title: Genome-Wide Survey of Genes Under Positive Selection in Avian Pathogenic Escherichia coli Strains.
abstract: The ability to obtain bacterial genomes from the same host has allowed for comparative studies that help in the understanding of the molecular evolution of specific pathotypes. Avian pathogenic Escherichia coli (APEC) is a group of extraintestinal strains responsible for causing colibacillosis in birds. APEC is also suggested to possess a role as a zoonotic agent. Despite its importance, APEC pathogenesis still has several cryptic pathogenic processes that need to be better understood. In this work, a genome-wide survey of eight APEC strains for genes with evidence of recombination revealed that ∼14% of the homologous groups evaluated present signs of recombination. Enrichment analyses revealed that nine Gene Ontology (GO) terms were significantly more represented in recombinant genes. Among these GO terms, several were noted to be ATP-related categories. The search for positive selection in these APEC genomes revealed 32 groups of homologous genes with evidence of positive selection. Among these groups, we found several related to cell metabolism, as well as several uncharacterized genes, beyond the well-known virulence factors ompC, lamB, waaW, waaL, and fliC. A GO term enrichment test showed a prevalence of terms related to bacterial cell contact with the external environment (e.g., viral entry into host cell, detection of virus, pore complex, bacterial-type flagellum filament C, and porin activity). Finally, the genes with evidence of positive selection were retrieved from genomes of non-APEC strains and tested as were done for APEC strains. The result revealed that none of the groups of genes presented evidence of positive selection, confirming that the analysis was effective in inferring positive selection for APEC and not for E. coli in general, which means that the study of the genes with evidence of positive selection identified in this study can contribute for the better understanding of APEC pathogenesis processes.
authors.affiliation: 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil .
authors.forename: Thaís Cabrera Galvão
authors.initials: TCG
authors.lastname: Rojas
authors.affiliation: 2 Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária , Campinas, Brazil .
authors.forename: Francisco Pereira
authors.initials: FP
authors.lastname: Lobo
authors.affiliation: 2 Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária , Campinas, Brazil .
authors.forename: Jorge Augusto
authors.initials: JA
authors.lastname: Hongo
authors.affiliation: 3 Systems Biology Laboratory, Centre for Molecular Biology and Genetic Engineering, State University of Campinas (UNICAMP) , Campinas, Brazil .
authors.forename: Renato
authors.initials: R
authors.lastname: Vicentini
authors.affiliation: 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil .
authors.forename: Renu
authors.initials: R
authors.lastname: Verma
authors.affiliation: 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil .
authors.forename: Renato Pariz
authors.initials: RP
authors.lastname: Maluta
authors.affiliation: 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil .
authors.forename: Wanderley Dias
authors.initials: WD
authors.lastname: da Silveira
mesh_terms: D000818:Animals; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics; D001715:Bird Diseases / Q000382:microbiology; D019729:Carbon-Oxygen Ligases / Q000235:genetics; D004269:DNA, Bacterial / Q000302:isolation & purification; D004926:Escherichia coli / Q000235:genetics*; D004927:Escherichia coli Infections / Q000662:veterinary*; D029968:Escherichia coli Proteins / Q000235:genetics*; D005408:Flagellin / Q000235:genetics; D005798:Genes, Bacterial; D018272:Porins / Q000235:genetics; D011991:Receptors, Virus / Q000235:genetics; D012641:Selection, Genetic; D016415:Sequence Alignment
chemical_list: D001425:Bacterial Outer Membrane Proteins; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; C516095:FliC protein, E coli; C113724:OmpC protein; D018272:Porins; D011991:Receptors, Virus; C472372:WaaZ protein, E coli; C016532:maltoporins; D005408:Flagellin; D019729:Carbon-Oxygen Ligases; C571195:WaaL protein, E coli
keywords: Avian E. coli; genetic characterization; zoonoses