Fig. 3

Composition of different categories of genomic scaffolds in each cohort. For each cohort, the assembled scaffolds are classified into one of the three categories: known, novel, and divergent. The classification is based on the degree of similarity between the predicted genes on scaffolds and known genes in the NCBI database. Novel scaffolds have BLASTn alignments that spanned less than 20% of bases and had an average gene identity below 60%. Known scaffolds had an average gene identity greater than 80%. Divergent scaffolds were all those that neither fit into novel or known (in Gene Prediction and Scaffold Divergence Classification section of Methods). The percentage of base pairs from scaffolds in each category relative to the total number of base pairs from all scaffolds is shown. Of note samples from the Fosfomycin cohort went through single-end sequencing while all other cohorts went through paired-end sequencing (see Methods and Discussion). The three categories of scaffolds (Novel, Known, and Divergent) were separately analyzed in downstream analysis