RT Journal Article
SR Electronic
T1 Identification and analysis of integrons and cassette arrays in bacterial genomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 030866
DO 10.1101/030866
A1 Jean Cury
A1 Thomas Jové
A1 Marie Touchon
A1 Bertrand Néron
A1 Eduardo PC Rocha
YR 2016
UL http://biorxiv.org/content/early/2016/04/26/030866.abstract
AB Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program – IntegronFinder – to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attl site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.