Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Genome Sequences

Complete Genome Sequence of Rice Tungro Bacilliform Virus Infecting Asian Rice (Oryza sativa) in Malaysia

Maathavi Kannan, Maisarah Mohamad Saad, Noraini Talip, Syarul Nataqain Baharum, Hamidun Bunawan
Simon Roux, Editor
Maathavi Kannan
aInstitute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Maisarah Mohamad Saad
bRice Research Centre, MARDI Seberang Perai, Kepala Batas, Penang, Malaysia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Noraini Talip
cSchool of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Syarul Nataqain Baharum
aInstitute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hamidun Bunawan
aInstitute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Simon Roux
DOE Joint Genome Institute
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.00262-19
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Rice tungro disease was discovered in Malaysia in the 1930s. The first and only genome of Rice tungro bacilliform virus (RTBV) isolated from rice in Malaysia was sequenced in 1999. After nearly two decades, here, we present the complete genome sequence of an RTBV isolate in rice from Seberang Perai, Malaysia.

ANNOUNCEMENT

Rice tungro disease (RTD) is known to be one of the most economically important viral diseases of rice (1). High incidences of RTD have been reported across South and Southeast Asia (2, 3). Every year, RTD causes losses of approximately $1.5 billion in rice yield (4). The disease results from an infection by two distinct viruses, Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV) (5, 6). The severity of tungro symptoms is driven by RTBV (7), while RTSV mainly plays a role as a helper virus in vector transmission of RTBV (8).

RTBV is a member of the genus Tungrovirus and family Caulimoviridae (9). RTBV has a circular double-stranded DNA genome of about 8 kb (10). The genome of RTBV (Philippines isolate) was sequenced for the first time in 1991 (11), followed by complete sequencing of five biological variants, Phi-2 (12), Phi-3 (13), Ic, G1, and G2 (14). Since then, several Indian isolates from Chinsura (15), Kanyakumari (2), Andra Pradesh, and West Bengal (16) were sequenced. Moreover, complete genomes of isolates from Punjab (17), Chainat, and Serdang (18) have also been reported.

Despite the importance of tungro viruses, less research work has been conducted on RTBV in Malaysia (19). The only genome of RTBV in Malaysia, RTBV-Serdang (GenBank accession no. AF076470), was sequenced in 1999 (18). Since then, no RTBV genome sequence has been reported in the past 19 years, although the disease is still endemic in Malaysia (9). In this study, we report the complete genomic sequence of an RTBV isolate obtained from an infected field. This will enable further studies regarding RTBV evolution and genome variability in Malaysia.

Rice plants exhibiting RTD symptoms were collected from a paddy field in Seberang Perai, Malaysia. The cetyltrimethylammonium bromide (CTAB) method was utilized in the extraction of DNA from infected leaves of rice plants (20). Designation of five overlapping primer pairs was done (Table 1) based on the aligned complete genome sequences of 13 RTBV isolates derived from GenBank (https://www.ncbi.nlm.nih.gov/nuccore/?term=rice+tungro+bacilliform+virus+complete+genome). PCR amplification of those five fragments covering the entire genome from the RTBV DNA template was carried out using PCRBIO HiFi polymerase, and the products were electrophoresed on a 1% agarose gel. Once the band size was confirmed, the products were purified from the gel using a QIAquick gel extraction kit (Qiagen, Malaysia) and cloned into pJET1.2 vector. A minimum of two recombinant plasmids for every fragment were sent to the First BASE Laboratories Sdn Bhd company for sequencing in forward and reverse directions using the Sanger sequencing method.

View this table:
  • View inline
  • View popup
TABLE 1

Primers used in PCR to amplify the complete genome of Rice tungro bacilliform virus

A total of 10 bidirectional reads were obtained. The program Clustal Omega version 1.2.4 with default parameters was used to align all obtained reads in pairs to generate respective consensus nucleotide sequences of five fragments (21). Adjacent segments with overlapping sequences were joined in order to generate the complete genome of RTBV.

The full-length genome sequence of RTBV isolated from Seberang Perai (RTBV-SP) was thus obtained and found to be 8,000 nucleotides in length, with a G+C content of 33.3%. Searches through BLASTN revealed that the nucleotide sequence of the RTBV-SP isolate is 81.45% to 95.44% identical to those of other RTBV complete genomes available in the GenBank database. The highest nucleotide similarity (95.44%) was observed with the Serdang isolate. Interestingly, the RTBV-SP genome is shorter than that of the Serdang isolate by 16 nucleotides.

This study revealed that the genetic makeup of RTBV-SP has remained stable despite a time gap of approximately 20 years between genome sequencing of the SP isolate and the Serdang isolate. Availability of the data on RTBV variability in Malaysia would be helpful in determining the resistance strategies against tungro.

Data availability.The complete genomic sequence of the RTBV-SP isolate was submitted to NCBI GenBank with the accession no. MK552377.

ACKNOWLEDGMENT

This work was supported by Universiti Kebangsaan Malaysia through grants GGPM-2017-072, DPP-2018-010, and GUP-2017-035.

FOOTNOTES

    • Received 19 March 2019.
    • Accepted 23 April 2019.
    • Published 16 May 2019.
  • Copyright © 2019 Kannan et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Shahjahan M,
    2. Imbe T,
    3. Jalani BS,
    4. Zakri AH,
    5. Othman O
    . 1991. Inheritance of resistance to rice tungro spherical virus in rice (Oryza sativa L.), p 247–254. In Rice genetics II. International Rice Research Institute, Manila, Philippines.
  2. 2.↵
    1. Sharma S,
    2. Rabindran R,
    3. Robin S,
    4. Dasgupta I
    . 2011. Analysis of the complete DNA sequence of rice tungro bacilliform virus from southern India indicates it to be a product of recombination. Arch Virol 156:2257–2262. doi:10.1007/s00705-011-1092-y.
    OpenUrlCrossRefPubMed
  3. 3.↵
    1. Shahjahan M,
    2. Jalani BS,
    3. Zakri AH,
    4. Imbe T,
    5. Othman O
    . 1990. Inheritance of tolerance to rice tungro bacilliform virus (RTBV) in rice (Oryza sativa L.). Theor Appl Genet 80:513–517. doi:10.1007/BF00226753.
    OpenUrlCrossRef
  4. 4.↵
    1. Dai S,
    2. Beachy RN
    . 2009. Genetic engineering of rice to resist rice tungro disease. In Vitro Cell Dev Biol 45:517. doi:10.1007/s11627-009-9241-7.
    OpenUrlCrossRef
  5. 5.↵
    1. Habibuddin H,
    2. Mahir AM,
    3. Ahmad IB,
    4. Jalani BS,
    5. Imbe T
    . 1997. Genetic analysis of resistance to rice tungro spherical virus in several rice varieties. J Trop Agric Food Sci 25:1–7.
    OpenUrl
  6. 6.↵
    1. Habibuddin H,
    2. Ahmad IB,
    3. Mahir AM,
    4. Jalani S,
    5. Omura T
    . 1995. Resistance in rice to multiplication of the two tungro viruses. MARDI Res J 23:27–36.
    OpenUrl
  7. 7.↵
    1. Blas N,
    2. David G
    . 2017. Dynamical roguing model for controlling the spread of tungro virus via Nephotettix virescens in a rice field. J Phys Conf Ser 893:012018. doi:10.1088/1742-6596/893/1/012018.
    OpenUrlCrossRef
  8. 8.↵
    1. Bunawan H,
    2. Dusik L,
    3. Bunawan SN,
    4. Amin NM
    . 2014. Rice tungro disease: from identification to disease control. World Appl Sci J 31:1221–1226.
    OpenUrl
  9. 9.↵
    1. Azzam O,
    2. Chancellor TCB
    . 2002. The biology, epidemiology, and management of rice tungro disease in Asia. Plant Dis 86:88–100. doi:10.1094/PDIS.2002.86.2.88.
    OpenUrlCrossRef
  10. 10.↵
    1. Bao Y,
    2. Hull R
    . 1992. Characterization of the discontinuities in rice tungro bacilliform virus DNA. J Gen Virol 73:1297–1301. doi:10.1099/0022-1317-73-5-1297.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Hay JM,
    2. Jones MC,
    3. Blakebrough ML,
    4. Dasgupta I,
    5. Davies JW,
    6. Hull R
    . 1991. An analysis of the sequence of an infectious clone of rice tungro bacilliform virus, a plant pararetrovirus. Nucleic Acids Res 19:2615–2621. doi:10.1093/nar/19.10.2615.
    OpenUrlCrossRefPubMedWeb of Science
  12. 12.↵
    1. Qu R,
    2. Bhattacharyya M,
    3. Laco GS,
    4. De Kochko A,
    5. Rao BLS,
    6. Kaniewska MB,
    7. Elmer JS,
    8. Rochester DE,
    9. Smith CE,
    10. Beachy RN
    . 1991. Characterization of the genome of rice tungro bacilliform virus: comparison with Commelina yellow mottle virus and caulimoviruses. Virology 185:354–364. doi:10.1016/0042-6822(91)90783-8.
    OpenUrlCrossRefPubMedWeb of Science
  13. 13.↵
    1. Kano H,
    2. Koizumi M,
    3. Noda H,
    4. Hibino H,
    5. Ishikawa K,
    6. Omura T,
    7. Cabauatan PQ,
    8. Koganezawa H
    . 1992. Nucleotide sequence of capsid protein gene of rice tungro bacilliform virus. Arch Virol 124:157–163. doi:10.1007/BF01314633.
    OpenUrlCrossRefPubMed
  14. 14.↵
    1. Cabauatan PQ,
    2. Melcher U,
    3. Ishikawa K,
    4. Omura T,
    5. Hibino H,
    6. Koganezawa H,
    7. Azzam O
    . 1999. Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships. J Gen Virol 80:2229–2237. doi:10.1099/0022-1317-80-8-2229.
    OpenUrlCrossRefPubMed
  15. 15.↵
    1. Banerjee A,
    2. Roy S,
    3. Tarafdar J
    . 2011. Phylogenetic analysis of Rice tungro bacilliform virus ORFs revealed strong correlation between evolution and geographical distribution. Virus Genes 43:398–408. doi:10.1007/s11262-011-0647-z.
    OpenUrlCrossRefPubMed
  16. 16.↵
    1. Nath N,
    2. Mathur S,
    3. Dasgupta I
    . 2002. Molecular analysis of two complete rice tungro bacilliform virus genomic sequences from India. Arch Virol 147:1173–1187. doi:10.1007/s00705-002-0801-y.
    OpenUrlCrossRefPubMed
  17. 17.↵
    1. Mathur S,
    2. Dasgupta I
    . 2013. Further support of genetic conservation in Indian isolates of Rice tungro bacilliform virus by sequence analysis of an isolate from North-Western India. Virus Genes 46:387–391. doi:10.1007/s11262-012-0857-z.
    OpenUrlCrossRef
  18. 18.↵
    1. Marmey P,
    2. Bothner B,
    3. Jacquot E,
    4. de Kochko A,
    5. Ong CA,
    6. Yot P,
    7. Siuzdak G,
    8. Beachy RN,
    9. Fauquet CM
    . 1999. Rice tungro bacilliform virus open reading frame 3 encodes a single 37-kDa coat protein. Virology 253:319–326. doi:10.1006/viro.1998.9519.
    OpenUrlCrossRefPubMed
  19. 19.↵
    1. Hashim M,
    2. Osman M,
    3. Abdullah R,
    4. Pillai V,
    5. Bakar UKA,
    6. Hashim H,
    7. Daud HM
    . 2002. Research and development of transgenic plants in Malaysia: an example from an Asian developing country. Food Nutr Bull 23:367–375. doi:10.1177/156482650202300410.
    OpenUrlCrossRefPubMed
  20. 20.↵
    1. Gambino G,
    2. Perrone I,
    3. Gribaudo I
    . 2008. A rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochem Anal 19:520–525. doi:10.1002/pca.1078.
    OpenUrlCrossRefPubMedWeb of Science
  21. 21.↵
    1. Sievers F,
    2. Wilm A,
    3. Dineen D,
    4. Gibson TJ,
    5. Karplus K,
    6. Li W,
    7. Lopez R,
    8. McWilliam H,
    9. Remmert M,
    10. Söding J,
    11. Thompson JD,
    12. Higgins DG
    . 2014. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. doi:10.1038/msb.2011.75.
    OpenUrlCrossRef
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Complete Genome Sequence of Rice Tungro Bacilliform Virus Infecting Asian Rice (Oryza sativa) in Malaysia
Maathavi Kannan, Maisarah Mohamad Saad, Noraini Talip, Syarul Nataqain Baharum, Hamidun Bunawan
Microbiology Resource Announcements May 2019, 8 (20) e00262-19; DOI: 10.1128/MRA.00262-19

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Complete Genome Sequence of Rice Tungro Bacilliform Virus Infecting Asian Rice (Oryza sativa) in Malaysia
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Complete Genome Sequence of Rice Tungro Bacilliform Virus Infecting Asian Rice (Oryza sativa) in Malaysia
Maathavi Kannan, Maisarah Mohamad Saad, Noraini Talip, Syarul Nataqain Baharum, Hamidun Bunawan
Microbiology Resource Announcements May 2019, 8 (20) e00262-19; DOI: 10.1128/MRA.00262-19
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENT
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X