McInerney, J. O., McNally, A. & O’Connell, M. J. Why prokaryotes have pangenomes. Nat. Microbiol. 2, 17040 (2017).
Tettelin, H., Riley, D., Cattuto, C. & Medini, D. Comparative genomics: the bacterial pan-genome. Curr. Opin. Microbiol. 11, 472–477 (2008).
Google Scholar
Bentley, S. Sequencing the species pan-genome. Nat. Rev. Microbiol. 7, 258–259 (2009).
Google Scholar
Bromham, L. & Penny, D. The modern molecular clock. Nat. Rev. Genet. 4, 216–224 (2003).
Google Scholar
Otto, S. P. & Whitlock, M. C. The probability of fixation in populations of changing size. Genetics 146, 723–733 (1997).
Google Scholar
Moura, A. et al. Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat. Microbiol. 2, 16185 (2016).
Linke, K. et al. Reservoirs of Listeria species in three environmental ecosystems. Appl. Environ. Microbiol. 80, 5583–5592 (2014).
Google Scholar
Liao, J., Wiedmann, M. & Kovac, J. Genetic stability and evolution of the sigB allele, used for Listeria sensu stricto subtyping and phylogenetic inference. Appl. Environ. Microbiol. 83, e00306–e00317 (2017).
Google Scholar
Duché, O., Trémoulet, F., Glaser, P. & Labadie, J. Salt stress proteins induced in Listeria monocytogenes. Appl. Environ. Microbiol. 68, 1491–1498 (2002).
Google Scholar
Mcclure, P. J., Roberts, T. A. & Oguru, P. O. Comparison of the effects of sodium chloride, pH and temperature on the growth of Listeria monocytogenes on gradient plates and in liquid medium. Lett. Appl. Microbiol. 9, 95–99 (1989).
Google Scholar
Schwarz, G., Mendel, R. R. & Ribbe, M. W. Molybdenum cofactors, enzymes and pathways. Nature 460, 839–847 (2009).
Google Scholar
Cordero, O. X. & Polz, M. F. Explaining microbial genomic diversity in light of evolutionary ecology. Nat. Rev. Microbiol. 12, 263–273 (2014).
Google Scholar
Iranzo, J., Wolf, Y. I., Koonin, E. V. & Sela, I. Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence. Nat. Commun. 10, 5376 (2019).
Google Scholar
Thomas, C. M. & Nielsen, K. M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3, 711–721 (2005).
Google Scholar
Smith, J. M., Feil, E. J. & Smith, N. H. Population structure and evolutionary dynamics of pathogenic bacteria. BioEssays 22, 1115–1122 (2000).
Google Scholar
Crits-Christoph, A., Olm, M. R., Diamond, S., Bouma-Gregson, K. & Banfield, J. F. Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. ISME J. 14, 1834–1846 (2020).
Google Scholar
Murrell, B. et al. Gene-wide identification of episodic selection. Mol. Biol. Evol. 32, 1365–1371 (2015).
Google Scholar
Angelastro, A. Chemoenzymatic synthesis of isotopically labelled folates. J. Am. Chem. Soc. 139, 13047–13054 (2017).
Google Scholar
Shapiro, B. J. et al. Population genomics of early events in the ecological differentiation of bacteria. Science 336, 48–51 (2012).
Google Scholar
Choudoir, M. J., Doroghazi, J. R. & Buckley, D. H. Latitude delineates patterns of biogeography in terrestrial Streptomyces. Environ. Microbiol. 18, 4931–4945 (2016).
Google Scholar
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Google Scholar
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Google Scholar
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).
Google Scholar
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Google Scholar
Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46 (2014).
Google Scholar
Black, C. A., Evans, D. D., Ensminger, L. E., White, J. L. & Clark, F. E. Methods of Soil Analysis Part 1: Physical and Mineralogical Properties, Including Statistics of Measurement and Sampling 128–151 (American Society of Agronomy, 1965).
Weller, D., Belias, A., Green, H., Roof, S. & Wiedmann, M. Landscape, water quality, and weather factors associated with an increased likelihood of foodborne pathogen contamination of New York streams used to source water for produce production. Food Sustain. Food Syst. 3, 124 (2020).
Google Scholar
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289–300 (1995).
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Google Scholar
Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, 309–314 (2018).
Google Scholar
Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).
Google Scholar
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
Google Scholar
Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609–W612 (2006).
Google Scholar
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Google Scholar
Pritchard, L., Glover, R. H., Humphris, S., Elphinstone, J. G. & Toth, I. K. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal. Methods 8, 12–24 (2016).
Google Scholar
Carlin, C. R. et al. Listeria cossartiae sp. nov., Listeria immobilis sp. nov., Listeria portnoyi sp. nov. and Listeria rustica sp. nov. isolated from agricultural water and natural environments. Int J. Syst. Evol. Microbiol. 71, 004795 (2021).
Google Scholar
Arevalo, P., VanInsberghe, D., Elsherbini, J., Gore, J. & Polz, M. F. A reverse ecology approach based on a biological definition of microbial populations. Cell 178, 820–834 (2019).
Google Scholar
Méric, G. et al. A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter. PLoS ONE 9, e92798 (2014).
Google Scholar
Gardner, S. N., Slezak, T. & Hall, B. G. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics 31, 2877–2878 (2015).
Google Scholar
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
Google Scholar
Kelly, J. K. A test of neutrality based on interlocus associations. Genetics 146, 1197–1206 (1997).
Google Scholar
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
Google Scholar
Martin, D. P., Murrell, B., Golden, M., Khoosal, A. & Muhire, B. RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol. 1, vev003 (2015).
Google Scholar
Liao, J. et al. Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica. BMC Evol. Biol. 19, 132 (2019).
Google Scholar
Pond, S. L. K., Posada, D., Gravenor, M. B., Woelk, C. H. & Frost, S. D. W. Automated phylogenetic detection of recombination using a genetic algorithm. Mol. Biol. Evol. 23, 1891–1901 (2006).
Google Scholar
Source: Ecology - nature.com
