Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins

Vale, Filipa F. and Nunes, Alexandra and Oleastro, Mónica and Gomes, João P. and Sampaio, Daniel A. and Rocha, Raquel and Vítor, Jorge M. B. and Engstrand, Lars and Pascoe, Ben and Berthenet, Elvire and Sheppard, Samuel K. and Hitchings, Matthew D. and Mégraud, Francis and Vadivelu, Jamuna and Lehours, Philippe (2017) Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins. Scientific Reports, 7 (1). p. 42471. ISSN 2045-2322, DOI

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Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6-33.0 Kbp, consisting of 27-39 open reading frames. A 36.6% GC was found in prophages in contrast to 39% in H. pylori genome. Remarkably a conserved integration site was found in over 50% of the cases. Nearly 40% of the prophages harbored insertion sequences (IS) previously described in H. pylori. Tandem repeats were frequently found in the intergenic region between the prophage at the 3′ end and the bacterial gene. Furthermore, prophage genomes present a robust phylogeographic pattern, revealing four distinct clusters: one African, one Asian and two European prophage populations. Evidence of recombination was detected within the genome of some prophages, resulting in genome mosaics composed by different populations, which may yield additional H. pylori phenotypes.

Item Type: Article
Uncontrolled Keywords: Genome, Viral; Genomics; Helicobacter pylori; Mosaicism; Mutagenesis, Insertional; Open Reading Frames; Phylogeny; Prophages; Sequence Analysis, DNA
Subjects: R Medicine
Divisions: Faculty of Medicine
Depositing User: Ms. Juhaida Abd Rahim
Date Deposited: 26 Oct 2019 03:56
Last Modified: 26 Oct 2019 03:56

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