a universal diagnostic tool in plant virology. Molecular Plant Pathology 10(4):537-545.
Crossref

 

Bag S, Druffel KL, Pappu HR (2010). Structure and genome organization of the large RNA of Iris yellow spot virus (genus Tospovirus, family Bunyaviridae). Archives of Virology 155:275-279.
Crossref

 
 

Bag S, Schwartz HF, Cramer CS, Harvey MJ, Pappu HR (2015). Iris yellow spot virus (Tospovirus: Bunyaviridae): from obscurity to research priority. Molecular Plant Pathology 16(3):224-237.
Crossref

 
 

Bag S, Schwartz HF, Pappu HR (2012). Identification and characterization of biologically distinct isolates of Iris yellow spot virus (genus Tospovirus, family Bunyaviridae), a serious pathogen of onion. European Journal of Plant Pathology 134:97-104.
Crossref

 
 

Bandla MD, Campbell LR, Ullman DE, Sherwood JL (1998). Interaction of Tomato spotted wilt tospovirus (TSWV) glycoproteins with a thrips midgut protein, a potential cellular receptor for TSWV. Phytopathology 88:98-104.
Crossref

 
 

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012). SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19:455-477.
Crossref

 
 

Bolger AM, Lohse M, Usadel B (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114-2120.
Crossref

 
 

Bushnell B (2014). BBMap short read aligner. 

View. Accessed on June 11, 2018.

 
 

CABI (2018). Iris yellow spot virus datasheet 28848. 

View. Accessed on July 7, 2018.

 
 

Cortês I, Livieratos IC, Derks A, Kormelink R (1998). Molecular and serological characterization of Iris yellow spot virus, a new and distinct Tospovirus species. Phytopathology 88:1276-1282.
Crossref

 
 

Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005). Protein identification and analysis tools on the ExPASy Server. In: The Proteomics Protocols Handbook. J.M. Walker (eds). Humana Press, USA.
Crossref

 
 

Gawande SJ, Gurav VS, Martin DP, Asokan R, Gopal J (2015). Sequence analysis of Indian Iris yellow spot virus ambisense genomic segments: evidence of interspecies RNA recombination. Archives of Virology 160:1285-1289.
Crossref

 
 

Karavina C, Gubba A (2017). Iris yellow spot virus in Zimbabwe: Incidence, severity and characterization of Allium-infecting isolates. Crop Protection 94:69-76.
Crossref

 
 

Karavina C, Ibaba JD, Gubba A (2016). First report of Iris yellow spot virus infecting onion in Zimbabwe. Plant Disease 100(1):235.
Crossref

 
 

King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (2012). Virus taxonomy- classification and nomenclature of viruses. Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, Amsterdam, The Netherlands pp. 725-741.

 
 

Kreuze JF, Perez A, Untiveros M, Quispe D, Fuentes S, Barker I, Simon R (2009). Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a genetic method for diagnosis discovery and sequencing of viruses. Virology 388:1-7.
Crossref

 
 

Lee J-S, Cho WK, Choi H-S, Kim K-H (2011). RT-PCR detection of five quarantine plant RNA viruses belonging to poty- and tospo-viruses. Plant Patholology Journal 27(3):291-296.
Crossref

 
 

Margaria P, Miozzi L, Ciuffo M, Pappu H, Turina M (2015). The first complete genome sequences of two distinct European Tomato spotted wilt virus isolates. Archives of Virology 160:591-595.
Crossref

 
 

Martin JA, Wang Z (2011). Next-generation transcriptome assembly. Nature Reviews Genetics 12:671-682.
Crossref

 
 

Pappu HR, Jones RAC, Jain RK (2009). Global status of tospovirus epidemics in diverse cropping systems: Successes achieved and challenges ahead. Virus Research 141:219-236.
Crossref

 
 

Srinivasan R, Sundaraj S, Pappu HR, Diffie S, Riley DG (2012). Transmission of Iris yellow spot virus by Frankliniella occidentalis and Thrips tabaci (Thysanoptera: Thripidae). Journal of Economic Entomology 105:40-47.
Crossref

 
 

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30:2725-2729.
Crossref

 
 

Walsh K, North J, Barker I, Boonham N (2001). Detection of different strains of Potato virus Y and their mixed infections using competitive fluorescent RT-PCR. Journal of Virological Methods 91:167-173.
Crossref

 
 

Zhang Z, Wang D, Yu C, Wang Z, Dong J, Shi K, Yuan X (2016). Identification of three new isolates of Tomato spotted wilt virus from different hosts in China: molecular diversity, phylogenetic and recombination analyses. Virology Journal 13:8.
Crossref