Abstract
Background: Vibrio cholerae, the etiologic agent of cholera, is indigenous to aquatic environments. The V. cholerae genome consists of two chromosomes; the smallest of these harbors a large gene capture and excision system called the superintegron (SI), of ~120 kbp. The flexible nature of the SI that results from gene cassette capture, deletion and rearrangement is thought to make it a hotspot of V. cholerae diversity, but beyond the basic structure it is not clear if there is a core genome in the SI and if so how it is structured. The aim of this study was to explore the core genome structure and the differences in gene content among strains of V. cholerae. Methods: From the complete genomes of seven V. cholerae and one Vibrio mimicus representative strains, we recovered the SI sequences based on the locations of the structural gene IntI4 and the V. cholerae repeats. Analysis of the pangenome, including cluster analysis of functional genes, pangenome profile analysis, genetic variation analysis of functional genes, strain evolution analysis and function enrichment analysis of gene clusters, was performed using a pangenome analysis pipeline in addition to the R scripts, splitsTree4 and genoPlotR. Results and conclusions: Here, we reveal the genetic architecture of the V. cholerae SI. It contains eight core genes when V. mimicus is included and 21 core genes when only V. cholerae strains are considered; many of them are present in several copies. The V. cholerae SI has an open pangenome, which means that V. cholerae may be able to import new gene cassettes to SI. The set of dispensable SI genes is influenced by the niche and type species. The core genes are distributed along the SI, apparently without a position effect.
Highlights
Vibrio cholerae is a diverse, environmental, gram-negative bacterial species that can be pathogenic and can cause cholera, a severe diarrheal disease that occurs most frequently in epidemic form[1,2]
The gene content was converted to a presence/ absence (0/1) matrix and the core, dispensable and unique genes were identified by in-house R scripts
SI regions were extracted from the seven V. cholerae and one V. mimicus genomes (Table 1)
Summary
Vibrio cholerae is a diverse, environmental, gram-negative bacterial species that can be pathogenic and can cause cholera, a severe diarrheal disease that occurs most frequently in epidemic form[1,2]. The 1.07 Mbp small chromosome contains few essential genes and the superintegron (SI), a large gene capture and excision system of ~120 kbp[2] (Figure 1). The V. cholerae genome consists of two chromosomes; the smallest of these harbors a large gene capture and excision system called the superintegron (SI), of ~120 kbp. Methods: From the complete genomes of seven V. cholerae and one Vibrio mimicus representative strains, we recovered the SI sequences based on the locations of the structural gene IntI4 and the V. cholerae repeats. Results and conclusions: Here, we reveal the genetic architecture of the V. cholerae SI It contains eight core genes when V. mimicus is included and 21 core genes when only V. cholerae strains are considered; many of them are present in several copies. The core genes are distributed along the SI, apparently without a position effect
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