Application of systems biology approach for investigation of pan genome and phylogenetics in various strains of anaplasma phagocytophilum

Pallavi Singh, Dipanshi Verma

Application of systems biology approach for investigation of pan genome and phylogenetics in various strains of anaplasma phagocytophilum

Číslo: 3/2020/2021
Periodikum: Journal of Microbiology, Biotechnology and Food Sciences
DOI: 10.15414/jmbfs.2020.10.3.445-448

Klíčová slova: Anaplasma phagocytophilum, pan genome, core genome, ClustAGE, SPINE

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Anotace: Anaplasma phagocytophilum, has been observed as an emerging human pathogen of public health importance and is commonly transmitted to humans by tick bites. The bacterium Anaplasma phagocytophilum has been known from decades to cause the disease, tick-borne fever (TBF) in domestic ruminants and cattles in various areas in northern Europe, China, Russian border and United Kingdom. In recent years, outbreak of A.phagocytophilum infection has enhanced multifold and is widely reported in I. persulcatus and engorged as D. silvarum ticks in north eastern regions of China. However, few genome sequences have been completed so far, thus observations on biological, ecological, and pathological differences between genotypes of this bacterium,are yet to be elucidated by molecular and experimental infection studies.

In our current work, We have investigated 4 completely sequenced Genomic strains of A.phagocytophilum using various insilico tools SPINE and AGENT to characterize the percentage of Core Genome, Accessory genome and Pan Genome of these species. Further, we have tried to characterize the serotype and find the resistance genes observed in these four strains using MLST and ResFinder tools available at centre of Genetic epidemiology, Denmark Technical University server. By application of ClustAGE tool, we have made a comparative assessment of accessory genes across these strains. Heatmaps using expression map of these 4 genomes was constructed to infer the conserved genes and variable genes across these strains. Our study led to conclusion that core genome across these strains varies from 1.43 Mbps to 1.47 Mbps and accessory genomes varies from 0.0410 Mbps to 0.0734 Mbps. Comparison of the Gene clusters led to conclusion that gene clusters led to core genome value of 318 and Pan Genome value of 1035. Our analysis characterizes the dominance of accessory genes during evolution of Anaplasma phagocytophilum and lesser conservation of genes as there is a phylogenetic variation observed.