Closing the Gaps in Rat Cytomegalovirus ALL-03 (Malaysian Strain) Genomic Scaffold
Krishnan Nair Balakrishnan, Ashwaq Ahmed Abdullah, Yusuf Abba, Jamilu Abubakar Bala, Faez Firdaus Jesse Abdullah, Farina Mustaffa Kamal, Zeenathul Allaudin Nazariah, Ideris Aini, Noordin Mohamed Mustapha and Mohd Azmi Mohd Lila
DOI : 10.3844/ajavsp.2015.133.140
American Journal of Animal and Veterinary Sciences
Volume 10, Issue 3
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 Rat Cytomegalovirus (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.
© 2015 Krishnan Nair Balakrishnan, Ashwaq Ahmed Abdullah, Yusuf Abba, Jamilu Abubakar Bala, Faez Firdaus Jesse Abdullah, Farina Mustaffa Kamal, Zeenathul Allaudin Nazariah, Ideris Aini, Noordin Mohamed Mustapha and Mohd Azmi Mohd Lila. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.