First report of naturally occurring recombinant non-coding DNA satellite associated with Tomato yellow leaf curl Kanchanaburi virus on eggplant in Indonesia

Abstract

Abstract. Kandito A, Hartono S, Sulandari S, Somowiyarjo S, Widyasari YA. 2019. First report of naturally occurring recombinant non-coding DNA satellite associated with Tomato yellow leaf curl Kanchanaburi virus on eggplant in Indonesia. Biodiversitas 20: 129-136. Begomovirus is a viral genus which is a major impediment in the cultivation of plants, especially Solanaceae. Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) is a member of the Begomovirus genus that is widely reported to infect eggplant and results in severe symptoms of chlorosis. In addition to the type of virus that infects, the severity of symptoms can also be caused by the presence of betasatellite associated with several begomovirus species. The presence of betasatellite that is related to several begomovirus species can lead to more severe symptoms. The aim of this study was to identify satellites associated with begomovirus in Indonesia. Eggplant samples from Bantul, Special Region of Yogyakarta show with mosaic and severe chlorotic symptoms due to Begomovirus infection. Total DNA samples were subject to PCR amplification using universal primer for begomovirus PALIV1978/PAR1C715 and specific primer for betasatellite β01/β02. The PCR amplification produced a DNA band measuring ± 1600bp, identical size of begomovirus. The amplification of the betasatellite specific primer produced a DNA band featuring ± 1300bp, identical size of betasatellites that were associated with begomovirus in the sample. The results of DNA sequencing, suggested that begomovirus in this study had a close relationship with TYLCKaV from Thailand and Indonesia. Characterization of the satellite-based on nucleotide sequence revealed the presence of stem-loop structures, satellite conservative regions, and adenine-rich regions that resembled structures present in the betasatellite, which were associated with Tomato leaf curl virus and Ageratum yellow vein virus, with no ORF found. These results indicated that the TYLCKaV could be associated with a non-coding satellite. This result is the first report regarding the TYLCKaV association with a non-coding satellite in Indonesia.

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

“…The nucleotide sequence of betasatellite shows that the satellite accompanies the infection resembling betasatel lites which associated with ToLCV and AYVV, and has similarities to the noncoding region part of DNAB on PepYLCIV. Phylogenetic analysis using the Neighbor joining method shows that this satellite is located in a clus ter with satellites associated with ToLCV and AYVV, and has proximity to the noncoding satellite previously re ported to be associated with TYLCKaV (Kandito et al 2020) (Figure 4). The sequencing and characterization results of the satellite showed a noncoding satellite that was thought to be a recombination of betasatellite with PepYLCIV DNAB.…”

Begomoviruses on two chili types in Southeast Sulawesi Indonesia: variation of symptom severity assessment and DNA-betasatellite identification

“…This container was then stored in a styrofoam box and sent to the Plant Virology Laboratory at Gadjah Mada University for a PCR test. The satellite DNA analysis followed the procedures from a previous study (Kandito et al, 2020).…”

“…It also influences symptom severity (Fiallo-Olivé et al, 2021). Satellite DNA has been reported in chili plants infected by Begomovirus in several areas, including Magelang and Yogyakarta (Kandito et al, 2019;Kandito et al, 2020).…”

“…In Indonesia, Begomovirus infections associated with beta-satellites have been previously reported. These include DNA-β associated with ToLJaV in Ageratum conyzoides weed, DNA-β01 associated with ToLCJaV, DNA-β associated with PepYLCIV in chili plants, DNA-β02 associated with AYVV [Java] in tomato plants, as well as non-coding satellites associated with TYLCKaV and PepYLCIV from eggplant and chili plants (Jamsari & Pedri, 2013;Kandito et al, 2019;Kandito et al, 2020;Kon et al, 2007). Ilyas et al (2010) reported that in Pakistan, Begomovirus associated with long bean plants causes yellow mosaic symptoms.…”

Begomovirus Associated with Yellow Mosaic Symptom on Eggplant Plant in Bengkulu

“…Daun muda bergejala diambil sebanyak lima lembar, selanjutnya daun dimasukkan ke dalam kantung plastik dan disimpan pada suhu -20 ℃ sebelum diekstraksi DNA totalnya. (Kon et al 2006(Kon et al dan 2007Kandito et al 2019Kandito et al , 2020Kandito et al , 2021. Analisis sikuen DNA dengan program BLAST menunjukkan Begomovirus isolat terung dari Bengkulu memiliki similaritas yang tinggi, sekitar 99% terhadap Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) asal Indonesia, Malaysia dan Thailand (Tabel 1).…”