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

摘要

> >Next generation sequencingtechnologies has revolutionized genomic research by producing a large volume ofsequence data and lowest per base cost compared to the traditional sangermethod. Although this technology offers many advantages, gap occurrences arecommonly found in draft assemblies. The sameproblem was observed with Rat Cytomegalovirus (RCMV) ALL-03 (Malaysia strain),where a complete genome sequence could not produce the complete genome due tothe presence of gaps in the draft genome. This restrains our ability to takefull advantage of genome data. This study aimed to identify the sequence datapresent in the gap regions and close these gaps in order to produce a completegenome sequence for RCMV ALL-03. Twenty sets of specific primers were designedbetween two adjacent contigs and PCR was carried out to obtain the appropriatesequences in respective gap regions. Sanger sequencing was employed in the PCRproduct to get the gap sequences. Out of the five identified gaps in the RCMVALL-03 genome sequence, only three were confirmed to be true gaps, while theother two were due to sequence repeats. In conclusion, all the gaps were closedsuccessfully and complete genome sequence of RCMV ALL-03 can now be explored infurther studies.