Detection and Molecular Characterization of Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) Infecting Chili Pepper (Capsicum annuum) in Bengkulu, Indonesia: Deteksi dan Karakterisasi Molekuler Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) yang Menginfeksi Cabai Merah (Capsicum annuum) di Bengkulu, Indonesia

Hengki Windra; Deri Gustian; Mimi Sutrawati; Yenny Sariasih; Sempurna Ginting; Duy-Hung Do; Nakachew  Minuye

doi:10.14692/jfi.22.1.12-22

Authors

Hengki Windra Department of Plant Protection, Faculty of Agriculture, University of Bengkulu
Deri Gustian Department of Plant Pathology, College of Agriculture and Natural Science, National Chung Hsing University
Mimi Sutrawati Department of Plant Protection, Faculty of Agriculture, University of Bengkulu
Yenny Sariasih Department of Plant Protection, Faculty of Agriculture, University of Bengkulu
Sempurna Ginting Department of Plant Protection, Faculty of Agriculture, University of Bengkulu
Duy-Hung Do Plant Protection Research Institute, Vinh Quynh, Thanh Tri District, Hanoi 100000, Vietnam
Nakachew Minuye Department of Biotechnology, College of Natural and Computational Science, Debre Markos University, P.O. Box 269, Debre Markos, Ethiopia

DOI:

https://doi.org/10.14692/jfi.22.1.12-22

Keywords:

Begomovirus, Capsicum annuum , TYLCKaV, host interaction, viral accumulation

Abstract

Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV), an emerging Begomovirus in Southeast Asia, has not previously been confirmed in chili pepper (Capsicum annuum) in Bengkulu, Indonesia. This study provides the first molecular evidence of TYLCKaV infecting chili in this region and characterizes its genomic variation, viral accumulation dynamics, and predicted host-interaction profiles. PCR amplification of the AC1-IR-AV1 region confirmed TYLCKaV in all symptomatic samples. Sequence analysis revealed the highest nucleotide identity (99%) with Indonesian-Bengkulu and Philippines isolates (PP990580), whereas the lowest identity (92%) was observed with the Cambodia isolate (KR073086), indicating regional sequence divergence within Southeast Asian populations. Quantitative PCR demonstrated significant variation in viral accumulation among isolates (p = 0.042), with no consistent correlation between symptom severity and viral DNA levels. Comparative analysis of AC1-AC4 proteins identified amino acid substitutions across functional domains, particularly within central and C-terminal regions. Structural prediction and protein-protein interaction modelling suggested isolate-specific differences in predicted binding affinities to Histone-3, IMPA1, and BTF3. These findings confirm the presence of TYLCKaV in chili from Bengkulu and demonstrate genomic micro-variation and predicted differences in host interaction characteristics, supporting the importance of molecular surveillance for effective disease management.

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