100+ years of phase variation: – the premier bacterial bet-hedging phenomenon - review for Microbiology - data file

This file contains the list of species names identified by three different searches. This data underpins Table 3 in the review.

Search 1 was :-Abstracts were obtained from PubMed for publications with titles containing ‘PV’ or similar phrasing (e.g. phase variable) with species names extracted from the text using an R script.

Search 2:- species names were extracted from supplementary information provided as part of Jiang et al. study using PhaseFinder. This program was used to search 54 875 bacterial genomes for invertible intergenic regions flanked by repeats. Jiang X, Hall AB, Arthur TD, Plichta DR, Covington CT, et al. Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. Science 2019;363:181–187. 10.1126/science.aau5238.

Search 3:- species names were extracted from supplementary information provided as part of Mrazek et al. Long simple sequence repeats (LSSR), as published by Mrazek et al., are defined as SSRs of repeat length k whose total length exceeds a cutoff derived from a random model, which reproduces key genomic sequence metrics. This latter dataset was generated from a search of 378 prokaryotic genomes for these repeats. Mrázek J, Guo X, Shah A. Simple sequence repeats in prokaryotic genomes. Proc Natl Acad Sci USA 2007;104:8472–8477. 10.1073/pnas.0702412104