Sequence and Phylogenetic Analysis of the First Complete Genome of Rice tungro spherical virus in Malaysia

Document Type : Research Paper

Authors

1 Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia

2 Institute of Rice Research Centre, MARDI Seberang Perai, Jalan Paya Keladi/ Pinang Tunggal, 13200 Kepala Batas, Penang, Malaysia

3 Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia; School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia

4 Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia

5 School of Environmental and Natural Resource Sciences, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia

Abstract

Background: Rice tungro disease (RTD) is a viral disease mainly affecting rice in Asia. RTD caused by Rice tungro bacilliform virus and Rice tungro spherical virus. To date, there are only 5 RTSV isolates have been reported.
Objectives: In this study, we aimed to report the complete nucleotide sequence of Malaysian isolate of Rice tungro spherical virus Seberang Perai (RTSV-SP) for the first time. RTSV-SP was characterized and its evolutionary relationship with previously reported Indian and Philippines isolates were elucidated.
Materials and Methods: RTSV-SP isolate was isolated from a recent outbreak in a paddy field in Seberang Perai zone of Malaysia. Its complete genome was amplified by RT-PCR, cloned and sequenced.
Results: Sequence analysis indicated that the genome of RTSV-SP consisted of 12,173 nucleotides (nt). Comparative analysis of 6 complete genome sequences using Clustal Omega showed that Seberang Perai isolate shared the highest nucleotide identity (96.04%) with Philippine-A isolate, except that the sORF-2 of RTSV-SP is shorter than RTSV Philippine-A by 27 amino acid residues. RTSV-SP found to cluster in Southeast Asia (SEA) group based on the whole genome sequence phylogenetic analysis using MEGA X software.
Conclusions: Phylogenetic classification of RTSV isolates based on the complete nucleotide sequences showed more distinctive clustering pattern with the addition of RTSV-SP whole genome to the available isolates. Present study described the isolation and molecular characterization of RTSV-SP.

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Iranian Journal of Biotechnology
Volume 18, Issue 4
December 2020
Pages 9-17

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