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

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.

Dermatopathology of Orf Virus (Malaysian Isolates) in Mice Experimentally Inoculated at Different Sites with and without Dexamethasone Administration

“…This method is recommended for proper detection and identification of pathogens by using specific gene; hence this successful confirmation of positive cases by PCR agrees with [ 21 , 44 , 45 ] whom both in separate studies confirmed CE virus detection by using major genes essential for orf virus replication. An amplified gene product can be used as important genetic materials for further genetic analysis and gene expression studies [ 46 – 49 ] especially for their gene functions. This approach has been adopted for studies on other viruses such as herpes viruses, bacteria, and fungi (Balakrishnan et al, 2017 [ 50 ]).…”

Comparative Genomics of Domesticated and Wild Sunflower: Complete Chloroplast and Mitochondrial Genomes

“…Whole Genome Sequencing (WGS) is now a common technique in contemporary plant research (Balakrishnan et al, 2015). WGS provides an opportunity to investigate nucleotide diversity much faster and more accurate than hybridization-based methods (molecular beacons, microarrays etc.…”