Bacterial pathogens dynamic during multi-species infections

Illumina gapA sequences of synthetic communities of plant bacterial pathogens: Pectobacterium and Dickeya genus. Sequencing was performed after growth on TSB synthetic medium (2 days post inoculation) or growth on potato tubers (5 days post infection).

The following files are available:

PT_table.txt: description of the potato tubers samples

TSB_table.txt: description of samples in synthetic medium (TSB)

gapA_PT.fasta.gz: Illumina fasta sequences after potato tubers infection (35,000 reads)

gapA_TSB.fasta.gz: Illumina fasta sequences after synthetic medium inoculation (35,000 reads)

gapA_without_primers.fasta: gapA sequences (without primers) of Pectobacterium and Dickeya strains used in this study (27 strains)

species.txt: list of bacterial species used in this study (9 species)

strains.txt: list of bacterial strains used in this study (27 strains)

count.py: python3 script used to analyse the output of blastn

R_script_FigureS1.R: R script for statistical analysis

R_script_Figure2b.R: R script for statistical analysis

R_script_Figure2a.R: R script for statistical analysis

Method (examplified with the gapA_TSB sequences at the species level):

• gapA sequences were blasted (blastn) against gapA sequences of Pectobacterium and Dickeya strains used in this study:

makeblastdb -in gapA_without_primers.fasta -dbtype nucl -out dbblastn

blastn -db dbblastn -query gapA_TSB.fasta -outfmt 6 -out blast.blastn -num_threads 12 -evalue 0.00001 -num_alignments 1

• Reads count. Reads matching (100% identity) with gapA sequences of Pectobacterium and Dickeya strains used in this study were counted using the count.py python script. The output is a tab-separated values (.tsv) file:

python3 count.py species.txt blast.blastn