Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution

Title	Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution
Authors	Jingqiu Liao, Xiaodong Guo, Daniel L. Weller, Shaul Pollak, Daniel H. Buckley, Martin Wiedmann, Otto X. Cordero
Magazine	Nature Microbiology
Date	07/15/2021
DOI	10.1038/s41564-021-00935-7
Introduction	Bacterial populations in natural environments exhibit extensive genomic diversity, largely due to gene content shifts from DNA exchange with their surroundings. The precise ecological factors driving this genomic variation and the influence of selection are subjects of ongoing debate. This study addresses these questions by compiling a nationwide atlas of 1,854 Listeria strains, systematically isolated from soils throughout the contiguous United States. It was observed that Listeria occupied diverse environmental conditions, primarily influenced by soil moisture, molybdenum, and salinity levels. Analysis of whole-genome data from 594 representative strains enabled the classification of Listeria diversity into 12 phylogroups, each showing distinct habitat ranges and degrees of endemism. Phylogroups with a broad environmental presence, termed 'cosmopolitan', possessed more expansive pangenomes and exhibited reduced linkage disequilibrium, indicative of elevated rates of gene acquisition, loss, and allele transfer compared to phylogroups adapted to narrower habitats. These cosmopolitan phylogroups also contained a significant proportion of genes impacted by positive selection. The impact of positive selection was particularly evident within the phylogroup-specific core genome, suggesting that these core genes are crucial for adaptation within specific lineages. These findings demonstrate that genomic adaptability and recombination are outcomes of selective pressures for persistence in varied environments.
Quote	Jingqiu Liao, Xiaodong Guo and Daniel L. Weller et al. Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution. Nat. Microbiol. 2021. DOI: 10.1038/s41564-021-00935-7
Element	Molybdenum (Mo) , Sodium (Na)
Industry	Agriculture , Research & Laboratory