The complete sequence of a Singapore isolate of odontoglossum ringspot virus and comparison with other tobamoviruses

Chng, C. G.; Wong, Sek‐Man; Mahtani, Parvesh; Loh, Chiang‐Shiong; Goh, C. J.; Kao, Ming Shan; Chung, Maxey C.M.; Watanabe, Yoshihisa

doi:10.1016/0378-1119(96)00046-7

Cited by 36 publications

(22 citation statements)

References 21 publications

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“…ORSV menyebabkan kerugian secara ekonomi akibat menurunnya kualitas bunga di Florida, Hawai, India, Taiwan, Thailand, Singapura, dan Australia (Zettler et al 1990;Hu et al 1993;Wong et al 1994;Barry et al 1996;Chang et al 1996;Sherpa et al 2006;Khentry et al 2006;Chang 2008;Ali et al 2014).…”

Section: Pendahuluanunclassified

Deteksi Odontoglossum ringspot virus pada Anggrek Asli Koleksi Kebun Raya di Indonesia

Mahfut

Daryono

Somowiyarjo

2017

J Fitopatol Indones

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ABSTRAKAnggrek asli merupakan salah satu kekayaan flora asli Indonesia yang memiliki peran penting sebagai induk persilangan dalam pemuliaan tanaman anggrek. Infeksi virus menjadi salah satu faktor pembatas dalam budi daya anggrek. Penelitian bertujuan mendeteksi dan mengidentifikasi Odontoglossum ringspot virus (ORSV) yang menginfeksi anggrek asli. Sampel dikoleksi dari tanaman bergejala asal 5 kebun raya di Indonesia, yaitu Bogor, Cibodas, Purwodadi, Balikpapan, dan Enrekang. Deteksi dan identifikasi dilakukan secara serologi menggunakan antiserum spesifik ORSV, dilanjutkan dengan metode reverse transcriptase-polymerase chain reaction (RT-PCR), dan perunutan DNA. Uji serologi menunjukkan 5 sampel bereaksi positif terhadap antiserum ORSV, yaitu pada Phalaenopsis amboinensis (KRB2) dan Phalaenopsis amabilis (KRB12) dari Kebun Raya Bogor, Phalaenopsis amabilis (KRP18) dan Dendrobium salacence (KRP20) dari Kebun Raya Purwodadi, dan Phalaenopsis modesta J. J. Sm. (KRBp5) dari Kebun Raya Balikpapan. Deteksi asam nukleat 5 sampel tersebut dengan RT-PCR menggunakan primer spesifik gen coat protein ORSV menghasilkan fragmen DNA berukuran ± 474 pb. Analisis homologi 5 isolat ORSV tersebut menunjukkan nilai indeks similaritas (IS) sebesar 99.8% dengan 14 isolat ORSV lain. Analisis filogenetika menunjukkan isolat KRB2 dan isolat KRP18 berada dalam satu kelompok dan terpisah dengan isolat ORSV dari negara-negara lain. Ini adalah laporan pertama adanya infeksi ORSV pada anggrek asli koleksi 5 kebun raya di Indonesia. Kata kunci: analisis filogenetika, homologi, serologi, RT-PCR ABSTRACTNative orchid is one of Indonesian natural resources which play important role as parental materials in breeding program. Virus infection is one of the limiting factors in the cultivation of orchid. The purpose of this study was to detect Odontoglossum ringspot virus (ORSV) from native orchid. Symptomatic orchids were collected from 5 botanical gardens, i.e. Bogor, Cibodas, Purwodadi, Balikpapan, and Enrekang Botanical Gardens. Detection and identification was conducted by serological method using ORSV specific antisera, followed by RT-PCR and DNA sequencing. The serological test showed that 5 samples gave positive reaction against ORSV antiserum, i.e. Phalaenopsis amboinensis (KRB2) and Phalaenopsis amabilis (KRB12) from Bogor Botanical Garden, Phalaenopsis amabilis (KRP18) and Dendrobium salacence (KRP20) from Purwodadi Botanical Garden, dan Phalaenopsis modesta J. J. Sm. (KRBp5) from Balikpapan Botanical Garden. RT-PCR of the 5 samples using specific primer of ORSV coat protein gene was successfully amplified fragment DNA with size ± 474 bp. Homology analysis of those 5 ORSV isolates showed the highest index similiarity of 99

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Section: Pendahuluanunclassified

Deteksi Odontoglossum ringspot virus pada Anggrek Asli Koleksi Kebun Raya di Indonesia

Mahfut

Daryono

Somowiyarjo

2017

J Fitopatol Indones

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“…ORSV-infected orchids often show a variety of symptoms such as color-breaking in flowers, diamond mottle, streak or stripe mosaic or necrotic spots, yellowing leaves, as well as symptomless conditions [3,6,9]. To date, the complete nucleotide (nt) sequences of three ORSV isolates have been reported [10][11][12], and the complete nt sequences for only two Taiwan isolates of ORSV are available in the GenBank database (accession numbers DQ139262 and AY571290). These studies using phylogenetic tree analysis demonstrated evolutionary convergence in RNA-dependent RNA polymerase, movement protein, and coat protein (CP) within each virus clusters.…”

Section: Introductionmentioning

confidence: 99%

High sequence conservation among Odotoglossum ringspot virus isolates from orchids

Yoon

Chung²,

Choi

2010

Virus Genes

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The variability in the nucleotide (nt) and amino acid (aa) sequences of the coat protein (CP) of Odontoglossum ringspot virus (ORSV), which naturally infects orchids worldwide, was investigated. The CP genes of 48 ORSV isolates originating from different locations in Korea were amplified using RT-PCR and sequenced. The encoded CP consists of 158 aa. The CP sequences of the Korean isolates were compared at the nt and aa levels with those of the previously published ORSV isolates originating from different countries. The Korean isolates share 94.8-100% and 92.4-100% CP identity to ORSV isolates from other countries at the nt and aa levels, respectively. No particular region of variability could be found in either sequence of the viruses. In the deduced aa sequence, the N-terminal region was more conserved than the C-terminal region in ORSV. The phylogenetic tree analysis and recombination analysis revealed that there was no distinct grouping between geographic locations and sequence identity, and nor distinct intra-specific recombination events among ORSV isolates.

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“…The CP sequences determined in this study are available in DDBJ/EMBL/GenBank databases with accession codes MG869629–MG869649. Three highly conserved RNA-binding motifs (I, II, and III) in tobamoviruses (Altschuh et al, 1987; Chng et al, 1996) were also observed from these ORSV CP gene sequences.…”

Section: Resultsmentioning

confidence: 84%

“…It has rod-shaped particles with a positive-sense single-stranded RNA genome. Similar to other tobamoviruses, ORSV encodes at least four proteins, such as the RdRp (126 kDa/183 kDa), movement protein (MP; 33 kDa MP), and coat protein (CP, 18 kDa) (Chng et al, 1996; Ryu and Park, 1995). ORSV induces ringspots, diamond-shaped mottle, and streaks or striped mosaicism symptom on leaves; and crinkle, color breaking and ringspots on orchids flowers (Jensen and Gold, 1951; Wong et al, 1994; Zheng et al, 2010).…”

mentioning

confidence: 99%

Evolutionary Rates and Phylogeographical Analysis of Odontoglossum Ringspot Virus Based on the 166 Coat Protein Gene Sequences

Dong

et al. 2019

Plant Pathol J

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The complete sequence of a Singapore isolate of odontoglossum ringspot virus and comparison with other tobamoviruses

Cited by 36 publications

References 21 publications

Deteksi Odontoglossum ringspot virus pada Anggrek Asli Koleksi Kebun Raya di Indonesia

Deteksi Odontoglossum ringspot virus pada Anggrek Asli Koleksi Kebun Raya di Indonesia

High sequence conservation among Odotoglossum ringspot virus isolates from orchids

Evolutionary Rates and Phylogeographical Analysis of Odontoglossum Ringspot Virus Based on the 166 Coat Protein Gene Sequences

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