title: Comparative Genomics of Listeria Sensu Lato: Genus-Wide Differences in Evolutionary Dynamics and the Progressive Gain of Complex, Potentially Pathogenicity-Related Traits through Lateral Gene Transfer.
abstract: Historically, genome-wide and molecular characterization of the genus Listeria has concentrated on the important human pathogen Listeria monocytogenes and a small number of closely related species, together termed Listeria sensu strictu. More recently, a number of genome sequences for more basal, and nonpathogenic, members of the Listeria genus have become available, facilitating a wider perspective on the evolution of pathogenicity and genome level evolutionary dynamics within the entire genus (termed Listeria sensu lato). Here, we have sequenced the genomes of additional Listeria fleischmannii and Listeria newyorkensis isolates and explored the dynamics of genome evolution in Listeria sensu lato. Our analyses suggest that acquisition of genetic material through gene duplication and divergence as well as through lateral gene transfer (mostly from outside Listeria) is widespread throughout the genus. Novel genetic material is apparently subject to rapid turnover. Multiple lines of evidence point to significant differences in evolutionary dynamics between the most basal Listeria subclade and all other congeners, including both sensu strictu and other sensu lato isolates. Strikingly, these differences are likely attributable to stochastic, population-level processes and contribute to observed variation in genome size across the genus. Notably, our analyses indicate that the common ancestor of Listeria sensu lato lacked flagella, which were acquired by lateral gene transfer by a common ancestor of Listeria grayi and Listeria sensu strictu, whereas a recently functionally characterized pathogenicity island, responsible for the capacity to produce cobalamin and utilize ethanolamine/propane-2-diol, was acquired in an ancestor of Listeria sensu strictu.
authors.affiliation: Dipartimento di Bioscienze, Università degli Studi di Milano, Italy Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Chiara
authors.affiliation: Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy.
authors.forename: Marta
authors.initials: M
authors.lastname: Caruso
authors.affiliation: Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Italy Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy.
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: D'Erchia
authors.affiliation: Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy.
authors.forename: Caterina
authors.initials: C
authors.lastname: Manzari
authors.affiliation: Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy.
authors.forename: Rosa
authors.initials: R
authors.lastname: Fraccalvieri
authors.affiliation: Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Goffredo
authors.affiliation: Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Latorre
authors.affiliation: Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy.
authors.forename: Angela
authors.initials: A
authors.lastname: Miccolupo
authors.affiliation: Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy.
authors.forename: Iolanda
authors.initials: I
authors.lastname: Padalino
authors.affiliation: Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy.
authors.forename: Gianfranco
authors.initials: G
authors.lastname: Santagada
authors.affiliation: Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy.
authors.forename: Doriano
authors.initials: D
authors.lastname: Chiocco
authors.affiliation: Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Italy Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy.
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
authors.affiliation: Dipartimento di Bioscienze, Università degli Studi di Milano, Italy david.horner@unimi.it parisi.izspb@gmail.com.
authors.forename: David S
authors.initials: DS
authors.lastname: Horner
authors.affiliation: Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy david.horner@unimi.it parisi.izspb@gmail.com.
authors.forename: Antonio
authors.initials: A
authors.lastname: Parisi
mesh_terms: D004269:DNA, Bacterial / Q000737:chemistry; D019856:Ethanolamine / Q000378:metabolism; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D007558:Italy; D008087:Listeria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D010802:Phylogeny; D011409:Propylene Glycols / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid; D012256:Riboflavin / Q000096:biosynthesis
chemical_list: D004269:DNA, Bacterial; D011409:Propylene Glycols; D019856:Ethanolamine; D012256:Riboflavin
keywords: Listeria; cobalamin; comparative genomics; ethanolamine metabolism; flagella; genome sequencing; lateral gene transfer; propane-2-diol metabolism