COMPUTATIONAL ANALYSIS OF CHILLI INFECTING PEPPER LEAF CURL LAHOREVIRUS  AND PEPPER LEAF CURL BANGLADESH VIRUS

M ATIF; F AHMAD; MT MANZOOR; K GILANI; Q ALI; M SARWAR; S ANJUM; MW ALAM; A HUSSAIN; N RAFAQAT

doi:10.54112/bcsrj.v2022i1.112

Authors

M ATIF Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab Lahore, Pakistan
F AHMAD School of Food Sciences and Technology, Minhaj University Lahore, Pakistan
MT MANZOOR Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
K GILANI Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore Pakistan
Q ALI Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab Lahore, Pakistan
M SARWAR Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab Lahore, Pakistan
S ANJUM Department of Botany, University of the Punjab, Lahore, Pakistan
MW ALAM Department of Plant Pathology, University of Okara, Okara, Pakistan
A HUSSAIN Department of Agronomy, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
N RAFAQAT Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan

DOI:

https://doi.org/10.54112/bcsrj.v2022i1.112

Keywords:

ChiLCD, Diversity, Geminiviruses, Mutation, Phylogenetic analysis

Abstract

Since a few decades ago, the pandemic of the Chilli Leaf Curl Disease Complexes (ChiLCD) has caused
enormous alarm. The investigations of various genomes isolated from various regions of the subcontinent in the
current study revealed a vast expansion of ChiLCD. According to evolutionary research, genomes from the pepper
leaf curl Lahore virus (PepLCLV) (JN880419 and JX524173) and the pepper leaf curl Bangladesh virus (PepLCBV)
(DQ116881 and KY420149) are ancestors while others are descendants. The accessions JN880419, JX524173,
DQ116881, and KY420149's sequences underwent evolution, giving rise to several strains and variations.
According to the findings, the Indian subcontinent's chilli crop may be most severely affected by the extremely
aggressive ChiLCV.

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References

Ahmed. (2010). Phylogenetic analysis of Bemisia tabaci (Hemiptera: Aleyrodidae) populations from cotton plants in Pakistan, China, and Egypt . Journal of Pest Science, 14, 135-141. DOI: https://doi.org/10.1007/s10340-009-0279-4

Ahmad. (2011). Characterization of Sun hemp begomo virus and its geographical origin based on in silico structural and functional analysis of recombinant coat protein. African Journal of Biotechnology, 10, 260-270. DOI: https://doi.org/10.5897/AJB10.1212

Balol, G.B. (2010). Sources of genetic variation in plant virus populations. Journal of Pure Applied Microbiology 4, 803-808.

Berriei, L.C., Rybicki, E.P., Rey, M.E.C. (2001). Complete nucleotide sequence and host range of South African cassava mosaic virus: further evidence for recombination amongst Begomoviruses. Journal of General Virology, 82, 53-58. DOI: https://doi.org/10.1099/0022-1317-82-1-53

Biebricher, C.K., & Eigen, M. (2006). ‘What is a Quasispecies?. Current Topics in Microbiology and Immunology, 299, 1–31. DOI: https://doi.org/10.1007/3-540-26397-7_1

Bisaro. (2006). Silencing suppression by Geminivirus proteins. Virology, 16,158-168. DOI: https://doi.org/10.1016/j.virol.2005.09.041

Bisimwa, E., Walangululu J., & Bragard, C. (2012). Occurrence and Distribution of cassava mosaic begomovirus related to agro-ecosystems in the Sud-kivu Province, Democratic Republic of Congo. Asian Journal of Plant Pathology, 6, 1–12. doi: 10.3923/ajppaj.2012.1.12. DOI: https://doi.org/10.3923/ajppaj.2012.1.12

Bosco. (2004). TYLCSV DNA, but not infectivity can be transovarially inherited by the progeny of the whitefly vector Bemisia tabaci (Gennadius). Virology,18, 276-283. DOI: https://doi.org/10.1016/j.virol.2004.03.010

Briddon. (2003). Diversity of DNA :a satellitemolecule associated with some monopartite begomoviruses. Virology, 106-121.

Briddon, R.W., Bull, S.E., Amin, I., Idris, A.M., Mansoor, S., Bedford, I.D., & Markham, P.G. (2003). Diversity of DNA β, a satellite molecule associated with some monopartite Begomoviruses. Virology, 312, 106-121. DOI: https://doi.org/10.1016/S0042-6822(03)00200-9

Briddon, R.W., & Stanley, J. (2006). Subviral agents associated with plant single-stranded DNA viruses. Virology, 344, 198-210. DOI: https://doi.org/10.1016/j.virol.2005.09.042

Castillo-Urquiza, G.P., Beserra, J.E.A., Bruckner, F.P., Lima, A.T., Varsani, A., Alfenas-Zerbini, P., & Zerbini, F.M. (2008). Six novel begomoviruses infecting tomato and associated weeds in Southeastern Brazil. Archives of viroogyl, 153(10), 1985-1989. DOI: https://doi.org/10.1007/s00705-008-0172-0

Duffy, S., & Holmes, E.C. (2008). Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus Tomato yellow leaf curl virus. Journal of General Virology, 82, 957-965. DOI: https://doi.org/10.1128/JVI.01929-07

Duffy, S., & Holmes, E.C. (2009). Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from east african cassava mosaic viruses. Journal of General Virology, 90, 1539-1547. DOI: https://doi.org/10.1099/vir.0.009266-0

Duffy, S., Shackelton, L.A., & Holmes, E.C. (2008). Rates of evolutionary change in viruses: patterns and determinants. Nature Reverse Genetics, 9, 267-276. DOI: https://doi.org/10.1038/nrg2323

Eigen, M., Winkler-Oswatitsch, R., Dress, A. (1988). Statistical geometry in sequence space: a method of quantitative comparative sequence analysis. Science USA, 85, 5913-5917. DOI: https://doi.org/10.1073/pnas.85.16.5913

Faria, J.C., & Maxwell, D.P. 1999. Variability in geminivirus isolatesa ssociated with Phaseolus spp. in Brazil. Phytopathology, 89, 262-268. DOI: https://doi.org/10.1094/PHYTO.1999.89.3.262

Fondong, V.N., Pita, J.S., Rey, M.E.C., de Kochko, A., Beachy, R.N., & Fauquet, C.M. (2000). Evidence of synergism between African cassava mosaic virus and a new double-recombinant geminivirus infecting cassava in Cameroon. Journal General Virology, 81, 287-297. DOI: https://doi.org/10.1099/0022-1317-81-1-287

Galvao, R.M., Mariano, A.C., & Luz, D. (2003). A naturally occurring recombinant DNA-A of a typical bipartite begomovirus does not require the cognate DNA-B to infect Nicotiana benthamiana systemically. Journal General Virology, 84, 715-726. DOI: https://doi.org/10.1099/vir.0.18783-0

Ge, L., Zhang, J., Zhou, X., & Li, H. (2007). Genetic structure and population variability of tomato yellow leaf curl China virus. Journal of virology, 81(11), 5902-5907. DOI: https://doi.org/10.1128/JVI.02431-06

Grigoras, I., Timchenko, T., Grande-Pérez, A., Katul, L., Vetten, H.J., & Gronenborn, B. (2010). High variability and rapid evolution of a nanovirus. Journal of virology, 84(18), 9105-9117. DOI: https://doi.org/10.1128/JVI.00607-10

Harkins, G.W., Delport, W., & Duffy, S. (2009). Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts. Virology Journal, 6, 104. DOI: https://doi.org/10.1186/1743-422X-6-104

Holland, J., Spindler, K., Horodyski, F., Grabau, E., Nichol, S., & Vande Pol, S. (1982). Rapid evolution of RNA genomes. Science, 215(4540), 1577-1585. DOI: https://doi.org/10.1126/science.7041255

Inoue-Nagata, A.K, Martin, D.P., Boiteux, L.S., Giordano, L.D., Bezerra, I.C., & De Avila, A.C. (2006). New species emergence via recombination among isolates of the Brazilian tomato infecting Begomovirus complex. Brazilian Journal of Agricultural Research, 41, 1329-1332. DOI: https://doi.org/10.1590/S0100-204X2006000800018

Jeske, H., Lutgemeier, M., & Preiss, W. (2001). DNA Forms Indicate Rolling Circle and Recombination-Dependent Replication of Abutilon Mosaic Virus, EMBO Journal, 20: 6158-6167. DOI: https://doi.org/10.1093/emboj/20.21.6158

Kumarvinoth, Tribhuwan, Y.V., & SaumikBasu. (2015). Complexity of Begomovirus and betasatellite populations associated with chili leaf curl disease in India. Journal of General Virology, 96, 3143-3158. DOI: https://doi.org/10.1099/jgv.0.000254

Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology Evolution, 33, 1870-1874. doi: 10.1093/molbev/msw054. DOI: https://doi.org/10.1093/molbev/msw054

Lefeuvre, P., Lett, J.M., Reynaud, B., Martin, D.P. (2007a). Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathology , 3:e181. DOI: https://doi.org/10.1371/journal.ppat.0030181

Lefeuvre., & Moriones. (2015). Recombination as a motor of host switches and virus emergence: Geminiviruses as case studies. Current Opinion in Virology,10, 14-19. DOI: https://doi.org/10.1016/j.coviro.2014.12.005

Lima, A. T., Sobrinho, R. R., Gonzalez-Aguilera, J., Rocha, C. S., Silva, S. J., Xavier, C. A., & Zerbini, F. M. (2013). Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts. Journal of General Virology, 94(2), 418-431. DOI: https://doi.org/10.1099/vir.0.047241-0

Lima, A., Silva, J. C., Silva, F. N., Castillo-Urquiza, G. P., Silva, F. F., Seah, Y. M., & Zerbini, F. M. (2017). The diversification of begomovirus populations is predominantly driven by mutational dynamics. Virus evolution, 3(1). DOI: https://doi.org/10.1093/ve/vex005

Liu, H., Boulton, M. I., & Davies, J. W. (1997). Maize streak virus coat protein binds single-and double-stranded DNA in vitro. Journal of general virology, 78(6), 1265-1270. DOI: https://doi.org/10.1099/0022-1317-78-6-1265

Mansoor, S., Khan, S.H., Bashir, A., Saeed, M., Zafar, Y., Malik, K.A., & Markham, P.G. (1999). Identification of a novel circular single-stranded DNA associated with cotton leaf curl disease in Pakistan. Virology, 259, 190-199. DOI: https://doi.org/10.1006/viro.1999.9766

Martin, D.P., Biagini, P., Lefeuvre, P., Golden, M., Roumagnac, P., & Varsani, A. (2011). Recombination in eukaryotic single stranded DNA viruses. Viruses, 3, 1699-1738. DOI: https://doi.org/10.3390/v3091699

Monci, F., Sánchez-Campos, S., Navas-Castillo, J., & Moriones, E. (2002). A natural recombinant between the geminiviruses Tomato yellow leaf curl Sardinia virus and Tomato yellow leaf curl virus exhibits a novel pathogenic phenotype and is becoming prevalent in Spanish populations. Virology, 303(2), 317-326. DOI: https://doi.org/10.1006/viro.2002.1633

Moriones, E., & Navas-Castillo, J. (2000). Tomato yellow leaf curl virus, an emerging virus complex causing epidemics worldwide. Virus Research, 71,123-134. DOI: https://doi.org/10.1016/S0168-1702(00)00193-3

Muhire, B. M., Varsani, A., & Martin, D. P. (2014). SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PloS one, 9(9), e108277. DOI: https://doi.org/10.1371/journal.pone.0108277

Padidam, M., Sawyer, S., & Fauquet, C. M. (1999). Possible emergence of new geminiviruses by frequent recombination. Virology, 265(2), 218-225. DOI: https://doi.org/10.1006/viro.1999.0056

Palukaitis., & García-Arenal F. (2003). Cucumoviruses. Advances in Virus Research, 62, 241-323. DOI: https://doi.org/10.1016/S0065-3527(03)62005-1

Paprotka, T., Metzler, V., & Jeske, H. (2010b). The first DNA 1-like alpha satellites in association with New World begomoviruses in natural infections. Virology, 404, 148-157. DOI: https://doi.org/10.1016/j.virol.2010.05.003

Pita, J. S., Fondong, V. N., Sangare, A., Otim-Nape, G. W., Ogwal, S., & Fauquet, C. M. (2001). Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda. Journal of General Virology, 82(3), 655-665. DOI: https://doi.org/10.1099/0022-1317-82-3-655

Patil, B.L., & Fauquet, C.M. (2009). Cassava mosaic geminiviruses: Actual knowledge and perspectives. Molecular Plant Pathology, 10, 685-701. DOI: https://doi.org/10.1111/j.1364-3703.2009.00559.x

Prasanna, H.C., & Rai, M. (2007). ‘Detection and Frequency of Recombination in Tomato-Infecting Begomoviruses of South and Southeast Asia’. Virology Journal, 4, 111. DOI: https://doi.org/10.1186/1743-422X-4-111

Ramos-Sobrinho, R., Silva, S.J.C., & Silva, T.A.L. (2010). Genetic structure of a population of the begomovirus Bean golden mosaic virus (BGMV) that infects lima bean (Phaseolus lunatus L.) in the state of Alagoas, Brazil. In: Program and Abstracts, 6th International Geminivirus Symposium and 4th International ssDNA Comparative Virology Workshop., 2010, Guanajuato, Mexico.

Ribeiro, S.G., Martin, D.P., Lacorte, C., Simoes, I.C., Orlandini, D.R.S., & Inoue-Nagata, A.K. (2007). Molecular and biological characterization of Tomato chlorotic mottle virus suggests that recombination underlies the evolution and diversity of Brazilian tomato begomoviruses. Phytopathology, 97, 702-711. DOI: https://doi.org/10.1094/PHYTO-97-6-0702

Roye, M.E., Spence, J., McLaughlin, W.A., & Maxwell, D.P. (1999). The common weed Macroptilium lathyroides is not a source of crop-infecting geminiviruses from Jamaica. Tropical Agriculture, 76, 256-262.

Saleem, H., Nahid, N., Shakir, S., Ijaz, S., Murtaza, G., Khan, A. A., & Nawaz-ul-Rehman, M. S. (2016). Diversity, mutation and recombination analysis of cotton leaf curl geminiviruses. PLoS One, 11(3), e0151161. DOI: https://doi.org/10.1371/journal.pone.0151161

Shackelton, & Holmes, E.C. (2006). Phylogenetic Evidence for the Rapid Evolution of Human B19 Erythrovirus. Journal of Virology, 80, 3666-3669. DOI: https://doi.org/10.1128/JVI.80.7.3666-3669.2006

Shakir, S., Nawaz-ul-Rehman, M.S., & Mubin, M. (2018). Characterization, phylogeny and recombination analysis of Pedilanthus leaf curl virus-Petunia isolate and its associated betasatellite. Virology Journal, 15, 134 https://doi.org/10.1186/s12985-018-1047-y . DOI: https://doi.org/10.1186/s12985-018-1047-y

Silva, F.N., Lima, A.T., Rocha, C.S., Castillo-Urquiza, G.P., Alves-Júnior, M., & Zerbini, F.M. (2014). Recombination and pseudorecombination driving the evolution of the begomoviruses Tomato severe rugose virus (ToSRV) and Tomato rugose mosaic virus (ToRMV): two recombinant DNA-A components sharing the same DNA-B. Virology journal, 11(1), 1-11. DOI: https://doi.org/10.1186/1743-422X-11-66

Unseld, S., Höhnle, M., Ringel, M., & Frischmuth, T. (2001). Subcellular targeting of the coat protein of African cassava mosaic geminivirus. Virology, 286(2), 373-383. DOI: https://doi.org/10.1006/viro.2001.1003

Worobey, M., & Holmes, E.C. (1999). Evolutionary Aspects of Recombination in RNA Viruses. Journal of General Virology, 80, 2535-2545. DOI: https://doi.org/10.1099/0022-1317-80-10-2535

Zaidi, S.S., Martin, D.P., Amin. I., Farooq, M., & Mansoor, S., (2016). Tomato leaf curl New Delhi virus; a widespread bipartite begomovirus in the territory of monopartite begomoviruses. Molecular Plant Pathology, 2016. DOI: https://doi.org/10.1111/mpp.12481

Zhang, Wei., Olson, N.H., Baker, T.S., Faulkner, L., Agbandje-McKenna, M., Boulton, M.I., Davies, J.W., & McKenna, R. (2001). Structure of the Maize streak virus geminate particle. Virology, 279, 471-477. DOI: https://doi.org/10.1006/viro.2000.0739

Zhou, X., Liu, Y., Calvert, L., Munoz, C., Otim-Nape, G.W., Robinson, D.J., & Harrison, B.D. (1997). Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination. Journal General Virology, 78(8), 2101-2111. DOI: https://doi.org/10.1099/0022-1317-78-8-2101

Zulfiqar, A., Zhang, J., Cui, X., Qian, Y., Zhou, X., & Xie, Y. (2012). A new Begomovirus associated with alpha- and betasatellite molecules isolated from Vernonia cinerea in China. Archives of Virology, 25,189-191. DOI: https://doi.org/10.1007/s00705-011-1137-2