Pyoverdine reads are available on Dryad at DOI: https://doi.org/10.5061/dryad.6963pj3, and were used to identify isolates with increased pyoverdine production, as presented in Appendix 1-Fig. 1 and Fig. 1. Sequencing data is previously published and available from GenBank. The mutation lists for the isolates from the Children's collection from Marvig et al., 2015, can be downloaded from https://www.nature.com/articles/ng.3148#supplementary-information. The mutation list for the transmissible clone type DK1 from Markussen et al., 2014, can be downloaded from https://mbio.asm.org/content/mbio/5/5/e01592-14/DC1/embed/inline-supplementary-material-1.pdf. The mutation lists for the transmissible clone type DK2 from Marvig et al., 2013, can be downloaded from https://doi.org/10.1371/journal.pgen.1003741.s009 and https://doi.org/10.1371/journal.pgen.1003741.s010. Datasets S03 and S04 from Andersen et al, 2015, with lists of mutations in the pyoverdine system, are downloadable from http://www.pnas.org/content/112/34/10756/tab-figures-data#fig-data-tables. The raw reads and mutation lists were used to identify mutations in five iron uptake systems, as presented in Supplementary Table 1C and D. Table S03 from Yang et al., 2011, is downloadable from http://www.pnas.org/content/108/18/7481/tab-figures-data, and was used to estimate the number of generations that Pseudomonas aeruginosa was followed for in cystic fibrosis patients.
Sequence Read ArchiveConvergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis.
NucleotideID CP003149.1. Deletion and acquisition of genomic content duringearly stage adaptation of Pseudomonas aeruginosa toa human host environment.
BioProjectID PRJEB8028. Long-term social dynamics drive loss of function in pathogenic bacteria.
Sequence Read ArchiveGenome analysis of a transmissible lineage of Pseudomonas aeruginosa reveals pathoadaptive mutations and distinct evolutionary paths of hypermutators.
NucleotideID AJHI00000000. Pseudomonas aeruginosa PADK2_CF510, whole genome shotgun sequencing project.