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• W4386572233 abstract "Studies of bacterial adaptation and evolution are hampered by the difficulty of measuring traits such as virulence, drug resistance and transmissibility in large populations. In contrast, it is now feasible to obtain high-quality complete assemblies of many bacterial genomes thanks to scalable and affordable long-read sequencing technology. To exploit this opportunity we introduce a phenotype- and alignment-free method for discovering co-selected and epistatically interacting genomic variation from genome assemblies covering both core and accessory parts of genomes. Our approach uses a compact coloured de Bruijn graph to approximate the intra-genome distances between pairs of loci for a collection of bacterial genomes to account for the impacts of linkage disequilibrium (LD). We demonstrate the versatility of our approach to efficiently identify associations between loci linked with drug resistance and adaptation to the hospital niche in the major human bacterial pathogens Streptococcus pneumoniae and Enterococcus faecalis ." @default.
• W4386572233 created "2023-09-10" @default.
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• W4386572233 date "2023-09-08" @default.
• W4386572233 modified "2023-09-30" @default.
• W4386572233 title "PAN-GWES: Pangenome-spanning epistasis and co-selection analysis via de Bruijn graphs" @default.
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• W4386572233 doi "https://doi.org/10.1101/2023.09.07.556769" @default.
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