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Abstract

Microbial species diversify into separate strains through mutation, recombination, and gene loss/acquisition. Elucidating mechanisms driving the genomic diversity of species residing within complex microbiomes remains biased towards mutation, because current strain tracking methods have low sensitivity to genomic structural differences. To overcome this and to complement existing strain tracking tools we developed SynTracker, a tool that compares strains using synteny, i.e., the conservation of the order of genomic markers in homologous regions in pairs of metagenomic assemblies or genomes. SynTrackers attributes include low SNP sensitivity, no database requirement, and a high comparative performance. The combined use of SynTracker and SNP-based tools in metagenome analysis allows the identification of species undergoing high rates of recombination with low rates of mutation, or conversely, high rates of structural change with low mutation rates. When used as a standalone, SynTracker can accurately track strains using a fraction of the total genome length, allowing strain tracking in low abundance taxa, plasmids and phages. Taken together, SynTracker, when used alone or combined with other existing tools, provides a novel window into different modes of evolution on a per species-basis in complex microbiomes.