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Closing the gaps in rat cytomegalovirus ALL-03 (Malaysian strain) genomic scaffold


Balakrishnan, Krishnan Nair and Abdullah, Ashwaq Ahmed and Abba, Yusuf and Bala, Jamilu Abubakar and Abdullah, Faez Firdaus Jesse and Mustaffa Kamal, Farina and Allaudin, Zeenathul Nazariah and Ideris, Aini and Mohamed Mustapha, Noordin and Mohd Lila, Mohd Azmi (2015) Closing the gaps in rat cytomegalovirus ALL-03 (Malaysian strain) genomic scaffold. American Journal of Animal and Veterinary Sciences, 10 (3). pp. 133-140. ISSN 1557-4555; ESSN: 1557-4563


Next generation sequencing technologies has revolutionized genomic research by producing a large volume of sequence data and lowest per base cost compared to the traditional sanger method. Although this technology offers many advantages, gap occurrences are commonly found in draft assemblies. The same problem was observed with RatCytomegalovirus (RCMV) ALL-03 (Malaysia strain), where a complete genome sequence could not produce the complete genome due to the presence of gaps in the draft genome. This restrains our ability to take full advantage of genome data. This study aimed to identify the sequence data present in the gap regions and close these gaps in order to produce a complete genome sequence for RCMV ALL-03. Twenty sets of specific primers were designed between two adjacent contigs and PCR was carried out to obtain the appropriate sequences in respective gap regions. Sanger sequencing was employed in the PCR product to get the gap sequences. Out of the five identified gaps in the RCMV ALL-03 genome sequence, only three were confirmed to be true gaps, while the other two were due to sequence repeats. In conclusion, all the gaps were closed successfully and complete genome sequence of RCMV ALL-03 can now be explored in further studies.

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Additional Metadata

Item Type: Article
Divisions: Faculty of Veterinary Medicine
Institute of Bioscience
DOI Number: https://doi.org/10.3844/ajavsp.2015.133.140
Publisher: Science Publications
Keywords: Cytomegalovirus; Genome; Next generation sequencing; PCR; Sanger sequencing
Depositing User: Nabilah Mustapa
Date Deposited: 08 Apr 2016 01:34
Last Modified: 08 Apr 2016 01:34
Altmetrics: http://www.altmetric.com/details.php?domain=psasir.upm.edu.my&doi=10.3844/ajavsp.2015.133.140
URI: http://psasir.upm.edu.my/id/eprint/16503
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