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.
Highlights
Cytomegalovirus (CMV), an important pathogen belongs to the betaherpesviruses subfamily of herpesviruses, which infects many living organisms including humans (Weller, 1971)
Confluent cells were infected with Rat Cytomegalovirus (RCMV) ALL-03 and frequently observed for morphological changes known as Cytopathic Effect (CPE)
About 5 gaps have been identified and each gap is located at different position with different sizes in draft genome
Summary
Cytomegalovirus (CMV), an important pathogen belongs to the betaherpesviruses subfamily of herpesviruses, which infects many living organisms including humans (Weller, 1971). CMV causes acute, persistent and latent infections in human and animal population but remain asymptomatic in healthy individuals. This virus can cause significant morbidity and mortality in immunocompromised and immunosuppresed patients, such as AIDS patients and organ transplant recipients, respectively (Livingston et al, 2001; Scalzo et al, 2009). A new strain of RCMV strain ALL-03, acquired from the uterus and placenta of the Rattus rattus diaardi (house rat) (Loh et al, 2003), confirms the ability of this strains’ vertical transmission in pregnant rats This ability of the virus makes it an appropriate model of choice to study the congenital infection of CMV in humans.
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