Article
Open Access
Volume 2 · Issue 3 · 2022
pp. 126–135
In silico Molecular Characterization of Helicobacter pylori based on Tandem Repeat Number and 16S rRNA gene
Arijit Sankar Mondal1, Ritu Sharma1, Arunava Das2, Ashish Warghane2
1
Department of Microbiology, Guru Nanak Institute of Pharmaceutical Science and Technology (Life Science), Kolkata, West Bengal, India
2
Faculty of Life Sciences, Mandsaur University, Mandsaur, Madhya Pradesh, India
Abstract
Objectives: Helicobacter pylori is the major cause of gastrointestinal carcinoma. The presence of tandem repeats are mainly responsible for increasing the mutation rate, thereby enhancing the virulence and adaptation of the pathogen to its host. Similarly, 16S ribosomal RNA sequence analysis has been widely used for determining the phylogenetic and taxonomic classification of bacterial strains.
Methods: The sequences of H. pylori were retrieved from GenBank, the National Centre for Biotechnology Information database, in order to identify specific tandem repeats. In our study, the genomic instability in H. pylori due to the presence of consecutive and non-consecutive sequences has been comparatively analyzed using MEGA X software, with consecutive sequences representing the tandem repeats.
Results: Based on the occurrence of Tandem repeats in the retrieved isolates of H. pylori, the consecutive sequences were classified into four different classes (Class I-IV). Further, the tandem repeat and 16S rRNA sequences were classified using phylogenetic analysis into two different clades for determining species variability and evolutionary relationships, respectively.
Conclusion: The data obtained from this study can be used to characterize different H. pylori strains, gain a better understanding of its genome variability leading to a higher mutation rate and depict the intra-species evolutionary relationship.
Methods: The sequences of H. pylori were retrieved from GenBank, the National Centre for Biotechnology Information database, in order to identify specific tandem repeats. In our study, the genomic instability in H. pylori due to the presence of consecutive and non-consecutive sequences has been comparatively analyzed using MEGA X software, with consecutive sequences representing the tandem repeats.
Results: Based on the occurrence of Tandem repeats in the retrieved isolates of H. pylori, the consecutive sequences were classified into four different classes (Class I-IV). Further, the tandem repeat and 16S rRNA sequences were classified using phylogenetic analysis into two different clades for determining species variability and evolutionary relationships, respectively.
Conclusion: The data obtained from this study can be used to characterize different H. pylori strains, gain a better understanding of its genome variability leading to a higher mutation rate and depict the intra-species evolutionary relationship.
Keywords: Tandem repeats, 16S rRNA, Helicobacter pylori, Mutation, Pathogenesis, Phylogenetic analysis
