Molecular Characterization of Mungbean yellow mosaic India virus and Tomato leaf curl New Delhi virus in Sukoharjo and Magelang Regencies, Indonesia

https://doi.org/10.22146/jpti.101371

Antama Surwadinata(1), Ananda Restu Putro(2), Adhi Pradhana(3), Filzah Shalihah(4), Muhammad Garda Pancasona(5), Rachmad Saputra(6), Mayadah A. Haj Ali(7), Adyatma Irawan Santosa(8*)

(1) Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jln. Flora No. 1, Sleman, Yogyakarta 55281, Indonesia
(2) Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jln. Flora No. 1, Sleman, Yogyakarta 55281, Indonesia
(3) Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jln. Flora No. 1, Sleman, Yogyakarta 55281, Indonesia; Central Java Animal, Fish, and Plant Quarantine Office, Indonesian Quarantine Agency, Jln. Jenderal Sudirman No.81, Krobokan, Semarang Barat, Semarang, Central Java 50141 Indonesia
(4) Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jln. Flora No. 1, Sleman, Yogyakarta 55281, Indonesia
(5) Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jln. Flora No. 1, Sleman, Yogyakarta 55281, Indonesia
(6) Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jln. Flora No. 1, Sleman, Yogyakarta 55281, Indonesia; Plant Protection Study Program, Faculty of Agriculture, Universitas Riau, Jln. H.R. Soebrantas km. 12,5 Kampus Bina Widya, Pekanbaru, Riau 28293 Indonesia
(7) Department of Plant Pathology, International Centre for Agricultural Research in the Dry Areas (ICARDA), 2 Port Said, Victoria Square, Ismail El-Shaaer Building, Maadi, Cairo 11728, Egypt; Department of Microbiology and Immunology, National Commission for Biotechnology (NCBT), Damascus, Syria
(8) Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jln. Flora No. 1, Sleman, Yogyakarta 55281, Indonesia
(*) Corresponding Author

Abstract


Diseases caused by Begomoviruses in black-eyed pea (Vigna unguiculata subsp. unguiculata) and cucumber (Cucumis sativus) are remains insufficiently explored in Indonesia. One symptomatic black-eyed pea and two cucumber samples were collected from Sukoharjo and Magelang Regencies, respectively, to be molecularly tested using Krusty/Homer and SPG1/SPG2 primer pairs for universal detection of Begomoviruses. NCBI BLAST analysis on the obtained nucleotide sequences confirmed mungbean yellow mosaic India virus (MYMIV, Begomovirus vignaradiataindiaense) infection in black-eyed pea sample and tomato leaf curl New Delhi virus (ToLCNDV, Begomovirus solanumdelhiense) infection in both cucumber samples. Sequences of partial AV1, and partial AC1 and AC2 genes of the three isolates were registered with accession nos. PQ539469-71 and PQ539476-78, respectively, in NCBI GenBank. No recombination signal was detected in the sequences of the new isolates according to scan by Recombination Detection Program (RDP v.5.30). In the phylogenetic trees built by MEGA 11 software with Tamura-Nei parameter model, MYMIV H-2 as well as ToLCNDV N-8 and V-97 isolates shared basal nodes with Indonesian isolates, indicated their close genetic relationship with other isolates also found in the country. While expanding our information regarding genetic diversity of Begomoviruses, this study also reported the first cases of MYMIV in black-eyed pea in Indonesia and ToLCNDV in cucumber in Magelang, to the best of our knowledge.


Keywords


Cucurbitaceae; Fabaceae; molecular variation; plant virus; polymerase chain reaction

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References

Cai, L., Mei, Y., Ye, R., Deng, Y., Zhang, X., Hu, Z., Zhou, X., Zhang, M., & Yang, J. (2023). Tomato leaf curl New Delhi virus: An Emerging Plant Begomovirus Threatening Cucurbit Production. aBIOTECH, 4(3), 257–266. https://doi.org/10.1007/s42994-023-00118-4

Defitra, N.K., Zahra, H.A., Surwadinata, A., Saputra, R., Subiastuti, A.S., Haj Ali, M.A., & Santosa, A.I. (2025). Evaluation of Krusty/Homer and SPG1/SPG2 Primer Pairs in Identification of Six Begomoviruses Commonly Found in Indonesia. Journal of Tropical Biodiversity and Biotechnology 10(2), jtbb15670. http://doi.org/10.22146/jtbb.15670

Duffy, S. & Holmes, E.C. (2007). Multiple Introductions of the Old World Begomovirus Tomato yellow leaf curl virus into the New World. Applied and Environmental Microbiology, 73(21), 7114-7. https://doi.org/10.1128/AEM.01150-07

Fiallo-Olivé, E. & Navas-Castillo, J. (2023). Begomoviruses: What is the Secret(s) of Their Success? Trends in Plant Science, 28(6), 715–727. https://doi.org/10.1016/j.tplants.2023.01.012

Fortes, I.M., Sánchez-Campos, S., Fiallo-Olivé, E., Díaz-Pendón, J.A., Navas-Castillo, J., & Moriones, E. (2016). A Novel Strain of Tomato leaf curl New Delhi virus Has Spread to the Mediterranean Basin. Viruses, 8(11), 307. https://doi.org/10.3390/v8110307

Haerunisa, R., Suastika, G., & Damayanti, T.A. (2016). Identifikasi Begomovirus yang Berasosiasi dengan Penyakit Kuning pada Mentimun di Jawa Barat dan Bali [Identification of Begomovirus Associated with Yellowing Disease on Cucumber Plants in West Java and Bali]. Jurnal Hortikultura Indonesia, 7(1), 9-20. https://doi.org/10.29244/jhi.7.1.9-20

Jyothsna, P., Haq, Q.M.I., Singh, P., Sumiya, K.V., Praveen, S., Rawat, R., & Malathi, V.G. (2013). Infection of Tomato leaf curl New Delhi virus (ToLCNDV), a Bipartite Begomovirus with Betasatellites, Results in Enhanced Level of Helper Virus Components and Antagonistic Interaction between DNA B and Betasatellites. Applied Microbiology and Biotechnology, 97(12), 5457-5471. https://doi.org/10.1007/s00253-012-4685-9

Kumar, J., Kumar, A., Roy, J.K., Tuli, R., & Khan, J.A. (2010). Identification and Molecular Characterization of Begomovirus and Associated Satellite DNA Molecules Infecting Cyamopsis tetragonoloba. Virus Genes, 41(1), 118-125. https://doi.org/10.1007/s11262-010-0482-7

Li, R., Salih S., & Hurtt, S. (2004). Detection of Geminiviruses in Sweetpotato by Polymerase Chain Reaction. Plant Disease 88(12), 1347–1351. https://doi.org/10.1094/PDIS.2004.88.12.1347

Listihani, L., Damayanti, T.A., Hidayat, S.H., & Wiyono, S. (2019). Molecular Characterization of Begomovirus on Cucumber in Java. Jurnal Perlindungan Tanaman Indonesia, 23(2), 197-204. https://doi.org/10.22146/jpti.41402

Martin, D.P., Varsani, A., Roumagnac, P., Botha, G., Maslamoney, S., Schwab, T., Kelz, Z., Kumar, V., & Murrell, B. (2021). RDP5: A Computer Program for Analyzing Recombination in, and Removing Signals of Recombination from, Nucleotide Sequence Datasets. Virus Evolution, 7(1), veaa087. https://doi.org/10.1093/ve/veaa087

Mizutani, T., Daryono, B.S., Ikegami, M., & Natsuaki, K.T. (2011). First Report of Tomato leaf curl New Delhi virus Infecting Cucumber in Central Java, Indonesia. Plant Disease, 95(11), 1485. https://doi.org/10.1094/PDIS-03-11-0196

Moriones, E., Praveen, S., & Chakraborty. S. (2017). Tomato leaf curl New Delhi virus: An Emerging Virus Complex Threatening Vegetable and Fiber Crops. Viruses, 9(10), 264. https://doi.org/10.3390/v9100264

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. https://doi.org/10.1371/journal.pone.0108277

Mulyadi, D., Sulandari, S., Hartono, S., & Somowiyarjo, S. (2021). Distribution, Host Range and Detection of Seed-borne Yellow Mosaic Disease on Yardlong Beans (Vigna unguiculata subsp. sesquipedalis L.) in the Special Region of Yogyakarta, Indonesia. Biodiversitas, 22(9), 3949-3957. https://doi.org/10.13057/biodiv/d220942

Nigam, D. (2021). Genomic Variation and Diversification in Begomovirus Genome in Implication to Host and Vector Adaptation. Plants, 10(8), 1706. https://doi.org/10.3390/plants10081706

Nurulita, S., Hidayat, S.H., Mutaqin, K.H., & Thomas, J. (2015). Molecular Characterization of Begomovirus Infecting Yard Long Bean (Vigna unguiculata subsp. sesquipedalis L.) in Java, Indonesia. Biotropia, 22(1), 53-60. https://doi.org/10.11598/btb.2015.22.1.401

Revill, P.A., Ha, C.V., Porchun, S.C., Vu, M.T., & Dale, J.L. (2003). The Complete Nucleotide Sequence of Two Distinct Geminiviruses Infecting Cucurbits in Vietnam. Archives of Virology, 148(8), 1523–1541. https://doi.org/10.1007/s00705-003-0109-6

Rojas, M.R., Macedo, M.A., Maliano, M.R., Soto-Aguilar, M., Souza, J.O., Briddon, R.W., Kenyon, L., Rivera Bustamante, R.F., Zerbini, F.M., Adkins, S., Legg, J.P., Kvarnheden, A., Wintermantel, W.M., Sudarshana, M.R., Peterschmitt, M., Lapidot, M., Martin, D.P., Moriones, E., Inoue-Nagata, A., & Gilbertson, R.L. (2018). World Management of Gemiviruses. Annual Review of Phytopathology, 56, 637-677. https://doi.org/10.1146/annurev-phyto080615-100327

Santosa, A.I., Irbati, A.H., Pratiwi, G.N.C., Surwadinata, A., Laeshita, P., Dharma, K.S., Jaya, R.S., Andriyani, A.L., A’yun, C.Q., & Fatika, C.N.S. (2024). Updates on Hosts and Distribution of Pepper yellow leaf curl Indonesia virus and Squash leaf curl China virus in Central Java Province, Indonesia. Jurnal Ilmiah Pertanian, 21(1), 11-20. https://doi.org/10.31849/jip.v21i1.18856

Santosa, A.I., & Somowiyarjo, S. (2023). Ageratum Yellow Vein Alphasatellite and Tomato Leaf Curl Java Betasatellite Association with Begomoviruses Infecting Crops and Weeds in Indonesia. Plant Protection Science, 59(4), 317–324. https://doi.org/10.17221/16/2023-PPS

Septariani, N.D., Hidayat, S.H., & Nurhayati, E. (2014). Identifikasi Penyebab Penyakit Daun Keriting Kuning pada Tanaman Mentimun [Identification of the Causal Agent of Yellow Leaf Curl Disease on Cucumbers]. Jurnal Hama dan Penyakit Tumbuhan Tropika, 14(1), 80–86. https://doi.org/10.23960/j.hptt.11480-86

Singh, S., Nirmalkar, V.K., & Awasthi, L.P. (2020). Recent Advances in Begomovirus Research in India. Applied Plant Virology, 493-513. https://doi.org/10.1016/B978-0-12-818654-1.00035-9

Supyani, Septariani, D.N., & Hadiwiyono. (2020). Symptoms Variation of Viral Infections in Yardlong Bean. Jurnal Hama dan Penyakit Tumbuhan Tropika 20(1), 28–36. https://doi.org/10.23960/j.hptt.12028-36

Sutrawati, M., Hidayat, S.H., Suastika, G., Sukarno, B.P.W., & Nurmansyah, A. (2020). Penyakit Mosaik Kuning pada Kedelai [Yellow Mosaic Disease on Soybean]. Jurnal Fitopatologi Indonesia 16(1), 30–36. https://doi.org/10.14692/jfi.16.1.30-36

Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120

Tamura, K. & Nei, M. (1993). Estimation of the Number of Nucleotide Substitutions in the Control Region of Mitochondrial DNA in Humans and Chimpanzees. Molecular Biology and Evolution, 10(3), 512-526. https://doi.org/10.1093/oxfordjournals.molbev.a040023

Tsai, W.S., Shih, S.L., Rauf, A., Safitri, R., Hidayati, N., Huyen, B.T.T., & Kenyon, L. (2013). Genetic Diversity of Legume Yellow Mosaic Begomoviruses in Indonesia and Vietnam. Annals of Applied Biology 163(3), 367-377. https://doi.org/10.1111/aab.12063

Wiratama, I.D.M.P., Wirya, G.N.A.S., Nyana, I.D.N, Adnyani, N.N.P., & Suastika, G. (2015). Laporan Pertama Infeksi Begomovirus pada Tanaman Mentimun di Bali [First Report on Begomovirus Infection on Cucumber in Bali]. Jurnal Fitopatologi Indonesia 11(5), 175–178. https://doi.org/10.14692/jfi.11.5.175



DOI: https://doi.org/10.22146/jpti.101371

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