A recombinant DNA‐satellite associated with Pepper yellow leaf curl Indonesia virus in highland area

https://doi.org/10.22146/ijbiotech.64817

Argawi Kandito(1), Sedyo Hartono(2*), Sri Sulandari(3), Susamto Somowiyarjo(4)

(1) Department of Plant Protection, Faculty of Agriculture, Gadjah Mada University, Jln. Flora 1, Bulaksumur, Sleman, Yogyakarta 55281
(2) Department of Plant Protection, Faculty of Agriculture, Gadjah Mada University, Jln. Flora 1, Bulaksumur, Sleman, Yogyakarta 55281
(3) Department of Plant Protection, Faculty of Agriculture, Gadjah Mada University, Jln. Flora 1, Bulaksumur, Sleman, Yogyakarta 55281
(4) Department of Plant Protection, Faculty of Agriculture, Gadjah Mada University, Jln. Flora 1, Bulaksumur, Sleman, Yogyakarta 55281
(*) Corresponding Author

Abstract


Yellow curl disease caused by begomovirus is a major threat for horticulture in Indonesia. Control mea‐ sures for the disease face several constraints, one of which is the association between begomovirus and DNA satellites which can affect the severity of symptoms. In this study, we detected the presence of a DNA satellite associated with begomovirus in a highland area. The sample was obtained from Ketep, Magelang, located approximately 1400 meters above sea level. Begomovirus was detected using primers PAL1V1978/PAR1C715 that resulted in an amplicon of ap‐ proximately 1600bp. The presence of this satellite was detected using primers CLB36F/CLB37R, resulting in full‐length satellite genome of approximately 1300bp. Sequence analysis showed the sample was infected by Pepper yellow leaf curl Indonesia virus (PepYLCIV) and a non‐coding satellite which resembled some characteristics of common betasatellites with imperfect putative ORF βC1. SimPlot analysis revealed the recombination event between betasatellites and DNA‐B of PepYLCIV. The satellite found in this study is thought to be the result of recombination due to multiple infections in plants.


Keywords


Begomovirus, DNA satellite, non-coding satellite, PepYLCIV, recombination

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References

Agnihotri AK, Mishra SP, Tripathi RC, Ansar M, Srivastava A, Tripathi IP. 2018. First natural co­occurrence of tomato leaf curl New Delhi virus DNA­A and chili leaf curl betasatellite on tomato plants (Solanum lycopersicum L.) in India. J Gen Plant Pathol. 84(6):414–417. doi:10.1007/s10327­018­0807­2.

Briddon RW, Mansoor S, Bedford ID, Pinner MS, Saunders K, Stanley J, Zafar Y, Malik KA, Markham PG. 2001. Identification of DNA components required for induction of cotton leaf curl disease. Virology. 285(2):234–243. doi:10.1006/viro.2001.0949.

Briddon RW, Patil BL, Bagewadi B, Nawaz­Ul­Rehman MS, Fauquet CM. 2010. Distinct evolutionary histories of the DNA­A and DNA­B components of bipartite begomoviruses. BMC Evol Biol. 10(1). doi:10.1186/1471­2148­10­97.

Briddon RW, Stanley J. 2006. Subviral agents associated with plant single­stranded DNA viruses 344(1):198– 210. doi:10.1016/j.virol.2005.09.042.

Dry IB, Krake LR, Rigden JE, Rezaian MA. 1997. A novel subviral agent associated with a geminivirus: The first report of a DNA satellite. Proc Natl Acad Sci USA. 94(13):7088–7093. doi:10.1073/pnas.94.13.7088.

Efron B, Halloran E, Holmes S. 1996. Bootstrap confidence levels for phylogenetic trees. Proc Natl Acad Sci USA. 93(23):13429–13434. doi:10.1073/pnas.93.23.13429.

Emmanuel CJ, Manohara S, Shaw MW. 2020. Molecular characterization of begomovirus–betasatellite– alphasatellite complex associated with okra enation leaf curl disease in Northern Sri Lanka. 3 Biotech 10(12). doi:10.1007/s13205­020­02502­z.

Fiallo­Olivé E, Navas­Castillo J. 2020. Molecular and Biological Characterization of a New World Mono­ /Bipartite Begomovirus/Deltasatellite Complex Infecting Corchorus siliquosus. Front Microbiol. 11. doi:10.3389/fmicb.2020.01755.

Giovanni AC, Hartono S, Sulandari S, Somowiyarjo S. 2020. Molecular Identification of Begomovirus Infecting Angled Luffa. Jurnal Perlindungan Tanaman Indonesia. 24(2):147. doi:10.22146/jpti.31073.

Hidayat S, Rusli E, Nooraidawati. 1999. Penggunaan primer universal dalam polymerase chain reaction untuk mendeteksi virus gemini pada cabe [The Use of Universal Primers on PCR to Detect Geminivirus on Chili]. In: Prosiding Seminar Ilmiah dan Kongres Nasional PFI XV. Purwokerto.

Huang C, Xie Y, Zhao L, Ren H, Li Z. 2013. A naturally occurring defective DNA satellite associated with a monopartite begomovirus: Evidence for recombination between alphasatellite and betasatellite. Viruses. 5(9):2116–2128. doi:10.3390/v5092116.

Idris AM, Shahid MS, Briddon RW, Khan AJ, Zhu JK, Brown JK. 2011. An unusual alphasatellite associated with monopartite begomoviruses attenuates symptoms and reduces betasatellite accumulation. J Gen Virol. 92(3):706–717. doi:10.1099/vir.0.025288­0.

Kandito A, Hartono S, Sulandari SRI, Somowiyarjo S, Widyasari YA. 2020. First report of naturally occurring recombinant non­coding dna satellite associated with tomato yellow leaf curl kanchanaburi virus on eggplant in Indonesia. Biodiversitas. 21(1):129–136. doi:10.13057/biodiv/d210117.

Kenyon L, Tsai WS, Shih SL, Lee LM. 2014. Emergence and diversity of begomoviruses infecting solanaceous crops in East and Southeast Asia. Virus Res. 186:104– 113. doi:10.1016/j.virusres.2013.12.026.

Kintasari T, DWN S, Sulandari S, Hidayat S. Tomato yellow leaf curl Kanchanaburi virus Associated with Yellow Mosaic Disease of Eggplant in Java. Jurnal Fitopatologi Indonesia. 9(4):127–131.

Kon T, Hidayat SH, Hase S, Takahashi H, Ikegami M. 2006. The natural occurrence of two distinct begomoviruses associated with DNAβ and a recombinant DNA in a tomato plant from Indonesia. Phytopathology. 96(5):517–525. doi:10.1094/PHYTO­96­0517.

Kumar R, Palicherla SR, Mandal B, Kadiri S. 2018. PCR based detection of betasatellite associated with the begomoviruses using improved universal primers. Australas Plant Pathol. 47(1):115–118. doi:10.1007/s13313­017­0537­5.

Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 33(7):1870–1874. doi:10.1093/molbev/msw054.

Kusumaningrum F, Hartono S, Sulandari S, Somowiyarjo S. 2017. Infeksi Ganda Begomovirus Dan Crinivirus Pada Tanaman Tomat Di Kabupaten Magelang , Jawa Tengah (Double Infections of Begomovirus and Crinivirus on Tomato Plants At Magelang Regency, Central Java). Jurnal Perlindungan Tanaman Indonesia. 19(2):60. doi:10.22146/jpti.17542.

Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC. 1999. Full­Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C­Infected Seroconverters in India, with Evidence of Intersubtype Recombination. J Virol. 73(1):152–160. doi:10.1128/jvi.73.1.152­160.1999.

Lozano G, Trenado HP, Fiallo­Olivé E, Chirinos D, Geraud­Pouey F, Briddon RW, Navas­Castillo J. 2016. Characterization of non­coding DNA satellites associated with sweepoviruses (Genus Begomovirus, Geminiviridae) ­ Definition of a distinct class of begomovirus­associated satellites. Front Microbiol. 7(FEB). doi:10.3389/fmicb.2016.00162.

Nawaz­ul Rehman MS, Mansoor S, Briddon RW, Fauquet CM. 2009. Maintenance of an Old World Betasatellite by a New World Helper Begomovirus and Possible Rapid Adaptation of the Betasatellite. J Virology. 83(18):9347–9355. doi:10.1128/jvi.00795­09.

Purwoko RR, Hartono S, Suputa, Lukman R, Wahyudin D. 2015. Emerging pepper yellow leaf curl virus and mungbean yellow mosaic virus of single Bemisia tabaci in Java, Indonesia. In: The 11th International Student Conference at Ibaraki University, volume 11. Japan. doi:10.13140/RG.2.1.4382.9849.

Rojas MR. 1993. Use of Degenerate Primers in the Polymerase Chain Reaction to Detect WhiteflyTransmitted Geminiviruses. Plant Dis. 77(4):340. doi:10.1094/pd­77­0340.

Saeed M, Zafar Y, Randles JW, Rezaian MA. 2007. A monopartite begomovirus­associated DNA beta satellite substitutes for the DNA B of a bipartite begomovirus to permit systemic infection. J Gen Virol. Pt 10:2881–2889. doi:10.1099/vir.0.83049­0.

Saunders K, Norman A, Gucciardo S, Stanley J. 2004. The DNA β satellite component associated with ageratum yellow vein disease encodes an essential pathogenicity protein (βC1). Virology. 324(1):37–47. doi:10.1016/j.virol.2004.03.018.

Sidik E, Hartono S, Sulandari S, Lukman R, Affifudin A, Wahyudin D, Santoso H. Molecular evidence for mixed infection of four begomovirus in common bean and yard long bean showing severe yellow symptoms in East Java, Indonesia. In: Proc 1st Intl Conf Trop Agric. Yogyakarta.

Sulandari S, Suseno R, Hidayat SH, Harjosudarmo K, Sosromarsono S. 2001. Deteksi virus Gemini pada cabai di Daerah Istimewa Yogyakarta [Detection of Geminivirus on Chili in Special Region of Yogyakarta]. In: Prosiding Kongres Nasional XVI dan Seminar Ilmiah PFI. Bogor. Indonesia.

Tahir MN, Hameed A, Amin I, Mansoor S. 2017. Characterization of a begomovirus­betasatellite complex, producing defective molecules in spinach (Spinacia oleracea L.), a new host for begomovirus and betasatellite complex in Pakistan. Plant Pathol J. 33(5):514–521. doi:10.5423/PPJ.NT.01.2017.0009.

Tsai WS, Shih SL, Green SK, Rauf A, Hidayat SH, Jan FJ. 2006. Molecular Characterization of Pepper yellow leaf curl Indonesia virus in Leaf Curl and Yellowing Diseased Tomato and Pepper in Indonesia. Plant Dis. 90(2):247–247. doi:10.1094/pd­90­0247b.

Wilisiani F, Somowiyarjo S, Hartono S. 2014. Molecular identification of virus causing leaf curl disease Bantul isolate on melon. JPTI 18(1):47–54. doi:10.22146/jpti.15602.

Yang X, Zhou X. 2017. Betasatellites of Begomoviruses. In: Viroids and Satellites. Elsevier Inc. p. 671–678. doi:10.1016/B978­0­12­801498­1.00062­0.

Zhang T, Luan JB, Qi JF, Huang CJ, Li M, Zhou XP, Liu SS. 2012. Begomovirus­whitefly mutualism is achieved through repression of plant defences by a virus pathogenicity factor. Mol Ecol. 21(5):1294– 1304. doi:10.1111/j.1365­294X.2012.05457.x.

Zhou X. 2013. Advances in understanding begomovirus satellites. Annu Rev Phytopathol. 51:357–381. doi:10.1146/annurev­phyto­082712­102234.



DOI: https://doi.org/10.22146/ijbiotech.64817

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