Genome-wide association testing of Biolog GenIII phenotypes vs. accessory genome presence/absence

The association of accessory gene occurrence with phenotypic profiles obtained with the Biolog GenIII (continuous values) was tested using the phylogenetic framework implemented in the ‘treeWAS’ R package (Collins & Didelot 2018). The test was performed on 9,621 non-trivial OG presence/absence profiles using the ML method for ancestral state reconstruction. Significance was assessed by comparing test scores to those obtained by simulating random genotype profiles along the 10-taxon species tree for 100 times more loci than the tested dataset (ca. 105 simulations) and scaling the p-values using FDR correction. Phenotypes with significant hits were then tested again with more stringent parameters, using 1,000 times more loci than the tested dataset and Bonferroni p-value correction.