Roselle bitkilerini enfekte eden Cotton leaf curl Multan virüsünün (CLCUMUV) moleküler karakterizasyonu ve evrimsel geçmiş analizi

Year 2023, Volume: 4 Issue: 1, 18 - 30, 30.06.2023

Muhammad Arif

Abstract

Roselle (Hibiscus sabidarrifa, Hibiscus esculentus) bitkileri, çok yönlü kullanımları için birçok tropikal ve subtropikal iklimde yetiştirilmektedir. Bitki virüsleri, tarımsal üretimde maksimum kayıplara neden olma konusunda önemli bir kapasiteye sahiptir. Dünya genelinde gıda güvenliği veya ekolojik bütünlük için büyük tehdit oluşturan bitki hastalıklarının yaklaşık yarısının ortaya çıkmasından bu virüslerin sorumlu olduğu varsayılmaktadır. Geminivirüsler, karakteristik ikiz yarı-ikosahedral viryonlara ve küçük, tek sarmallı dairesel bir DNA genomuna sahip bitki virüsleri ailesidir. Begomovirüslerin karakteristik semptomlarını gösteren bazı Roselle bitkileri gözlemlendi. Enfekte bitkilerden 550 bp'lik bir amplikon boyutu elde edildi. Sekans analizi, bu semptomatik bitkilerde Cotton leaf curl Multan virüsünün varlığını kanıtlamıştır. 2.4-2.5 kb tam uzunlukta bir genom boyutu elde edildi. Bir filogenetik analiz ve evrimsel tarih analizi, bu virüsün diğer hizalanmış virüslerle ilişkisini doğrulamıştır. Genel olarak, belirli bir bölgede yeni bir begomovirüs konakçısı belirledik.

Keywords

Roselle, Begomovirus, AC2 geni, Filogenetik analiz, evrimsel tarih, nükleotit karşılaştırması

The Molecular Characterization and Evolutionary History Analysis of Cotton leaf curl Multan virus (CLCUMUV) Infecting (Hibiscus sabidarrifa, Hibiscus rosa-sinensis) in Punjab Province of Pakistan

Abstract

The plants (Hibiscus sabidarrifa and Hibiscus rosa-sinensis) are cultivated in many tropical and
subtropical climates for their versatile usage. Plant viruses have a significant capacity to cause the
maximum losses in agricultural production. It is assumed that these viruses are responsible for the
emergence of about half of plant diseases which are a major threat to food safety or ecological integrity
worldwide. Geminiviruses are family of plant viruses with characteristic twinned quasi-icosahedral
virions and a small, single-stranded circular DNA genome. Some plants (H. sabidarrifa and H. rosasinensis) showing the characteristic symptoms of viruses were observed. The presence of whitefly vector presumed that these plants might have begomovirus. A 550 bp of amplicon size as a plasmid was
obtained from the infected plants after PCR reaction. The obtained amplicon was amplified with
sequence specific primers to get the full length genome. The sequence analysis has proved the existence
of Cotton leaf curl Multan virus (CLCUMUV) from symptomatic plants. The full genome sequence
analysis revealed a 2.4-2.5 kb full genome of CLCUMUV infecting Roselle species. A phylogenetic and
evolutionary history analysis has confirmed the association of this virus with other aligned viruses.
Overall, we have identified one new species as host of begomovirus in this area.

Keywords

Roselle, Begomovirus, AC2 gene, Phylogenetic analysis, nucleotide comparison

References

• 1. [1] N. O. Anderson, "Flower breeding and genetics: issues, challenges and opportunities for the 21st century" Springer Science & Business Media 2006.
• 2. [2] M. Ansari, T. Eslaminejad, Z. Sarhadynejad, T. Eslaminejad "An Overview of the Roselle Plant with Particular Reference to Its Cultivation, Diseases and Usages" European Journal of Medicinal Plants 3(1) (2013) 135.
• 3. [3] Y.W. Mak, L.O. Chuah, R. Ahmad, R. Bhat, "Antioxidant and antibacterial activities of hibiscus (Hibiscus rosa-sinensis L.) and Cassia (Senna bicapsularis L.) flower extracts" Journal of King Saud University-Science 25(4) (2013) 275-282.
• 4. [4] P. Ruban, K. Gajalakshmi, "In vitro antibacterial activity of Hibiscus rosa–sinensis flower extract against human pathogens" Asian pacific journal of tropical biomedicine 2(5) (2012) 399-403.
• 5. [5] Y. Xie, Y. Liu, M. Meng, L. Chen, Z. Zhu, "Isolation and identification of a super strong plant promoter from cotton leaf curl Multan virus" Plant molecular biology 53(1-2) (2003) 1-14.
• 6. [6] A.T. Lima, R.R. Sobrinho, J. Gonzalez-Aguilera, C.S. Rocha, S.J. Silva, C.A. Xavier, F.N. Silva, S. Duffy, F.M. Zerbini, "Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts" Journal of General Virology 94(2) (2013) 418-431.
• 7. [7] M. Arif, S. Atta, M.A. Bashir, A. Hussain, M.I. Khan, S. Farooq, A. Hannan, S. ul Islam, U. ud din Umar, M. Khan, "Molecular characterization and RSV Co-infection of Nicotiana benthamiana with three distinct begomoviruses" Methods 183 (2020) 43-49.
• 8. [8] M.-u.-. Rahman, A.Q. Khan, Z. Rahmat, M.A. Iqbal, Y. Zafar, "Genetics and genomics of cotton leaf curl disease, its viral causal agents and whitefly vector: a way forward to sustain cotton fiber security" Frontiers in Plant Science 8 (2017) 1157.
• 9. [9] S. Yogindran, M. Kumar, L. Sahoo, K. Sanatombi, S. Chakraborty, "Occurrence of Cotton leaf curl Multan virus and associated betasatellites with leaf curl disease of Bhut-Jolokia chillies (Capsicum chinense Jacq.) in India" Molecular Biology Reports 48 (2021) 2143-2152.
• 10. [10] R. Briddon, M. Pinner, J. Stanley, P. Markham, "Geminivirus coat protein gene replacement alters insect specificity" Virology 177(1) (1990) 85-94.
• 11. [11] L. Hanley-Bowdoin, S.B. Settlage, B.M. Orozco, S. Nagar, D. Robertson, "Geminiviruses: models for plant DNA replication, transcription, and cell cycle regulation" Critical Reviews in Bioch. and Molecular Bio. 35(2) (2000) 105-140.
• 12. [12] C.P. Priyadarshini, M. Ambika, R. Tippeswamy, H. Savithri, "Functional characterization of coat protein and V2 involved in cell to cell movement of Cotton leaf curl Kokhran virus-Dabawali" PLoS One 6(11) (2011) e26929.
• 13. [13] B. Krenz, K. Deuschle, T. Deigner, S. Unseld, G. Kepp, C. Wege, T. Kleinow, H. Jeske, "Early function of the Abutilon mosaic virus AC2 gene as a replication brake" Journal of virology 89(7) (2015) 3683-3699.
• 14. [14] S. Mansoor, R. Briddon, S. Bull, I. Bedford, A. Bashir, M. Hussain, M. Saeed, Y. Zafar, K. Malik, C. Fauquet, "Cotton leaf curl disease is associated with multiple monopartite begomoviruses supported by single DNA β" Archives of virology 148(10) (2003) 1969-1986.
• 15. [15] S. Barreto, M. Hallwass, O. Aquino, A. Inoue-Nagata, "A study of weeds as potential inoculum sources for a tomato-infecting begomovirus in central Brazil" Phytopathology 103(5) (2013) 436-444.
• 16. [16] M.S. Nawaz-ul-Rehman, C.M. Fauquet, "Evolution of geminiviruses and their satellites" FEBS letters 583(12) (2009) 1825-1832.
• 17. [17] M. Mubin, M. Shahid, M. Tahir, R. Briddon, S. Mansoor, "Characterization of begomovirus components from a weed suggests that begomoviruses may associate with multiple distinct DNA satellites" Virus Genes 40(3) (2010) 452-457.
• 18. [18] G. Moissiard, O. Voinnet, "Viral suppression of RNA silencing in plants" Molecular plant pathology 5(1) (2004) 71-82.
• 19. [19] R. Vanitharani, P. Chellappan, J.S. Pita, C.M. Fauquet, "Differential roles of AC2 and AC4 of cassava geminiviruses in mediating synergism and suppression of posttranscriptional gene silencing" Journal of virology 78(17) (2004) 9487-9498.
• 20. [20] L. Hanley-Bowdoin, S.B. Settlage, B.M. Orozco, S. Nagar, D. Robertson, "Geminiviruses: models for plant DNA replication, transcription, and cell cycle regulation" Critical Reviews in Plant Sciences 18(1) (1999) 71-106.
• 21. [21] R.W. Briddon, S.E. Bull, I. Amin, A.M. Idris, S. Mansoor, I.D. Bedford, P. Dhawan, N. Rishi, S.S. Siwatch, A.M. Abdel-Salam, "Diversity of DNA β, a satellite molecule associated with some monopartite begomoviruses" Virology 312(1) (2003) 106-121.
• 22. [22] I. Amin, K. Hussain, R. Akbergenov, J.S. Yadav, J. Qazi, S. Mansoor, T. Hohn, C.M. Fauquet, R.W. Briddon, "Suppressors of RNA silencing encoded by the components of the cotton leaf curl begomovirus-betasatellite complex" Molecular plant-microbe interactions 24(8) (2011) 973-983.
• 23. [23] J. Kumar, S. Gunapati, A. Alok, A. Lalit, R. Gadre, N.C. Sharma, J.K. Roy, S.P. Singh, "Cotton leaf curl Burewala virus with intact or mutant transcriptional activator proteins: complexity of cotton leaf curl disease" Archives of virology 160(5) (2015) 1219-1228.
• 24. [24] S.S.-e.-A. Zaidi, M. Shafiq, I. Amin, B.E. Scheffler, J.A. Scheffler, R.W. Briddon, S. Mansoor, "Frequent occurrence of Tomato leaf curl New Delhi virus in cotton leaf curl disease affected cotton in Pakistan" Plos one 11(5) (2016) e0155520.
• 25. [25] M.J. Iqbal, M. Zia-Ur-Rehman, M. Ilyas, U. Hameed, H.W. Herrmann, N. Chingandu, M.T. Manzoor, M.S. Haider, J.K. Brown, "Sentinel plot surveillance of cotton leaf curl disease in Pakistan-a case study at the cultivated cotton-wild host plant interface" Virus Research 333 (2023) 199144.
• 26. [26] M. Zubair, S.S.-e.-A. Zaidi, S. Shakir, M. Farooq, I. Amin, J.A. Scheffler, B.E. Scheffler, S. Mansoor, "Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton" Scientific reports 7(1) (2017) 680.
• 27. [27] J.J. Doyle, "Isolation of plant DNA from fresh tissue" Focus 12 (1990) 13-15.
• 28. [28] C. Biswas, P. Dey, S. Satpathy, S. Sarkar, A. Bera, B. Mahapatra, "A simple method of DNA isolation from jute (Corchorus olitorius) seed suitable for PCR‐based detection of the pathogen Macrophomina phaseolina (Tassi) Goid" Letters in applied microbiology 56(2) (2013) 105-110.
• 29. [29] R. Briddon, S. Bull, S. Mansoor, I. Amin, P. Markham, "Universal primers for the PCR-mediated amplification of DNA β" Molecular biotechnology 20(3) (2002) 315-318.
• 30. [30] K. Birnbaum, J.W. Jung, J.Y. Wang, G.M. Lambert, J.A. Hirst, D.W. Galbraith, P.N. Benfey, "Cell type–specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines" Nat. met. 2(8) (2005) 615-619.
• 31. [31] J. Felsenstein, "Confidence limits on phylogenies: an approach using the bootstrap" Evolution (39) (1985) 783-791.
• 32. [32] S. Kumar, G. Stecher, K. Tamura, "MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets" Molecular biology and evolution 33(7) (2016) 1870-1874.
• 33. [33] J.H. Cai, K. Xie, L. Lin, B. Qin, B. Chen, J. Meng, Y. Liu, "Cotton leaf curl Multan virus newly reported to be associated with cotton leaf curl disease in China" Plant pathology 59(4) (2010) 794-795.
• 34. [34] M.-J. Mao, Z.-F. He, H. Yu, H.-P. Li, "Molecular characterization of cotton leaf Curl Multan virus and its satellite DNA that infects Hibiscus rosa-sinensis" Bing du xue bao= Chinese Journal of Virology 24(1) (2008) 64-68.
• 35. [35] X. She, Y. Tang, Z. He, G. Lan, "Molecular Characterization of Cotton leaf curl Multan virus and its associated betasatellite infecting Hibiscus rosa-sinensis in the Philippines" Journal of Plant Pathology (2017) 765-768.
• 36. [36] K. Akhtar, R. Ullah, M. Saeed, N. Sarwar, S. Mansoor, China rose (Hibiscus rosa-sinensis): a new natural host of Cotton leaf curl Burewala virus in Pakistan" Journal of Plant Pathology 96(2) (2014) 385-389.
• 37. [37] A. Srivastava, S. Kumar, M. Jaidi, S. Raj, "Association of Cotton leaf curl Multan virus and its associated betasatellite with leaf curl disease of Hibiscus rosa-sinensis in India" New Disease Reports 33(4) (2016) 2044-0588.2016.
• 38. [38] J.K. Brown, F.M. Zerbini, J. Navas-Castillo, E. Moriones, R. Ramos-Sobrinho, J.C. Silva, E. Fiallo-Olivé, R.W. Briddon, C. Hernández-Zepeda, A. Idris, "Revision of Begomovirus taxonomy based on pairwise sequence comparisons" Archives of Virology 160(6) (2015) 1593-1619.
• 39. [39] M. Arif, W. Lin, L. Lin, W. Islam, Z. Jie, Z. He, Z. Du, Z. Wu, "Cotton leaf curl Multan virus infecting Hibiscus sabdariffa in China" Canadian Journal of Plant Pathology 40(1) (2018) 128-131.
• 40. [40] M. Arif, S. Farooq, A. Alasmari, M.A. Alshehri, M. Hashem, S. Alamri, H.A. Hemeg, N.M. Alabdallah, "Molecular study of geminiviruses with its complex biology, host-vector interactions, and increasing diversity" Journal of King Saud University-Science (2022) 102051.
• 41. [41] M. Zubair, S.S.-e.-A. Zaidi, S. Shakir, I. Amin, S. Mansoor, "An insight into Cotton leaf curl Multan betasatellite, the most important component of cotton leaf curl disease complex" Viruses 9(10) (2017) 280.
• 42. [42] W. Islam, K.S. Akutse, M. Qasim, K.A. Khan, H.A. Ghramh, A. Idrees, S. Latif, "Bemisia tabaci-mediated facilitation in diversity of begomoviruses: Evidence from recent molecular studies" Microbial pathogenesis 123 (2018) 162-168.
• 43. [43] W. Islam, W. Lin, M. Qasim, S.U. Islam, H. Ali, M. Adnan, M. Arif, Z. Du, Z. Wu, "A nation-wide genetic survey revealed a complex population structure of Bemisia tabaci in Pakistan" Acta Tropica 183 (2018) 119-125.
• 44. [44] M. Van Regenmortel, "Virologists, taxonomy and the demands of logic" Springer, 2006.
• 45. [45] F.M. Zerbini, R.W. Briddon, A. Idris, D.P. Martin, E. Moriones, J. Navas-Castillo, R. Rivera-Bustamante, P. Roumagnac, A. Varsani, "ICTV Virus Taxonomy Profile: Geminiviridae" Journal of General Virology 98(2) (2017) 131-133.
• 46. [46] E. Rybicki, "A phylogenetic and evolutionary justification for three genera of Geminiviridae" Archives of virology 139(1-2) (1994) 49-77.
• 47. [47] B. Harrison, H. Barker, K. Bock, E. Guthrie, G. Meredith, M. Atkinson, "Plant viruses with circular single-stranded DNA" Nature 270(5639) (1977) 760.
• 48. [48] H. Jeske, "Replication of geminiviruses and the use of rolling circle amplification for their diagnosis, Tomato yellow leaf curl virus disease" Springer 2007, pp. 141-156.
• 49. [49] K. Saunders, N. Salim, V.R. Mali, V.G. Malathi, R. Briddon, P.G. Markham, J. Stanley, "Characterisation of Sri Lankan cassava mosaic virus and Indian cassava mosaic virus: evidence for acquisition of a DNA B component by a monopartite begomovirus" Virology 293(1) (2002) 63-74.
• 50. [50] A. Varma, V. Malathi, "Emerging geminivirus problems: a serious threat to crop production" Annals of Applied Biology 142(2) (2003) 145-164.