Marin Michel A, Vicente Ana Carolina P
Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute (IOC), Rio de Janeiro, 4365, PO Box 926 CEP 21045-900, Brazil.
F1000Res. 2013 Feb 27;2:63. doi: 10.12688/f1000research.2-63.v1. eCollection 2013.
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.
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.
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.
霍乱弧菌是霍乱的病原体，原产于水生环境。霍乱弧菌基因组由两条染色体组成；其中最小的一条含有一个约120千碱基对的大型基因捕获和切除系统，称为超级整合子（SI）。由于基因盒的捕获、缺失和重排，超级整合子具有灵活的性质，这被认为使其成为霍乱弧菌多样性的热点，但除了基本结构外，尚不清楚超级整合子中是否存在核心基因组，如果存在，其结构如何。本研究的目的是探索霍乱弧菌菌株的核心基因组结构以及基因含量的差异。
从七株霍乱弧菌和一株副溶血弧菌代表性菌株的完整基因组中，我们根据结构基因IntI4的位置和霍乱弧菌重复序列回收了超级整合子序列。除了使用R脚本、splitsTree4和genoPlotR外，还使用泛基因组分析管道对泛基因组进行了分析，包括功能基因的聚类分析、泛基因组图谱分析、功能基因的遗传变异分析、菌株进化分析和基因簇的功能富集分析。
在此，我们揭示了霍乱弧菌超级整合子的遗传结构。当包括副溶血弧菌时，它包含八个核心基因；当仅考虑霍乱弧菌菌株时，包含21个核心基因；其中许多基因有多个拷贝。霍乱弧菌超级整合子具有开放的泛基因组，这意味着霍乱弧菌可能能够将新的基因盒导入超级整合子。可缺失的超级整合子基因集受生态位和物种类型的影响。核心基因沿超级整合子分布，显然没有位置效应。
