Competition and coevolution drive the evolution and the diversification of CRISPR immunity

Data for the paper :

"Competition and coevolution drive the evolution and the diversification of CRISPR immunity"

Does NOT contain sequencing data (they are available on NCBI, BioProject PRJNA843584)

Bacteria_density.csv
Density of bacteria (cfu/ml) in all replicates at all times. B: Treatment A ; Pw: Treatment B ; PR: Treatment C

Phages_density.csv
Density of phages (pfu/ml) in all replicates at all times. B: Treatment A ; Pw: Treatment B ; PR: Treatment C

NC_007019.1.fasta
Genome of bacteriophage 2972 downloaded from https://www-ncbi-nlm-nih-gov.inee.bib.cnrs.fr/nuccore/66391759

NC_007019.1_T0.fasta
Genome of bacteriophage 2972, updated to include the mutations observed in the mix of phages at T0 in treatment B.

Mutations.xlsx
This file shows the mutations in the genome of the 16 starting resistant bacteria compared to the sensitive ancestor DGCC 7710. All mutations were confirmed via Sanger sequencing of PCR products amplified from the chromosome of the BIMs. The sheet ‘BIM mutation details’ shows for each resistant bacteria details on the mutations detected, as well as the annotation of the protein produced by the mutated gene or the name of the gene when possible. As some mutations are observed in several bacteria, the sheet ‘Simplified combined mutations’ synthetically shows the presence/absence of mutations to the locus tag/gene level precision in each bacterial genotype. The effect of the mutation is shown with a color code, described below the table.

Processed data:

The following files are here as starting point to analyze data without having to process of raw data.

Bacteria_data.csv
Sequencing of bacteria populations: This file contains the frequency of each host genotype through time in all replicates. For the Genotypes, ‘start-end’ corresponds to the susceptible DGCC 7710. Any ‘PAM\_XXX’ between ‘start’ and ‘end’ indicates the presence of spacer XXX in this genotype. This pattern can be present several times for multi-resistant genotypes. Spacers are named according to the middle position of the corresponding protospacer in the phage. 

Phage_data.csv
Sequencing of phage populations: This file contains the frequency of each phage mutation through time in all replicates. It contains the type, the position on the genome, the reference allele, the mutated allele and the frequency of each mutations. The column with time 0 do not show replicate number next to the treatment as the sequencing was done for the phage mix used at the beginning of all replicates for each treatment.

Matching_data.csv
Dynamics of phage mutations that escape CRISPR immunity: This file contains the host spacer frequency and the corresponding phage mutation frequency through time in all replicates. Spacers are named according to the middle position of the corresponding protospacer in the phage. Many lines contain frequencies of 0 as they were not filtered for computation purposes.