{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T08:56:57Z","timestamp":1760345817790,"version":"3.32.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and\/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics.<\/jats:p><jats:p>Results: YAPI, a Yersinia PAI, and related islands were compared with measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera.<\/jats:p><jats:p>Contact: \u00a0claude-alain.roten@unil.ch<\/jats:p><jats:p>Supplementary information: \u00a0<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti793","type":"journal-article","created":{"date-parts":[[2005,11,23]],"date-time":"2005-11-23T01:24:56Z","timestamp":1132709096000},"page":"1072-1079","source":"Crossref","is-referenced-by-count":16,"title":["Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics"],"prefix":"10.1093","volume":"22","author":[{"given":"F.","family":"Collyn","sequence":"first","affiliation":[{"name":"Inserm E0364\u2014Universit\u00e9 de Lille II, Facult\u00e9 de M\u00e9decine Henri Warembourg, Institut Pasteur de Lille 1 \u00a0 1 \u00a0 \u00a0 1 rue du Pr Calmette, F-59021 Lille, France"},{"name":"D\u00e9partement de Microbiologie Fondamentale, B\u00e2timent de Biologie, Facult\u00e9 de Biologie et de M\u00e9decine, Universit\u00e9 de Lausanne 2 \u00a0 2 \u00a0 \u00a0 CH-1015 Dorigny, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L.","family":"Guy","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Microbiologie Fondamentale, B\u00e2timent de Biologie, Facult\u00e9 de Biologie et de M\u00e9decine, Universit\u00e9 de Lausanne 2 \u00a0 2 \u00a0 \u00a0 CH-1015 Dorigny, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Marceau","sequence":"additional","affiliation":[{"name":"Inserm E0364\u2014Universit\u00e9 de Lille II, Facult\u00e9 de M\u00e9decine Henri Warembourg, Institut Pasteur de Lille 1 \u00a0 1 \u00a0 \u00a0 1 rue du Pr Calmette, F-59021 Lille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Simonet","sequence":"additional","affiliation":[{"name":"Inserm E0364\u2014Universit\u00e9 de Lille II, Facult\u00e9 de M\u00e9decine Henri Warembourg, Institut Pasteur de Lille 1 \u00a0 1 \u00a0 \u00a0 1 rue du Pr Calmette, F-59021 Lille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C.-A. 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