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本文件收录经三种不同检索方式鉴定得到的物种名称列表，该数据为综述中的表3提供支撑。 检索1：从PubMed数据库中获取标题包含"PV"或类似表述（如相变异（phase variable））的出版物摘要，随后通过R脚本从文本中提取物种名称。 检索2：借助PhaseFinder工具，从Jiang等学者的研究补充材料中提取物种名称。该程序用于在54875个细菌基因组中检索侧翼带有重复序列的可逆基因间区。参考文献：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. 检索3：从Mrazek等学者的研究补充材料中提取物种名称。Mrazek等人定义的长简单序列重复（Long Simple Sequence Repeats, LSSR）为：重复单元长度为k、总长度超过基于随机模型推导的截断值的简单序列重复，该定义可复现关键基因组序列指标。本数据集通过检索378个原核生物基因组中的此类重复序列构建得到。参考文献：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