Research Article Open Access

Closing the Gaps in Rat Cytomegalovirus ALL-03 (Malaysian Strain) Genomic Scaffold

Krishnan Nair Balakrishnan1, Ashwaq Ahmed Abdullah2, Yusuf Abba1, Jamilu Abubakar Bala1, Faez Firdaus Jesse Abdullah1, Farina Mustaffa Kamal1, Zeenathul Allaudin Nazariah1, Ideris Aini1, Noordin Mohamed Mustapha1 and Mohd Azmi Mohd Lila1
  • 1 Universiti Putra Malaysia, Malaysia
  • 2 University Putra Malaysia, Malaysia
American Journal of Animal and Veterinary Sciences
Volume 10 No. 3, 2015, 133-140

DOI: https://doi.org/10.3844/ajavsp.2015.133.140

Submitted On: 25 March 2015 Published On: 8 June 2015

How to Cite: Balakrishnan, K. N., Abdullah, A. A., Abba, Y., Bala, J. A., Jesse Abdullah, F. F., Kamal, F. M., Nazariah, Z. A., Aini, I., Mustapha, N. M. & Mohd Lila, M. A. (2015). Closing the Gaps in Rat Cytomegalovirus ALL-03 (Malaysian Strain) Genomic Scaffold. American Journal of Animal and Veterinary Sciences, 10(3), 133-140. https://doi.org/10.3844/ajavsp.2015.133.140

Abstract

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.

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Keywords

  • Next Generation Sequencing
  • Cytomegalovirus
  • Sanger Sequencing
  • Genome
  • PCR