Identity and Sequence Diversity of Begomovirus Associated with Yellow Leaf Curl Disease of Tomato in Indonesia

Abstract

Infection of tomato by Begomovirus is known to cause serious disease and yield losses. Samples of tomato plants showing typical symptoms of begomovirus infection were collected from eight locations in Java and Sumatra. Amplification of a putative AV1 gene was performed using AV1 specific primers for Geminivirus, total nucleic acid isolated from tomato samples exhibiting leaf curl disease as the template, and the PCR technique. Direct sequencing of PCR product was carried out, followed by nucleotide and predicted amino acid sequence analysis using the BLAST program. Positive results were obtained, the PCR amplification proved that diseased tomato samples collected from eight locations in Java and Sumatra were infected with Begomovirus. When nucleic acid and amino acid sequences of the eight isolates were compared to other begomovirus's sequences present in the GenBank it was found that the isolates determined in this research were Indonesian isolates of AYVV. Further phylogenetic analysis of eight Begomovirus isolates identified in this study indicated they belonged into two different clades. Results of this research also suggest that the existence of Begomovirus genetic diversity in various regions in Indonesia needs further investigation. Moreover, the prevalence of distinct Begomovirus species or isolates also need investigation.

Detection and Sequence Diversity of Begomovirus Associated with Yellow Leaf Curl Disease of Pepper (Capsicum annuum) in West Sumatra, Indonesia

“…Both the hairpinloop structure and iteron have been found in all geminivirus sequenced to date and this might be used for analysis of their genetic diversity. It was known that differences in the common region may indicate a different begomovirus strain (Hidayat et al 1999;Chatchawankanphanich and Maxwell 2002;Sukamto et al 2005;Ribeiro et al 2006;Santoso et al 2008). It was found in our present research that three isolates of begomovirus infecting pepper in West Sumatra (PepPYK1-1, PepAg2-1 and PepAg2-4) have a hairpin loop those found in Java, which commonly caused bright yellow colouring (Sulandari 2004).…”

Deteksi Molekuler Asosiasi Begomovirus dengan Penyakit Keriting Kuning Cabai di Pakis dan Banyuurip, Magelang Indonesia

“…Polymerase chain reaction (PCR) yang berbasis asam nukleat dengan menggunakan primer universal dapat digunakan untuk mendeteksi dan mengidentifikasi Begomovirus dari tanaman yang berbeda dan tempat yang berbeda (Rojas et al, 1993). Deteksi dengan PCR mudah dilakukan karena virus ini melakukan replikasi menggunakan sebuah DNA intermediet yang berbentuk sirkuler dan utas ganda yang dapat bertindak sebagai sebuah cetakan untuk amplifikasi PCR (Santoso et al, 2008).…”

Konstruksi Kandidat Gen AV1 Begomovirus pada pBI121 dan Introduksinya ke dalam Tembakau Menggunakan Vektor Agrobacterium tumefaciens

“…Amplifikasi PCR menggunakan asam nukleat total tanaman dan primer spesifik gen AV1 Begomovirus dari isolat Kaliurang (CP8) dan Brastagi (CP11) menghasilkan fragmen DNA berukuran 780 bp (Gambar 1A). Pemilihan isolat ini berdasarkan dari hasil percobaan sebelumnya di mana kedua isolat tersebut mewakili dua kelompok yang berbeda dari hasil analisis filogenetik delapan isolat Begomovirus (Santoso et al, 2008).…”