April 2021, updated July 2021, updated September 2021
Full analysis scripts associated with this raw data can be found at github.com/jpjh/COMPMUT.
Now published in PLoS Biology:
Hall, J. P. J., Wright, R. C. T., Harrison, E., Muddiman, K. J., Jamie Wood, A., Paterson, S., & Brockhurst, M. A. (2021). Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. PLoS Biology, 19(10), e3001225. https://doi.org/10.1371/journal.pbio.3001225
COMPMUT_exp_data_1.csv. Competition data from knockout strains. Columns indicate experimental replicate (experiment), transconjugant replicate (replicate), host genotype (host), plasmid variant (plasmid), whether measurement was from the start or the end of the competition (timepoint), dilution factor (dilution), volume spread in µl (spread) and the counts of white and blue colonies on that plate (count_white, count_blue).COMPMUT_exp_data_2.csv. Competition data from plasmid mutants. Columns are the same as for COMPMUT_exp_data_1.csv, except marker indicates the antibiotic marker used in the plasmid-bearing strain. Gm = gentamicin-resistant, Sm = streptomycin resistant.COMPMUT_exp_data_3.csv. Competition data from knockouts and plasmid mutants. Columns are the same as COMPMUT_exp_data_1.csv.COMPMUT_exp_data_3-1.csv. Conjugation data from knockouts and plasmid mutants. Columns are the same as from COMPMUT_exp_data_1.csv except recipient refers to the species of the recipient (Pf = P. fluorescens, Pp = P. putida), and timepoint explains not only whether the plate contained start or end counts, but also what it was selecting for (DR = donors and recipients, T = transconjugants). COMPMUT_exp_data_4.csv. Competition data from expressing PQBR57_0059 variants in trans. Columns are the same as COMPMUT_exp_data_1.csv , except exp_rep refers to experimental replicate and tc_rep refers to transconjugant replicate. plasmid_pucp refers to the PQBR57_0059 allele on the pUCP18 variant, whereas plasmid_pq refers to the pQBR57 variant.COMPMUT_exp_data_5.csv. Competition data from expressing pQBR57 par genes in trans alongside pQBR57. Columns are the same as COMPMUT_exp_data_4.csv . COMPMUT_exp_data_5-1.csv is similar but from expressing alongside pQBR103.COMPMUT_exp_data_6.csv. Count data from medium-term cultures of different plasmid variants in soil. Data was collected by selective plating and replica plating. replicate indicates different transconjugants; variant is an abbreviated name referring to the population from which the clone came; marker indicates the antibiotic marker of the plasmid-bearing strain (Gm = plasmid initially in the gentamicin-resistant background; Sm = plasmid initially in the streptomycin-resistant lacZ background); media indicates the selective media (KB = no antibiotics, Gm3 = gentamicin at 3 µg/ml, Sm50 = streptomycin at 50 µg/ml); dilution indicates the dilution factor; spread indicates the volume spread in µl; count_white indicates the number of white (gentamicin-resistant) colonies; count_blue indicates the number of blue (streptomycin-resistant) colonies; hg_kept indicates the number of colonies from the originally-plasmid-free strain that had become mercury resistant; hg_lost indicates the number of colonies from the originally-plasmid-bearing strain that had become mercury sensitive.COMPMUT_exp_data_7.csv. Growth curve data. exp refers to the plate in which the experiment was performed; well refers to plate well; cycle is the measurement cycle; time is time in seconds; t_rep is transformant replicate; exp_rep is experimental replicate; pME6032 is the insert (if any); IPTG is IPTG concentration (0 µM or 100 µM); OD600_corr is the corrected OD600 (OD600 minus the mean blank well measurement).COMPMUT_exp_data_8.csv. pQBR57 par segregation data. code is a shorthand for each experimental condition, timepoint is transfer number, replicate is independent transconjugant/transformant replicate, par is whether pUCP18 was empty or whether it carried pQBR57 par, plasmid is whether it carried pQBR57 or pQBR103, spread is volume of dilution spread on plate, dilution is (log10) dilution factor), count is total colonies counted, count_hgs is sensitive colonies as assessed by replica plating.COMPMUT_exp_data_9.csv. Ectopic PFLU4242 expression in ∆gacS strains growth curve data. well is the well in the plate, cycle is measurement cycle (measurements taken every 15 mins), replicate is independent transformant/transconjugant replicate, pME6032 is whether pME6032 was empty or whether it carried PFLU4242, plasmid is the pQBR plasmid carried, IPTG is whether or not cells were induced with IPTG, OD600_corr is the OD600 reading for that well, with blank values subtracted.COMPMUT_RNAseq_1_de_table_chr_vanc.csv. Differential expression of chromosomal genes relative to the plasmid-free, unameliorated ancestral strain, as determined by edgeR. Data is in 'wide' format, with rows referring to PFLU locus tags, and columns referring to each treatment. For each treatment, there is a column for log2 fold-change (logFC), log2 counts-per-million-per-gene (logCPM), test statistic for the quasi-likelihood F test (F), associated p-value (PValue), and Benjamini-Hochberg adjusted p-value (FDR). COMPMUT_RNAseq_2_de_table_chr_vanc.csv. Differential expression of chromosomal genes relative to the plasmid-bearing, unameliorated ancestral strain, as determined by edgeR. Columns are similar to COMPMUT_RNAseq_1_de_table_chr_vanc.csv.COMPMUT_RNAseq_3_de_table_pQ57.csv. Differential expression of pQBR57 genes, relative to the unameliorated condition. Columns are similar to COMPMUT_RNAseq_1_de_table_chr_vanc.csv.COMPMUT_RNAseq_4_de_table_pQ103.csv. Differential expression of pQBR103 genes, relative to the unameliorated condition. Columns are similar to COMPMUT_RNAseq_1_de_table_chr_vanc.csv.COMPMUT_RNAseq_5_tpm.csv. Table with values of mean transcripts-per-million (TPM) for each gene, averaged over replicates. Column pc refers to whether the gene is on the plasmid (pla) or chromsome (chr); amelioration refers to the amelioration; plasmid refers to the plasmid, trt is a code referring to the combination of plasmid and amelioration; locus_tag refers to the locus tag for the corresponding GenBank file; group is a combination of the amelioration and plasmid columns; tpm is mean transcripts-per-million across replicates; n gives number of replicates; se is standard error; ci is 95% confidence intervals; and log2tpm is a log2 transformation of tpm.COMPMUT_mutations.csv. Compensatory mutations aggregated from published studies. Note: data was not available for all columns for all mutations. COMPMUT_RsmA_prediction.txt. Predicted RsmA binding sites in the P. fluorescens SBW25 chromosome. Output from running the script CSRA_TARGET.pl from Kulkarni et al. 2014.