Transposon insertion mapping with PIMMS - Pragmatic Insertional Mutation Mapping System

CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data

Summary

Sequencing of transposon insertion libraries is used to determine the relative fitness of individual mutants at a large scale. However, there is a lack of tools for specifically analyzing data from such experiments with paired sample designs. Here, we introduce CAFE—Coefficient-based Analysis of Fitness by read Enrichment—a software package that can analyze data from paired transposon mutant sequencing experiments, generate fitness coefficients for each gene and condition and perform appropriate statistical testing on these fitness coefficients.

Availability and implementation

CAFE is implemented in Perl and R. The source code is freely available for download under the MIT License from https://github.com/bengtssonpalme/cafe and http://microbiology.se/software/cafe/

Supplementary information

Supplementary data are available at Bioinformatics online.

PIMMS (Pragmatic Insertional Mutation Mapping System) Laboratory Methodology a Readily Accessible Tool for Identification of Essential Genes in Streptococcus

The Pragmatic Insertional Mutation Mapping (PIMMS) laboratory protocol was developed alongside various bioinformatics packages (Blanchard et al., 2015) to enable detection of essential and conditionally essential genes in Streptococcus and related bacteria. This extended the methodology commonly used to locate insertional mutations in individual mutants to the analysis of mutations in populations of bacteria. In Streptococcus uberis, a pyogenic Streptococcus associated with intramammary infection and mastitis in ruminants, the mutagen pGhost9:ISS1 was shown to integrate across the entire genome. Analysis of >80,000 mutations revealed 196 coding sequences, which were not be mutated and a further 67 where mutation only occurred beyond the 90th percentile of the coding sequence. These sequences showed good concordance with sequences within the database of essential genes and typically matched sequences known to be associated with basic cellular functions. Due to the broad utility of this mutagen and the simplicity of the methodology it is anticipated that PIMMS will be of value to a wide range of laboratories in functional genomic analysis of a wide range of Gram positive bacteria (Streptococcus, Enterococcus, and Lactococcus) of medical, veterinary, and industrial significance.