Updates on hosts and distribution of pepper yellow leaf curl Indonesia virus and squash leaf curl China virus in Central Java Province, Indonesia

Adyatma Irawan Santosa; Adenisa Hanifah Irbati; Geby Nandita Cahyaning Pratiwi; Antama Surwadinata; Putri Laeshita; Krisnanda Surya Dharma; Reko Saputra Jaya; Annisa Lisa Andriyani; Chilya Qurrota A'yun; Chusnu Naura Syifa Fatika

doi:10.31849/jip.v21i1.18856

Adyatma Irawan Santosa Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia https://orcid.org/0000-0002-2826-5444
Adenisa Hanifah Irbati Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia http://orcid.org/0009-0008-9629-9655
Geby Nandita Cahyaning Pratiwi Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia https://orcid.org/0009-0001-9716-3169
Antama Surwadinata Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia https://orcid.org/0009-0008-3117-3314
Putri Laeshita Department of Agrotechnology, Faculty of Agriculture, Universitas Tidar, Magelang 56114, Indonesia https://orcid.org/0009-0008-5945-6228
Krisnanda Surya Dharma Directorate of Horticulture Protection, Directorate General of Horticulture, Ministry of Agriculture, DKI Jakarta, Indonesia http://orcid.org/0009-0006-8635-8979
Reko Saputra Jaya Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia http://orcid.org/0009-0003-2496-9406
Annisa Lisa Andriyani Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia http://orcid.org/0009-0009-0067-6944
Chilya Qurrota A'yun Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia http://orcid.org/0009-0009-6102-8318
Chusnu Naura Syifa Fatika Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia https://orcid.org/0009-0005-6825-276X

DOI: https://doi.org/10.31849/jip.v21i1.18856

Keywords: coat protein, mechanical inoculation, molecular characterization, percentage identity, phylogenetic analysis

Abstract

Chili pepper, tomato, and squash cultivated in Magelang Regency, Central Java Province, Indonesia showed severe viral symptoms. Three samples were taken then molecularly tested against begomovirus, potyvirus, tobamovirus, and polerovirus. However, PCR test confirmed only begomovirus infections. BLAST analysis concluded that the chili pepper and tomato isolates were pepper yellow leaf curl Indonesia virus (PepYLCIV) while the squash isolate was squash leaf curl China virus (SLCCNV). The 552 bp partial AV1 gene sequences of the three isolates were given NCBI GenBank acc nos. OR924278-80. PepYLCIV OR924279 and OR924280 formed a subgroup with LC542629 from Bali in the phylogenetic tree constructed using MEGA11, and shared 95.8 – 96.7% identities at nucleotide (nt) and 98.4 – 99.5% at amino acid (aa) levels according to Sequence Demarcation Tool v1.2 software. Meanwhile, SLCCNV OR924278 was clustered, and shared 95.8 – 96.7% nt and 98.4 – 99.5% aa identities with three Malaysian isolates (MW248685, MW248687, and MW248689). Different plant species inoculated with SLCCNV OR924278 remained symptomless up to four weeks observation, suggesting that the isolate is not mechanically transmissible. This study contributed additional knowledge on molecular variation while expanding hosts and distribution of PepYLCIV and SLCCNV in Central Java Province.

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References

Brown, J. K., Zerbini, F. M., Navas-Castillo, J., Moriones, E., Ramos-Sobrinho, R., Silva, J. C. F., Fiallo-Olivé, E., Briddon, R. W., Hernández-Zepeda, C., Idris, A., Malathi, V. G., Martin, D. P., Rivera-Bustamante, R., Ueda, S., & Varsani, A. (2015). Revision of begomovirus taxonomy based on pairwise sequence comparisons. Achieves of Virology, 160(6), 1593–1619. https://doi.org/10.1007/s00705-015-2398-y

Cheewachaiwit, S., Warin, N., Phuangrat, B., Rukpratanporn, S., Gajanandana, O., Balatero, C. H., & Chatchawankanphanich, O. (2017). Incidence and molecular diversity of poleroviruses infecting cucurbit crops and weed plants in Thailand. Achieves of Virology, 162(7), 2083–2090. https://doi.org/10.1007/s00705-017-3332-2

Chen, Y. J., Lai, H. C., Lin, C. C., Neoh, Z. Y., & Tsai, W. S. (2021). Genetic diversity, pathogenicity and pseudo recombination of cucurbit-infecting begomoviruses in Malaysia. Plants, 10(11), 2396. https://doi.org/10.3390/plants10112396

Dovas, C. I., Efthimiou, K., & Katis, N. I. (2004). Generic detection and differentiation of tobamoviruses by a spot nested RT-PCR-RFLP using dI-containing primers along with homologous dG-containing primers. Journal of Virological Methods, 117(2), 137–144. https://doi.org/10.1016/j.jviromet.2004.01.004

Fadhila, C., Lal, A., Vo, T. T. B., Hidayat, S. H., Lee, J., Kil, E. J., & Lee, S. (2020). The threat of seed-transmissible pepper yellow leaf curl Indonesia virus in chili pepper. Microbial Pathogenesis, 143, 104132. https://doi.org/10.1016/j.micpath.2020.104132

FAO. (2024, February 24). Food and agriculture data. Food and Agriculture Organization of the United Nations. http://www.fao.org/faostat/en/

Kesumawati, E., Okabe, S., Khalil, M., Alfan, G., Bahagia, P., Pohan, N., Zakaria, S., & Koeda, S. (2020). Molecular characterization of begomoviruses associated with yellow leaf curl disease in solanaceae and cucurbitaceae crops from Northern Sumatra, Indonesia. The Horticulture Journal, 89(4), 410–416. https://doi.org/10.2503/hortj.UTD-175

Khairi, A., Jayaputra, Padusung, Tejowulan, S., & Nurrachman. (2023). Combination of bio-organo-mineral fertilizers on optimizing the growthand production of tomatoes (Solanum lycopersicum L.). Jurnal Ilmiah Pertanian, 20(2), 127-138. https://doi.org/10.31849/jip.v20i2.10901

Koeda, S., Homma, K., Tanaka, Y., Onizaki, D., Kesumawati, E., Zakaria, S., & Kanzaki, S. (2018). Inoculation of capsicums with pepper yellow leaf curl Indonesia virus by combining agroinoculation and grafting. The Horticulture Journal, 87(3), 364–371. https://doi.org/10.2503/hortj.OKD-137

Langeveld, S. A., Dore, J. M., Memelink, J., Derks, A. F. L. M., Van, C. I. M., Asjes, C. J., & Bol, J. F. (1991). Identification of potyviruses using the polymerase chain reaction with degenerate primers. Journal of General Virology, 72(7), 1531–1541. https://doi.org/10.1099/0022-1317-72-7-1531

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

Neoh, Z. Y., Lai, H. C., Lin, C. C., Suwor, P., & Tsai, W. S. (2023). Genetic diversity and geographic distribution of cucurbit-infecting begomoviruses in the Philippines. Plants, 12(2), 272. https://doi.org/10.3390/plants12020272

Neriya, Y., Izumi, R., Wilisiani, F., & Hartono, S., Wirya, G. N. A. S., Nishigawa, H., & Natsuaki, T. (2020). Complete genome sequence of a pepper yellow leaf curl Indonesia virus isolated from tomato in Bali, Indonesia. Microbiology Resource Announcements, 9(25), 10-20. https://doi.org/10.1128/mra.00486-20

Piyatassee, W., & Hongprayoon, R. (2021). Genetic diversity and recombination event of begomoviruses infecting pumpkin in Thailand. Journal of the International Society for Southeast Asian Agricultural Sciences (ISSAAS Journal), 27(1), 56–68. https://kukr.lib.ku.ac.th/kukr_es/KPS_CAB/search_detail/result/414849

Qiu, Y., Zhang, H., Tian, W., Fan, L., Du, M., Yuan, G., Wang, D., Wen, C., & Xu, X. (2022). First report of squash leaf curl China virus infecting tomato in China. Plant Disease, 106(9), 2539. https://doi.org/10.1094/PDIS-10-21-2192-PDN

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, 1523–1541. https://doi.org/10.1007/s00705-003-0109-6

Rojas, M. R., Hagen, C., Lucas, W. J., & Gilbertson, R. L. (2005). Exploiting chinks in the plant's armor: evolution and emergence of geminiviruses. Annual Review of Phytopathology, 43, 361–394. https://doi.org/10.1146/annurev.phyto.43.040204.135939

Sakata, Jj., Shibuya, Y., Sharma, P., & Ikegami, M. (2008). Strains of a new bipartite begomovirus, pepper yellow leaf curl Indonesia virus, in leaf-curl-diseased tomato and yellow-vein-diseased ageratum in Indonesia. Archives of Virology, 153, 2307–2313. https://doi.org/10.1007/s00705-008-0254-z

Santosa, A. I., Al-Shahwan, I. M., Abdalla, O. A., Al-Saleh, M. A., & Amer, M. A. (2018). Characterization of a watermelon mosaic virus isolate inducing a severe disease in watermelon in Saudi Arabia. Journal of Agricultural Science and Technology A, 8(4), 220–229. http://doi.org/10.17265/2161-6256/2018.04.005

Santosa, A. I., Irbati, A. H., Dharma, K. S., Winona, B., Jaya, R. S., Andriyani, A. L., & A'yun, C. Q. (2024). Potato virus y and shallot latent virus of Kajoran horticultural production center, Magelang regency, Indonesia: molecular characterization case study. Caraka Tani: Journal of Sustainable Agriculture, 39(1), 1–9. http://doi.org/10.20961/carakatani.v39i1.76737

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

Selangga, D. G. W., & Listhihani. (2021). Molecular identification of pepper yellow leaf curl Indonesia virus on chili pepper in Nusa Penida Island. Jurnal Hama dan Penyakit Tropika, 21(2), 97–102. https://doi.org/10.23960/j.hptt.22197-102

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. Jurnal Fitopatologi Indonesia, 17(6), 217–224. https://doi.org/10.14692/jfi.17.6. 217–224

Sipriyadi, S., Rahman, A. N. A., Darwis, W., Wibowo, R. H., Sutrawati, M., Hutasoit, C. M., Kristiani, Y., & Setiawan, R. (2022). Pencirian genetik pepper yellow leaf curl virus pada tanaman cabai merah (Capsicum annuum) di Bengkulu (in Bahasa Indonesia). Jurnal Ilmu Pertanian Indonesia, 27(4), 574–581. https://doi.org/10.18343/jipi.27.4.574

Subiastuti, A. S., Hartono, S., & Daryono, B. S. (2019). Detection and identification of Begomovirus infecting Cucurbitaceae and Solanaceae in Yogyakarta, Indonesia. Biodiversitas, Journal of Biological Diversity, 20(3), 738–744. https://doi.org/10.13057/biodiv/d200318

Sutrawati, M., Nadrawati, Ganefianti, D. W., & Listihani. (2022, August). Squash leaf curl China virus associated with yellow mosaic disease of pumpkin in Bengkulu, Indonesia. 9th International Conference on Sustainable Agriculture and Environment (ICSAE-IX), Surakarta, Indonesia. https://2022.icsae.id/id114-squash-leaf-curl-china-virus-associated/

Tamura, K. (1992). Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Molecular Biology and Evolution, 9(4), 678–687. https://doi.org/10.1093/oxfordjournals.molbev.a040752

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

Tsai, W. S., Shih, S. L., Green, S. K., Rauf, A., Hidayat, S. H., & Jan F.-J. (2006). Molecular characterization of Pepper yellow leaf curl Indonesia virus in leaf curl and yellowing diseased tomato and pepper in Indonesia. Plant Disease, 90(2), 247. https://doi.org/10.1094/PD-90-0247B

Venkataravanappa, V., Kumar, H. V., Nandan, M., Hiremath, S., Shankarappa, K. S., Reddy, M. K., & Reddy, C.L. (2021a). Characterization of squash leaf curl China virus associated with mosaic and vein clearing disease of pointed gourd (Trichosanthes dioica Roxb.) and its vector whitefly cryptic species. Indian Phytopathology, 75, 573–581. https://doi.org/10.1007/s42360-021-00450-z

Venkataravanappa, V., Reddy, C. L., Nandan, M., Hiremath, S., Ashwathappa, K. V., Shankarappa, K. S., Kumar, H. D. V., & Reddy, M. K. (2021b). Transmission, characterization and occurrence of recombination in Indian strain of squash leaf curl China virus associated with yellow mosaic and leaf curl disease of summer squash. 3 Biotech, 11(6), 265. https://doi.org/10.1007/s13205-021-02821-9

Wahyono, A., Murti, R. H., Hartono, S., Nuringtyas, T. R., Wijonarko, A., Mulyantoro, M., Firmansyah, D., Afifuddin, A., & Purnama, I. C. G. (2023). Current status and complexity of three begomovirus species in pepper plants in lowlands and highlands in Java Island, Indonesia. Viruses, 15(6), 1278. https://doi.org/10.3390/v15061278

Widodo, C. J., Taufik, M., Khaeruni, A., & Mallarangeng, R. (2023). Determination of begomovirus on chili plants (Capsicum sp.) in Buton and Muna Islands, Southeast Sulawesi, Indonesia. Biodiversitas, Journal of Biological Diversity, 24(2), 741–751. https://doi.org/10.13057/biodiv/d240209

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 (in Bahasa Indonesia). Jurnal Fitopatologi Indonesia, 11(5), 176–179. https://doi.org/10.14692/jfi.11.5.175

Wu, H. J., Meng, L. I., Ni, H. O. N. G., Bin, P. E. N. G., & Gu, Q. S. (2020). Molecular and biological characterization of melon-infecting squash leaf curl China virus in China. Journal of Integrative Agriculture, 19(2), 570–577. https://doi.org/10.1016/S2095-3119(19)62642-0