A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes

ABSTRACT

Insertion Sequences (ISs) are mobile pieces of DNA that are widespread in bacterial genomes. IS movements typically involve (i) excision of the IS element, (ii) cutting of the target site DNA, and (iii) IS element insertion. This process generates a new copy of the IS element, and a short duplication at the target site. It has been noted that for some extant IS element copies there are no Target Site Duplication (TSD) readily identifiable. The absence of TSDs has been attributed to degeneration of the TSD at some point after the insertion event, recombination between identical insertion sequences, or adjacent deletions. Indeed, the latter two - recombination between IS copies and adjacent deletions - are frequent causes for the absence of TSDs, which we demonstrate here in an analysis of genome sequence data from the Lenski long term evolution experiment. Furthermore, we propose that some IS movement events – namely, those that occur in association with large-scale genome rearrangements – do not generate TSDs, and occur without evidence for recombination between IS copies or adjacent deletions. In support of this hypothesis, we provide two direct, empirical observations of such IS transposition events: an IS481 movement occurring with a large duplication in Pseudomonas fluorescens SBW25, and an IS5 movement plus a large deletion in Escherichia coli C. Although unlikely, it is possible that the observed deletion and associated IS movement may have occurred in two successive events in a single overnight culture a novel insertion followed by an adjacent deletion. However, the presence of an IS at the center of a large-scale duplication is not readily explained, and suggests that IS element activity may not only cause large-scale deletions, but may also affect the likelihood of duplications. 

REPOSITORY CONTENTS

This entry contains additional raw data and background information for the manuscript entitled: A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes

01_SBW25_Dup_IS: contains the background files for work on the SBW25-Dup-IS strain, including:- electrophoresis gel images- genome sequencing data and analysis files- junction sequence files and Sanger sequencing traces- stability test R code and output

02_Ec_Del_IS: contains the background files for work on the Ec-Del-IS strain, including:- electrophoresis gel images- genome sequencing data and analysis files- junction sequence files and Sanger sequencing traces

03_LTEE: contains the background files for work on 3x LTEE populations (at 60,000 generations), including:- raw sequencing reads (downloaded from NCBI BioProject database; accession number PRJNA380528)- breseq output for Ara-3, Ara-6, and Ara+1 populations- reference alignment file (NCBI RefSeq NC_012967.1)