Current Status and Complexity of Three Begomovirus Species in Pepper Plants in Lowlands and Highlands in Java Island, Indonesia
Abstract
:1. Introduction
2. Materials and Methods
2.1. Field Survey and Samples Collection
2.2. DNA Extraction and Identification of Begomovirus Species and Bemisia tabaci Biotypes
2.3. Statistical Analysis
3. Results
3.1. Disease Symptoms, Incidence, and Severity
3.2. Biotypes of B. tabaci
3.3. Identification of Three Begomovirus Species
3.4. Phenotypic Symptoms of Single and Mixed begomovirus Infection
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Primers | Sequence (5′-3′) | Target | DNA Target (bp) | Target Region | References |
---|---|---|---|---|---|
Begomovirus | |||||
PepYLCIV_4-F | ACCTTGGGGCTCAAGTCAAG | PepYLCIV | ±997 | DNA A Protein AC1 | [20] |
PepYLCIV_4-R | GGTCCCTATCTTTATAGTGGGCG | ||||
TLCV-CPI | ATGGCGAAGCGACCAG | ToLCNDV | ±771 | DNA A Protein AV1 | [21] |
TLCV-CPT | TTAATTTGTGACCGAATCAT | ||||
TYLCKaV-F | GTAACAGCCGAAGTGCACG | TYLCKaV | ±1668 | DNA B Protein BC1 and BV1 | [22] |
TYLCKaV-R | AATGGAGAGACACCAGTCTGCC | ||||
Biotypes of B. tabaci | |||||
BaAF | GTGAAATCACTGTCCTCAGTTAGGT | biotype A | ±812 | DNA | [23] |
BaAR | AAAGCCATAGACAAAGAAGTAGACG | ||||
BaBF | CCACTATAATTATTGCTGTTCCCACA | biotype B | ±661 | Mitochondrial DNA mtCO1 | |
L2-N-3014R | TCCAATGCACTAATCTGCCATATTA | ||||
BaANF | GGTTATTGCTGTTCCAACTGGG | biotype AN | ±665 | Mitochondrial DNA mtCO1 | |
L2-N-3014R | TCCAATGCACTAATCTGCCATATTA | ||||
BaQF | GAAGCAACGCACTACTTACAA | biotype Q | ±892, 700,400 | DNA | |
BaQR | TTCTCGGCGTTTTTACCAA | ||||
BaNaF | GGCTTTGGTTTACTGGATTCTTTT | biotype Nauru | ±578 | Mitochondrial DNA mtCO1 | |
L2-N-3014R | TCCAATGCACTAATCTGCCATATTA | ||||
BaSF | CTCGCAACATTGGGTGGTATAAAGT | biotype S | ±613 | Mitochondrial DNA mtCO1 | |
L2-N-3014R | TCCAATGCACTAATCTGCCATATTA |
Location (District) | Altitude (m asl) | Observed Symptoms 1 | Disease Incidence (%) * | Disease Severity (%) * |
---|---|---|---|---|
Lowlands | ||||
Cirebon (West Java) | 24 | y, ym, lf, cp | 86.00 | 29.50 |
Pangandaran 1 (West Java) | 254 | y, ym, gm, lf, cp, vb, st | 93.00 | 57.50 |
Pangandaran 2 (West Java) | 122 | y, ym, gm, lf, cp, sl | 93.00 | 45.75 |
Bantul (Yogyakarta) | 9 | y, ym, gm, lf, cp, vb | 98.00 | 72.75 |
Kulon Progo (Yogyakarta) | 11 | y, ym, gm, lf, cp, vb, st | 82.00 | 35.25 |
Sragen (Central Java) | 163 | y, ym, gm, lf, cp | 97.00 | 60.00 |
Banyuwangi 1 (East Java) | 141 | y, ym, gm, lf, cp | 90.00 | 44.75 |
Banyuwangi 2 (East Java) | 108 | y, ym, gm, lf, cp | 98.00 | 63.75 |
Kediri (East Java) | 176 | y, ym, gm, lf, cp, vb, vc, st | 100.00 | 81.25 |
Mean | 93.00 a | 54.50 a | ||
Highlands | ||||
Sukabumi (West Java) | 872 | y, ym, lf, cp | 90.00 | 46.25 |
Bandung Barat (West Java) | 1200 | y, ym, gm, lf, cp | 94.00 | 43.25 |
Garut (West Java) | 1418 | y, ym, gm, lf, cp | 85.00 | 36.25 |
Banjarnegara (Central Java) | 1167 | y, ym, lf, cp, st | 95.00 | 44.75 |
Wonosobo (Central Java) | 1326 | y, lf | 69.00 | 22.50 |
Karanganyar (Central Java) | 848 | y, ym, lf, cp | 88.00 | 31.75 |
Malang (East Java) | 1185 | y, ym, gm, lf, cp | 94.00 | 49.50 |
Batu (East Java) | 881 | y, ym, gm, lf, cp | 92.00 | 34.75 |
Magetan (East Java) | 1024 | y, ym, gm, lf, cp | 92.00 | 34.00 |
Mean | 88.78 a | 38.11 b |
Location (District) | Biotype of B. tabaci | |||||
---|---|---|---|---|---|---|
A | B | AN | Q | Nauru | S | |
Lowlands | ||||||
Cirebon (West Java) | + | - | - | + | - | - |
Pangandaran 1 (West Java) | - | - | - | + | - | - |
Pangandaran 2 (West Java) | - | + | - | - | - | - |
Bantul (Yogyakarta) | - | + | - | - | - | - |
Kulon Progo (Yogyakarta) | - | + | - | - | - | - |
Sragen (Central Java) | - | + | - | - | - | - |
Banyuwangi 1 (East Java) | - | + | - | - | - | - |
Banyuwangi 2 (East Java) | + | - | - | - | - | - |
Kediri (East Java) | + | - | + | - | - | - |
Highlands | ||||||
Sukabumi (West Java) | - | - | - | + | - | - |
Bandung Barat (West Java) | - | + | - | - | - | - |
Garut (West Java) | - | - | - | - | - | - |
Banjarnegara (Central Java) | - | + | - | - | - | - |
Wonosobo (Central Java) | - | - | - | - | - | - |
Karanganyar (Central Java) | - | - | - | - | - | - |
Malang (East Java) | + | - | - | - | - | - |
Batu (East Java) | - | + | - | - | - | - |
Magetan (East Java) | - | - | - | + | - | - |
Location (District) | Results of PCR Detection | Percentage of Virus-Infected Plants (%) * | |||||||
---|---|---|---|---|---|---|---|---|---|
No Detectable Product | Single Infection | Mixed Infections | |||||||
PepYLCIV | ToLCNDV | TYLCKaV | PepYLCIV–ToLCNDV | PepYLCIV–TYLCKaV | ToLCNDV–TYLCKaV | PepYLCIV–ToLCNDV–TYLCKaV | |||
Lowlands | |||||||||
Cirebon (West Java) | 20 | 100.00 | |||||||
Pangandaran 1 (West Java) | 18 | 2 | 100.00 | ||||||
Pangandaran 2 (West Java) | 18 | 2 | 100.00 | ||||||
Bantul (Yogyakarta) | 20 | 100.00 | |||||||
Kulon Progo (Yogyakarta) | 11 | 6 | 1 | 2 | 100.00 | ||||
Sragen (Central Java) | 1 | 19 | 95.00 | ||||||
Banyuwangi 1 (East Java) | 4 | 16 | 80.00 | ||||||
Banyuwangi 2 (East Java) | 8 | 12 | 60.00 | ||||||
Kediri (East Java) | 5 | 3 | 1 | 8 | 3 | 75.00 | |||
Mean | 90.00 a | ||||||||
Highlands | |||||||||
Sukabumi (West Java) | 15 | 5 | 100.00 | ||||||
Bandung Barat (West Java) | 20 | 100.00 | |||||||
Garut (West Java) | 20 | 100.00 | |||||||
Banjarnegara (Central Java) | 19 | 1 | 100.00 | ||||||
Wonosobo (Central Java) | 1 | 19 | 95.00 | ||||||
Karanganyar (Central Java) | 1 | 19 | 95.00 | ||||||
Malang (East Java) | 1 | 19 | 95.00 | ||||||
Batu (East Java) | 1 | 19 | 95.00 | ||||||
Magetan (East Java) | 9 | 10 | 1 | 55.00 | |||||
Mean | 92.78 a |
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Wahyono, A.; Murti, R.H.; Hartono, S.; Nuringtyas, T.R.; Wijonarko, A.; Mulyantoro, M.; Firmansyah, D.; Afifuddin, A.; Purnama, I.C.G. Current Status and Complexity of Three Begomovirus Species in Pepper Plants in Lowlands and Highlands in Java Island, Indonesia. Viruses 2023, 15, 1278. https://doi.org/10.3390/v15061278
Wahyono A, Murti RH, Hartono S, Nuringtyas TR, Wijonarko A, Mulyantoro M, Firmansyah D, Afifuddin A, Purnama ICG. Current Status and Complexity of Three Begomovirus Species in Pepper Plants in Lowlands and Highlands in Java Island, Indonesia. Viruses. 2023; 15(6):1278. https://doi.org/10.3390/v15061278
Chicago/Turabian StyleWahyono, Andi, Rudi Hari Murti, Sedyo Hartono, Tri Rini Nuringtyas, Arman Wijonarko, Mulyantoro Mulyantoro, Deni Firmansyah, Ahmad Afifuddin, and Innez Candri Gilang Purnama. 2023. "Current Status and Complexity of Three Begomovirus Species in Pepper Plants in Lowlands and Highlands in Java Island, Indonesia" Viruses 15, no. 6: 1278. https://doi.org/10.3390/v15061278
APA StyleWahyono, 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