First report of Tomato leaf curl New Delhi virus (a bipartite begomovirus) from round gourd plant in Swat region of Pakistan: its phylogenetic and biogeographic analysis
Abstract
Background: The family Geminiviridae contains plant viruses commonly referred to as geminiviruses, which cause diseases in numerous important plants. Geminiviridae is one of the most important family of plant-infecting viruses that has been divided into fourteen recognized genera. Amongst these, the genus Begomovirus is the largest and economically most important one, viruses of the genus are further categorized into bipartite (two genomic components called DNA-A and DNA-B) and monopartite (single genomic component or DNA-A) begomoviruses.
Method: The genomic DNA was extracted from symptomatic plant samples and both the DNA-(B and A) components of a bipartite begomovirus were amplified via rolling circular amplification (RCA) and PCR. The amplified DNA-A and DNA-B were cloned and sequenced by Primer walking, Sanger sequencing, and Illumina sequencing methods. The phylogenetic and biogeographic analyses of both components were performed by various bioinformatics tools.
Results: DNA-A (accession number MW722701) and DNA-B (accession number MW722782) of begomoviruses that were sequenced shared >95% sequence similarity with the bipartite begomovirus known as Tomato Leaf Curl New Delhi virus (TLCuNDV). Phylogenetic and biogeographic analyses proposed several possible ancestors, and multiple dispersal and vicariance events may be involved in the evolution of this virus.
Conclusions: This is the first time a bipartite begomovirus has been found to infect a plant in the study area (District Swat, Pakistan). The existence of ToLCNDV may pose a major danger to other important crops in the region.
Keywords: Bipartite Begomoviruses; Phylogeny; Biogeography; BLAST; S-DIVA; BBM; DEC
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Gutierrez C. Geminivirus DNA replication. Cellular and Molecular Life Sciences, (1999); 56: 313–329.
Ha. C, Coombs S, Revill P, Harding R, Vu M, Dale J.A. Molecular characterization of begomoviruses and DNA satellites from Vietnam: additional evidence that the NW geminiviruses were present in the OW prior to continental separation. Journal of General Virology, (2008); 89: 312–326.
Yu Y, Harris AJ, Xingjian H. RASP version 2.1b. 2011, Available at http:/mnh.scu.edu.cn/soft/blog/RASP.
Brown G. Public participation GIS (PPGIS) for regional and environmental planning: Reflections on a decade of empirical research. Journal Of the Urban & Regional Information Systems Association, (2012); 24(2).
Uniyal, A P, Mansotra K, Yadav S K, Kumar V. An overview of designing and selection of sgRNAs for precise genome editing by the CRISPR-Cas9 system in plants. 3 Biotech, (2019); 9(6): 1-19.
Varsani, A, Roumagnac P, Fuchs M, Navas-Castillo J, Moriones E, Idris A, Martin D. P. Capulavirus and Grablovirus: two new genera in the family Geminiviridae. Archives of Virology, (2017); 162 (6): 1819-1831.
Roumagnac, P, Granier M, Bernardo P, Deshoux M, Ferdinand R, Galzi S, Mesléard F. Alfalfa leaf curl virus: An aphid-transmitted geminivirus. Journal of Virology, (2015);89(18):9683-8.
Roumagnac, P, Lett J. M.; Fiallo-Olivé E, Navas-Castillo J, Zerbini F. M.; Martin D. P.; Varsani A. Establishment of five new genera in the family Geminiviridae: Citlodavirus, Maldovirus, Mulcrilevirus, Opunvirus, and Topilevirus. Archives of virology, (2021); 1-16.
Varsani, A, Roumagnac P, Fuchs M, Navas-Castillo J, Moriones E, Idris A, Martin D. P. Capulavirus and Grablovirus: two new genera in the family Geminiviridae. Archives of Virology, (2017); 162 (6): 1819-1831.
Zerbini, F M, Briddon R W, Idris A, Martin D P, Moriones E, Navas-Castillo J, Consortium I.R. ICTV virus taxonomy profile: Geminiviridae. Journal of General Virology, (2017); 98 (2): 131.
Mansoor, S, Zafar Y, Briddon, R. W. Geminivirus disease complexes: the threat is spreading. Trends in plant science, (2006); 11(5): 209-212.
Navas-Castillo, J, Fiallo-Olivé E, Sánchez-Campos S. Emerging virus diseases transmitted by whiteflies. Annual Review of Phytopathology, (2011); 49: 219-248.
Padidam, M, Sawyer S, Fauquet C. M. Possible emergence of new geminiviruses by frequent recombination. Virology, (1999); 265(2): 218-225.
Paximadis, M, Idris A. M.; Torres-Jerez, I, Villarreal A, Rey M. E. C.; Brown J. K. Characterization of tobacco geminiviruses in the Old and New World. Archives of Virology, (1999);144 (4): 703-717.
Rybicki E. P. A phylogenetic and evolutionary justification for three genera of Geminiviridae. Archives of Virology, (1994); 139 (1-2): 49-77.
Briddon, R. W . Effects of genetic changes to the begomovirus/betasatellite complex causing cotton leaf curl disease in South Asia post-resistance breaking. Virus Res. (2014);186: 114–119
Rojas, M R, Hagen C, Lucas W J, Gilbertson R L. Exploiting chinks in the plant's armor: Evolution and emergence of geminiviruses. Annual Review of Phytopathology, (2005); 43: 361-394
Ali, S S, Pfosser M, Wetschnig W, Martínez‐Azorín M, Crespo M.B, Yu Y. Out of Africa: Miocene Dispersal, Vicariance, and Extinction within Hyacinthaceae Subfamily Urgineoideae. Journal of Integrative Plant Biology, (2013); 55 (10): 950–964.
Ali, S S, Yan Yu, Martin P, Wetschnig W. Inferences of biogeographical histories within subfamily Hyacinthoideae using S-DIVA and Bayesian binary MCMC analysis implemented in RASP (Reconstruct Ancestral State in Phylogenies). Annals of Botany, (2012); 109 (1): 95–107.
Rehman S U, Muhammad K, Sher H, Que Y, Ali R, Ali S, Hassan I, Rahat MA. Molecular Analysis of Cold Responsive (COR) Genes in Selected Sugarcane and Saccharum spontaneum L. Advancements in Life Sciences. (2023)
;9(4):547-51.
Habile D, Kober S, Jeske H. Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. Virol Methods. (2006); 135 (1): 9-16.
Drummond A J, Suchard M. A, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, (2012); 29 (8): 1969-1973.
Posada D. j ModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 2008; 25 (7): 1253-1256.
Rocha C S, Castillo-Urquiza G P, Lima A T, Silva F N, Xavier C. A, Hora-Júnior B. T, Zerbini F M. Brazilian begomovirus populations are highly recombinant, rapidly evolving, and segregated based on geographical location. Journal of virology, (2013); 87(10): 5784-5799.
Moyle RG. Andersen MJ, Oliveros CH, Steinheimer FD, Reddy SD. Phylogeny and biogeographic of the core babblers (Aves: Timaliidae). Systematic Biology, (2012); 61: 631-651.
Saeed ST, Samad A. Emerging threat of begomoviruses to the cultivation of medicinal and aromatic crops and their management strategies. Virus Disease (2017); 28(1): 1-17.
Uniyal, AP, Mansotra K, Yadav S. K, Kumar V. An overview of designing and selection of sgRNAs for precise genome editing by the CRISPR-Cas9 system in plants. 3 Biotech, (2019); 9(6): 1-19.
Inoue-Nagata, AK, Bassanezi R B, Belasque J, Amorim L, Macedo MA, Barbosa JC, Savary S. The importance of primary inoculum and area-wide disease management to crop health and food security. Food Security, (2016); 8(1): 221-238.
Mansoor S, Amin I, Briddon RW. Geminiviral diseases of cotton. Stress Physiology in Cotton. 2011:125.
Moriones E, Praveen S, Chakraborty S. Tomato leaf curl New Delhi virus: an emerging virus complex threatening vegetable and fiber crops. Viruses. (2017); 9 (10): 264.
Ali Z, Ali S, Tashkandi M, Zaidi SS, Mahfouz MM. CRISPR/Cas9-mediated immunity to geminiviruses: differential interference and evasion. Scientific reports. (2016); 6(1):26912.
Sahu AK, Sanan-Mishra N. Complete genome sequence of a new bipartite begomovirus associated with leaf curl disease of Capsicum annum. 3 Biotech (2020); 10 (5):235.
Rodríguez-Negrete EA, Morales-Aguilar JJ, Domínguez-Duran G, Torres-Devora G, Camacho-Beltrán E, Leyva-López NE, Voloudakis AE, Bejarano ER, Méndez-Lozano J. High-throughput sequencing reveals differential begomovirus species diversity in non-cultivated plants in Northern-Pacific Mexico. Viruses. (2019);11(7):594.
Srivastava A, Pandey V, Al-Sadi AM, Shahid MS, Gaur RK. An insight into emerging begomoviruses and their satellite complex causing papaya leaf curl disease. Current Genomics. (2023);24(1):2.
Nawaz-ul-Rehman MS, Fauquet CM. Evolution of geminiviruses and their satellites. FEBS letters. (2009); 583 (12):1825-32.
DOI: http://dx.doi.org/10.62940/als.v11i2.2459
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