Supplementary data for the paper "Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance", Microbial Genomics, 2020
Creators: name: Leyn, Semen
name: Zlamal, Jaime E.
name: Kurnasov, Oleg
name: Xiaoqing Li
name: Elane, Marinela
name: Myjak, Lourdes
name: Godzik, Mikolaj
name: Crecy, Alban De
name: Garcia-Alcalde, Fernando
name: Ebeling, Martin
Publisher: name: figshare
Year: 2021
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Supplementary Figure S1. Apparent “population-wide” IC90 values were determined by a standard growth curve method and presented as fold-change in comparison to IC90 of the unevolved culture shown as dashed line.<br>Supplementary Figure S2. CFU analysis of collected sample of evolving populations. Cells show percent of colonies grown on agar plates at different TCS concentrations as compared to the counts of colonies from the same sample grown in the absence of TCS. Note that the observed MIC of the unevolved culture in LB agar plates (0.15 uM) was ~ 5-fold lower than in liquid culture (possibly due to “inoculum effect”).<br>Supplementary Figure S3. Correlation of FimE L65Q mutation and fim switch in ON position frequencies. Each dot represents one sample. Line is a linear regression. 95% confidence interval is shown as a shaded area.<br>Supplementary Figure S4. A homology-based model of FimE 3D structure was built using E.coli BW25113 FimE amino acid sequence (BW25113_4313) with Phyre2 server (1) (coverage 92%; confidence 100%). Residues forming FimE active site are colored green (2) and the mutated L65 residue is colored red.<br>Supplementary Figure S5. IC90 values for mutants isolated from the early stage of evolution.<br>Supplementary Figure S6. IC90 for FabI mutant isolates that possess single FabI mutation or FabI mutation supplemented by secondary mutations. 95% confidence intervals shown by error bars.<br>Table S1. Sequencing metrics of bacterial population samples: mean coverage, fraction of mapped reads, number of reads and median insertion size.<br> Table S2. List of IS elements found by BLASTn of the <i>E. coli</i> BW25113 reference genome against ISfinder database. The list was used to estimate IS element rearrangement frequencies by iJump tool.<br> Table S3. Observed variant frequencies estimation in the 25 samples that represent four time points collected from the six reactors and unevolved culture. The SNPs, small InDels and IS elements rearrangements are shown.<br> Table S4. Mutations in the unevolved population of <i>E. coli</i> BW25113 D<i>uxaC::kan</i>. Annotations shown according to the PATRIC database.<br>Table S5. Primers used for PCR amplification of selected genomic loci for Sanger sequencing.<br>Table S6. Clone selection for Sanger sequencing and sequencing results.<br> Table S7. Comparison of observed and known mechanisms of TCS resistance.<br>Supplementary methods S1. Description of NGS data processing software and post-processing filtering.<br>References:(1) Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. 2015. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10:845-58. (2) Smith SG, Dorman CJ. 1999. Functional analysis of the FimE integrase of Escherichia coli K-12: isolation of mutant derivatives with altered DNA inversion preferences. Mol Microbiol 34:965-79.