Main Article Content
Abstract
Pepper yellow leaf curl Aceh virus (PepYLCAV) and pepper yellow leaf curl Indonesia virus (PepYLCIV) are begomoviruses that dominate chili cultivation in Indonesia. Characterization of these two begomoviruses is essential as basic information for the development of virus control technologies. The symptoms on chili plants indicate that PepYLCIV is more severe than PepYLCAV, with severe mosaic, curling, and yellowing, whereas PepYLCAV causes only mild mosaic and yellowing. Sequencing results also show that the nucleotides and amino acids between PepYLCAV and PepYLCIV are significantly different. This suggests that the pathogenicity of the two viruses on chili plants differs. Protein structure predictions using AlphaFold3 also show significant differences. Based on available data, control of PepYLCAV and PepYLCIV can be achieved using different approaches, as these viruses have distinct sequences that may affect their pathogenicity.
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Copyright (c) 2025 Deri Gustian, Mimi Sutrawati, Ariffatchur Fauzi, Ilmi Hamidi, Nakachew Minuye Mengesha, Duy-Hung Do, Nitchayamon RATTANA

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References
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- Chhapekar, S. S., Jaiswal, V., Ahmad, I., Gaur, R., & Ramchiary, N. (2018). Progress and Prospects in Capsicum Breeding for Biotic and Abiotic Stresses. In S. K. Singh & J. L. Karihaloo (Eds.), Spices and Herbs: Genetics and Genomics (pp. 317-347). Springer.
- DaPalma, T., Doonan, B. P., Trager, N. M., & Kasman, L. M. (2010). A systematic approach to virus–virus interactions. Virus Research, 149(1), 1–9.
- Faria, J. C., & Maxwell, D. P. (1999). Variability in geminivirus isolates associated with Phaseolus spp. In Brazil. Virology, 89: 262-268.
- Fiallo-Olivé, E., Lett, J. M., Martin, D. P., Roumagnac, P., Varsani, A., Zerbini, F. M., Navas-Castillo, J. (2021). ICTV Virus Taxonomy Profile: Geminiviridae 2021. Journal of General Virology, 102: 001696.
- Gao, M., & Lozano-Durán, R. (2025). Symptom Development in Plant Viral Diseases: What, How, and Why? Annual Review of Phytopathology, 63(1), 431-450.
- Garcia-Arenal, F., Zerbini, F. M. (2019). Life on the edge: geminiviruses at the interface between crops and wild plants host. Annual Review of Virology, 6: 411-433.
- Hanley‐Bowdoin, L., Settlage, S. B., Orozco, B. M., Nagar, S., Robertson, D. (1999). Geminiviruses: models for plant DNA replication, transcription, and cell cycle regulation. Critical Reviews in Plant Science, 18: 71-106.
- Hidayat, S. H., Sulandari, S., & Sulyo, S. (1999). Penyakit Virus Kuning pada Tanaman Cabai di Indonesia dan Strategi Pengendaliannya. Jurnal Hama dan Penyakit Tumbuhan Tropika, 3(2), 1-10.
- Ji, Y., Scott, J. W., Hanson, P. M. (2009). Ty-3, a Begomovirus resistance locus on chromosome 6 of tomato, is not effective against all strains of Tomato yellow leaf curl virus. Journal of the American Society for Horticultural Science, 134(1), 108–114.
- Jones, C. D., & Brown, E. F. (2020). Specificity of Viral Receptors in Plant Cell Membranes. Frontiers in Virology, 10(4), 50-65.
- Kesumawati, E., Okabe, S., Homma, K., Fujiwara, I., Zakaria, S., Kanzaki, S., Koeda, S. (2019). Pepper yellow leaf curl Aceh virus: a novel bipartite begomovirus isolated from chili pepper, tomato, and tobacco plants in Indonesia. Archives of Virology, 164(9), 2379–2383.
- Ko, D. C., & Smith, C. M. (2020). These Are the Genes You're Looking For: Finding Host Resistance Genes. Molecular Cell, 78(2), 237–249.
- Koeda, S., Kesumawati, E., Okabe, S., Homma, K., Fujiwara, I., Zakaria, S., & Kanzaki, S. (2019). Pepper yellow leaf curl Aceh virus: a novel bipartite begomovirus isolated from chili pepper, tomato, and tobacco plants in Indonesia. Archives of Virology, 164(8), 2207–2212.
- Koeda, S., Onouchi, M., Mori, N., Pohan, N. S., Nagano, A. J., Kesumawati, E. (2021). A recessive gene pepy-1 encoding Pelota confers resistance to begomovirus isolates of PepYLCIV and PepYLCAV in Capsicum annuum. Theoretical and Applied Genetics, 134(9), 2947–2964.
- Kundu, J. K., Zhang, H. M., Chakraborty, S. (2024). Editorial: Plant-virus interactions: crop resistance in focus. Frontiers in Plant Science, 14.
- Lee, C-H., Zheng, Y-X., Chan, C-H., Ku, H-M., Chang, C-J., Jan, F-J. (2020). Single amino acid substitution in movement protein enables the mechanical transmission of a geminivirus. Molecular Plant Pathology, 21: 571-588.
- Moffat, A. S. (1999). Geminiviruses emerge as a serious crop threat. Science, 286: 1835.
- Nauly, D. (2016). Fluktuasi dan Disparitas Harga Cabai di Indonesia. Jurnal Sains, Teknologi, Urban, dan Arsitektur (SINTESIS), 10(1), 1-10.
- Nigam, D. (2021). Genomic variation and diversification genome in implication to host and vector adaptation. Plants, 10: 1706.
- Orellana-Escobedo, R., & Lopez-Maltez, A. (2022). Capsaicinoids: Analgesic, Anti-inflammatory, and Metabolic Properties. Food Chemistry and Toxicology, 160, 112789.
- Pakkianathan, BC., Kontsedalov, S., Lebedev, G., Mahadav, A., Zeidan, M., Czosnek, H., Ghanim, M. (2015). Replication of tomato yellow leaf curl virus in its vector Bemisia tabacci. Journal of Virology, 89: 791-803.
- Ramírez-Bello, J., and Jiménez-Morales, M. (2017). Implicaciones funcionales de los polimorfismos de un solo nucleótido (SNP) en genes codificantes de proteínas y no codificantes en enfermedades multifactoriales [Functional implications of single nucleotide polymorphisms (SNPs) in protein-coding and non-coding RNA genes in multifactorial diseases]. Gaceta medica de Mexico, 153(2), 238–250.
- Robert, F., and Pelletier, J. (2018). Exploring the Impact of Single-Nucleotide Polymorphisms on Translation. Frontiers in genetics, 9, 507.
- Sanchez-Campos, S., Rodriguez-Negrete, E., Cruzado, L., Grande-Perez, A., Bejarano, E. R., Navas-Castillo, J., Moriones, E. (2016). Tomato yellow leaf curl virus: no evidence for replication in the insect vector Bemisia tabacci. Scientific Reports, 6: 30942.
- Selangga, D. G. W., Wiyono, S., Susila, A. D., & Hidayat, S. H. (2021). Distribution and Identification of Pepper yellow leaf curl Indonesia virus Infecting Chili Pepper in Bali Island. Jurnal Fitopatologi Indonesia, 17(6), 217–224.
- Shastry B. S. (2009). SNPs: impact on gene function and phenotype. Methods in molecular biology (Clifton, N.J.), 578, 3–22.
- Smith, A. B. (2018). Viral Protein Structures and Host-Pathogen Interaction. Journal of Plant Pathology, 50(2), 115-130.
- Syamsidi, Nainggolan, P., & Harti, R. (1997). Pengaruh Infeksi Virus terhadap Pertumbuhan dan Produksi Tanaman Cabai. Jurnal Ilmu Pertanian, 13(2), 97-105.
- Taufik, M., Hidayat, S. H., Mallarangeng, R., Khaeruni, A., Botek, M., Hartono, S., Aidawati, N., Hidayat, P. (2023). Sebaran Penyakit Daun Keriting Kuning pada Pertanaman Cabai di Sulawesi Tenggara dan Identifikasi Penyebabnya. Jurnal Fitopatologi Indonesia, 19(3), 89–98.
- Trisno, J., Hidayat, S. H., Jamsari, Habazar, T., & Manti, I. (2010). Identifikasi Molekuler Begomovirus Penyebab Penyakit Kuning Keriting pada Tanaman Cabai (Capsicum annum L.) di Sumatera Barat. Jurnal Natur Indonesia, 13(1), 41–46.
- Varma, A., Malathi, V. G. (2003). Emerging geminivirus problem: a serious threat to crop production. Annals of Applied Biology, 142: 145-164.
- Wang, L-L., Wang, X-R., Wei, X-M., Huang, H., Wu, J-X., Chen, X-X., Liu, S-S., Wang, X-W. (2016). The autophagy pathway participates in resistance to tomato yellow leaf curl virus infection in whiteflies. Autophagy, 12: 1560-1574.
- White, G., Harris, H., & Lee, I. (2019). Movement Proteins and Systemic Spread of Plant Viruses. Molecular Plant-Microbe Interactions, 32(1), 10-25.
References
Aulia, E., Sutrawati, M., Pamekas, T. (2022). Deteksi Molekuler dan Analisis Genetik Begomovirus Pada Tanaman Cabai di Desa Pematang Donok. Jurnal Ilmu-Ilmu Pertanian Indonesia, 24(2), 69–74.
Becker, N., Rimbaud, L., Chiroleu, F., Reynaud, B., Thebaud, G., Lett, J. M. (2015). Rapid accumulation and low degradation: key parameters for tomato yellow leaf curl virus persistence in its insect vector Bemisia tabacci. Scientific Reports, 2: 17696.
Chhapekar, S. S., Jaiswal, V., Ahmad, I., Gaur, R., & Ramchiary, N. (2018). Progress and Prospects in Capsicum Breeding for Biotic and Abiotic Stresses. In S. K. Singh & J. L. Karihaloo (Eds.), Spices and Herbs: Genetics and Genomics (pp. 317-347). Springer.
DaPalma, T., Doonan, B. P., Trager, N. M., & Kasman, L. M. (2010). A systematic approach to virus–virus interactions. Virus Research, 149(1), 1–9.
Faria, J. C., & Maxwell, D. P. (1999). Variability in geminivirus isolates associated with Phaseolus spp. In Brazil. Virology, 89: 262-268.
Fiallo-Olivé, E., Lett, J. M., Martin, D. P., Roumagnac, P., Varsani, A., Zerbini, F. M., Navas-Castillo, J. (2021). ICTV Virus Taxonomy Profile: Geminiviridae 2021. Journal of General Virology, 102: 001696.
Gao, M., & Lozano-Durán, R. (2025). Symptom Development in Plant Viral Diseases: What, How, and Why? Annual Review of Phytopathology, 63(1), 431-450.
Garcia-Arenal, F., Zerbini, F. M. (2019). Life on the edge: geminiviruses at the interface between crops and wild plants host. Annual Review of Virology, 6: 411-433.
Hanley‐Bowdoin, L., Settlage, S. B., Orozco, B. M., Nagar, S., Robertson, D. (1999). Geminiviruses: models for plant DNA replication, transcription, and cell cycle regulation. Critical Reviews in Plant Science, 18: 71-106.
Hidayat, S. H., Sulandari, S., & Sulyo, S. (1999). Penyakit Virus Kuning pada Tanaman Cabai di Indonesia dan Strategi Pengendaliannya. Jurnal Hama dan Penyakit Tumbuhan Tropika, 3(2), 1-10.
Ji, Y., Scott, J. W., Hanson, P. M. (2009). Ty-3, a Begomovirus resistance locus on chromosome 6 of tomato, is not effective against all strains of Tomato yellow leaf curl virus. Journal of the American Society for Horticultural Science, 134(1), 108–114.
Jones, C. D., & Brown, E. F. (2020). Specificity of Viral Receptors in Plant Cell Membranes. Frontiers in Virology, 10(4), 50-65.
Kesumawati, E., Okabe, S., Homma, K., Fujiwara, I., Zakaria, S., Kanzaki, S., Koeda, S. (2019). Pepper yellow leaf curl Aceh virus: a novel bipartite begomovirus isolated from chili pepper, tomato, and tobacco plants in Indonesia. Archives of Virology, 164(9), 2379–2383.
Ko, D. C., & Smith, C. M. (2020). These Are the Genes You're Looking For: Finding Host Resistance Genes. Molecular Cell, 78(2), 237–249.
Koeda, S., Kesumawati, E., Okabe, S., Homma, K., Fujiwara, I., Zakaria, S., & Kanzaki, S. (2019). Pepper yellow leaf curl Aceh virus: a novel bipartite begomovirus isolated from chili pepper, tomato, and tobacco plants in Indonesia. Archives of Virology, 164(8), 2207–2212.
Koeda, S., Onouchi, M., Mori, N., Pohan, N. S., Nagano, A. J., Kesumawati, E. (2021). A recessive gene pepy-1 encoding Pelota confers resistance to begomovirus isolates of PepYLCIV and PepYLCAV in Capsicum annuum. Theoretical and Applied Genetics, 134(9), 2947–2964.
Kundu, J. K., Zhang, H. M., Chakraborty, S. (2024). Editorial: Plant-virus interactions: crop resistance in focus. Frontiers in Plant Science, 14.
Lee, C-H., Zheng, Y-X., Chan, C-H., Ku, H-M., Chang, C-J., Jan, F-J. (2020). Single amino acid substitution in movement protein enables the mechanical transmission of a geminivirus. Molecular Plant Pathology, 21: 571-588.
Moffat, A. S. (1999). Geminiviruses emerge as a serious crop threat. Science, 286: 1835.
Nauly, D. (2016). Fluktuasi dan Disparitas Harga Cabai di Indonesia. Jurnal Sains, Teknologi, Urban, dan Arsitektur (SINTESIS), 10(1), 1-10.
Nigam, D. (2021). Genomic variation and diversification genome in implication to host and vector adaptation. Plants, 10: 1706.
Orellana-Escobedo, R., & Lopez-Maltez, A. (2022). Capsaicinoids: Analgesic, Anti-inflammatory, and Metabolic Properties. Food Chemistry and Toxicology, 160, 112789.
Pakkianathan, BC., Kontsedalov, S., Lebedev, G., Mahadav, A., Zeidan, M., Czosnek, H., Ghanim, M. (2015). Replication of tomato yellow leaf curl virus in its vector Bemisia tabacci. Journal of Virology, 89: 791-803.
Ramírez-Bello, J., and Jiménez-Morales, M. (2017). Implicaciones funcionales de los polimorfismos de un solo nucleótido (SNP) en genes codificantes de proteínas y no codificantes en enfermedades multifactoriales [Functional implications of single nucleotide polymorphisms (SNPs) in protein-coding and non-coding RNA genes in multifactorial diseases]. Gaceta medica de Mexico, 153(2), 238–250.
Robert, F., and Pelletier, J. (2018). Exploring the Impact of Single-Nucleotide Polymorphisms on Translation. Frontiers in genetics, 9, 507.
Sanchez-Campos, S., Rodriguez-Negrete, E., Cruzado, L., Grande-Perez, A., Bejarano, E. R., Navas-Castillo, J., Moriones, E. (2016). Tomato yellow leaf curl virus: no evidence for replication in the insect vector Bemisia tabacci. Scientific Reports, 6: 30942.
Selangga, D. G. W., Wiyono, S., Susila, A. D., & Hidayat, S. H. (2021). Distribution and Identification of Pepper yellow leaf curl Indonesia virus Infecting Chili Pepper in Bali Island. Jurnal Fitopatologi Indonesia, 17(6), 217–224.
Shastry B. S. (2009). SNPs: impact on gene function and phenotype. Methods in molecular biology (Clifton, N.J.), 578, 3–22.
Smith, A. B. (2018). Viral Protein Structures and Host-Pathogen Interaction. Journal of Plant Pathology, 50(2), 115-130.
Syamsidi, Nainggolan, P., & Harti, R. (1997). Pengaruh Infeksi Virus terhadap Pertumbuhan dan Produksi Tanaman Cabai. Jurnal Ilmu Pertanian, 13(2), 97-105.
Taufik, M., Hidayat, S. H., Mallarangeng, R., Khaeruni, A., Botek, M., Hartono, S., Aidawati, N., Hidayat, P. (2023). Sebaran Penyakit Daun Keriting Kuning pada Pertanaman Cabai di Sulawesi Tenggara dan Identifikasi Penyebabnya. Jurnal Fitopatologi Indonesia, 19(3), 89–98.
Trisno, J., Hidayat, S. H., Jamsari, Habazar, T., & Manti, I. (2010). Identifikasi Molekuler Begomovirus Penyebab Penyakit Kuning Keriting pada Tanaman Cabai (Capsicum annum L.) di Sumatera Barat. Jurnal Natur Indonesia, 13(1), 41–46.
Varma, A., Malathi, V. G. (2003). Emerging geminivirus problem: a serious threat to crop production. Annals of Applied Biology, 142: 145-164.
Wang, L-L., Wang, X-R., Wei, X-M., Huang, H., Wu, J-X., Chen, X-X., Liu, S-S., Wang, X-W. (2016). The autophagy pathway participates in resistance to tomato yellow leaf curl virus infection in whiteflies. Autophagy, 12: 1560-1574.
White, G., Harris, H., & Lee, I. (2019). Movement Proteins and Systemic Spread of Plant Viruses. Molecular Plant-Microbe Interactions, 32(1), 10-25.