Phylogenetic analysis of coat protein gene of CYDV-RPV strain from Wheat

Madiha Zamurrad, Shahid Hameed, Kamran Saleem, Irfan ul Haque, Samra Kausar


Background: Keeping in view the potential damage caused by viruses to production of different crops and possible ‘directed damages’ by manipulated viral attack in/across border collectively make phylogenetic analysis of any attacking viral specie important. Cereal yellow dwarf viruses (CYDV) are highly important viruses in wheat causing significant yield loss.

Methods: Double antibody sandwich ELISA and reverse transcription polymerase chain reaction (RT-PCR) was used to detect and confirm the polerovirus i.e. CYDV-rhopalosiphum padi virus (RPV), and unassigned viruses (SGV, RMV) in Punjab and NWFP provinces. The PCR products were inserted into a pGEM®-T easy vector, which then transformed in JM-107 cells of Escherichia coli. Recombinant plasmids were sequenced. Nucleotide and predicted amino acid sequences were aligned, analyzed and compared with other RPV isolates of the family. The nucleotide sequence data were used to make a phylogenetic tree.

Results: Sequencing of 600 bp of coat protein gene confirmed the presence of CYDV-RPV strain. Pakistani isolate has close phylogenetic relationship with RPV-Mexcio and RPV-Yolo (USA). They had 99.95% similarity with RPV-Pakistan. The RPV-Aus, RPV-IR, and RPV-Cal (USA) had 99.94% identities with RPV-Pakistan.

Conclusion: This work led to a conclusion that there is very low genetic diversity in RPV-Pakistan. Now it is in our future interest to clarify the identity of RPV-PK with more sequencing. The current study may help scientists to formulate appropriate management strategies against CYDV-RPV.

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Miller and WA, Rasochová L. Barley yellow dwarf viruses. Annual review of phytopathology, (1997); 35(1): 167-190.

Guy P, Johnstone G, Morris D. Barley yellow dwarf viruses in, and aphids on, grasses (including cereals) in Tasmania. Crop and Pasture Science, (1987); 38(1): 139-152.

Watson MA, Mulligan T. Cereal yellow dwarf virus in Great Britain. Plant Pathology, (1957); 6(1): 12-14.

Siddiqui NN, Ilyas M, Mansoor S, Azhar A, Saeed M. Cloning and phylogenetic analysis of coat protein of barley yellow dwarf virus isolates from different regions of pakistan. Journal of Phytopathology, (2012); 160(1): 13-18.

Takahashi T, Kojima M, Ohshima K, Uyeda I, Shikata E. Physical and chemical properties of japanese isolate of barley yellow dwarf virus. Journal of the Faculty of Agriculture, Hokkaido University, (1988); 63(4): 363-372.

Irwin M, Thresh J. Epidemiology of barley yellow dwarf: a study in ecological complexity. Annual review of phytopathology, (1990); 28(1): 393-424.

Chapin JW, Thomas JS, Gray SM, Smith DM, Halbert SE. Seasonal abundance of aphids (Homoptera: Aphididae) in wheat and their role as barley yellow dwarf virus vectors in the South Carolina coastal plain. Journal of economic entomology, (2001); 94(2): 410-421.

Ahmad YA, Rassaby L, Royer M, Borg Z, Braithwaite K, et al. Yellow leaf of sugarcane is caused by at least three different genotypes of sugarcane yellow leaf virus, one of which predominates on the Island of Réunion. Archives of virology, (2006); 151(7): 1355-1371.

Murphy JF, D'Arcy CJ, Clark JM. Barley yellow dwarf virus RNA has a 5′-terminal genome-linked protein. Journal of general virology, (1989); 70(8): 2253-2256.

Mayo M, Ziegler-Graff V. Molecular biology of luteoviruses. Advances in virus research, (1996); 46(1): 413-460.

Dinesh-Kumar S, Brault V. Precise mapping and in vitro translation of a trifunctional subgenomic RNA of barley yellow dwarf virus. Virology, (1992); 187(2): 711-722.

Kelly L, Gerlach WL, Waterhouse PM. Characterisation of the subgenomic RNAs of an Australian isolate of barley yellow dwarf luteovirus. Virology, (1994); 202(2): 565-573.

Allen Miller W, Hercus T, Waterhouse PM, Gerlach WL. A satellite RNA of barley yellow dwarf virus contains a novel hammerhead structure in the self-cleavage domain. Virology, (1991); 183(2): 711-720.

Miller WA, Dinesh-Kumar S, Paul CP. Luteovirus gene expression. Critical Reviews in plant sciences, (1995); 14(3): 179-211.

Gibbs A, Mackenzie A. A primer pair for amplifying part of the genome of all potyvirids by RT-PCR. Journal of Virological Methods, (1997); 63(1): 9-16.

Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in bioinformatics, (2008); 9(4): 299-306.

Chay C, Gunasinge U, Dinesh-Kumar S, Miller W, GRAY SM. Aphid transmission and systemic plant infection determinants of barley yellow dwarf luteovirus-PAV are contained in the coat protein readthrough domain and 17-kDa protein, respectively. Virology, (1996); 219(1): 57-65.

Lazarowitz SG, Beachy RN. Viral movement proteins as probes for intracellular and intercellular trafficking in plants. The Plant Cell Online, (1999); 11(4): 535-548.

Malmstrom CM, Shu R. Multiplexed RT-PCR for streamlined detection and separation of barley and cereal yellow dwarf viruses. Journal of virological methods, (2004); 120(1): 69-78.

Saleem K, Hameed S, Ul-Haque I. Phylogenetic analysis of coat protein gene of BYDV-MAV strain from wheat. Archives of Phytopathology and Plant Protection, (2013); 46(14): 1747-1755.

Rastgou M, Khatabi B, Izadpanah K, Kvarnheden A. Nucleotide sequences of a part of Barley yellow dwarf virus-PAV and Cereal yellow dwarf virus-RPV genome from Iran. Parasitica, (2005); 61(1): 89-94.

Wang M-B, Cheng Z, Keese P, Graham M, Larkin P, et al. Comparison of the coat protein, movement protein and RNA polymerase gene sequences of Australian, Chinese, and American isolates of barley yellow dwarf virus transmitted by Rhopalosiphum padi. Archives of virology, (1998); 143(5): 1005-1013.

Vincent J, Ueng P, Lister R, Larkins B. Nucleotide sequences of coat protein genes for three isolates of barley yellow dwarf virus and their relationships to other luteovirus coat protein sequences. Journal of general virology, (1990); 71(12): 2791-2799.

Miller WA, Liu S, Beckett R. Barley yellow dwarf virus: Luteoviridae or Tombusviridae? Molecular Plant Pathology, (2002); 3(4): 177-183.


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