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COMPMUT_index.md

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Compensatory mutations manuscript: Index page

jpjh compiled Mar 2021, edited Jul 2021

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

Experimental measurements of relative fitness, plasmid cost, etc

  1. Knockout fitness (COMPMUT_exp_1_knockouts.Rmd)
  2. Plasmid mutant fitness (COMPMUT_exp_2_plasmids.Rmd)
  3. Knockout and plasmid mutant fitness (COMPMUT_exp_3_knopla.Rmd)
  4. Fitness of strains expressing of PQBR57_0059 variants in trans (COMPMUT_exp_4_PQ57-59.Rmd)
  5. Fitness and segregation of strains expressing of par genes in trans (COMPMUT_exp_5_par.Rmd)
  6. Dynamics of plasmid-bearing strains in the medium term (COMPMUT_exp_6_dynamics.Rmd)
  7. Growth curve experiments from expression of plasmid-upregulated genes (COMPMUT_exp_7_growthcurves.Rmd)
  8. Growth curve experiments from expression of PFLU4242 in ∆gacS background (COMPMUT_exp_8_growth_gac_4242.Rmd)

RNAseq analysis

  1. Quality control and overview analyses (COMPMUT_RNAseq_1_QC.Rmd)
  2. Alignment of reads to reference sequences (COMPMUT_RNAseq_2_Alignment.Rmd)
  3. Counting of reads mapping to features using Rsubread featurecounts (COMPMUT_RNAseq_3_Rsubread.Rmd)
  4. Analysing differential expression with edgeR (COMPMUT_RNAseq_4_edgeR.Rmd)
  5. Preparing files with gene information (COMPMUT_RNAseq_5_gene_info.Rmd)
  6. Analysis of differential expression: Chromosomal differential expression (COMPMUT_RNAseq_6a_analysis.Rmd). pQBR57 differential expression (COMPMUT_RNAseq_6b_analysis.Rmd). pQBR103 differential expression (COMPMUT_RNAseq_6c_analysis.Rmd)
  7. Identification of SOS-associated genes (COMPMUT_RNAseq_7_lexA.Rmd)

Compensatory mutations from previous studies

  1. Compensatory mutations (COMPMUT_seqs_1_compmuts.Rmd)