Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics.

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Serval ID
serval:BIB_4CBE419539E7
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics.
Journal
Bioinformatics
Author(s)
Collyn F., Guy L., Marceau M., Simonet M., Roten C.A.
ISSN
1367-4803[print], 1367-4803[linking]
Publication state
Published
Issued date
2006
Volume
22
Number
9
Pages
1072-1079
Language
english
Abstract
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. 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.
Keywords
Chromosome Mapping/methods, Evolution, Molecular, Gene Transfer, Horizontal/genetics, Genome, Bacterial, Genomic Islands/genetics, Nucleotides/genetics, Phylogeny, Sequence Alignment/methods, Sequence Analysis, DNA/methods, Virulence Factors/genetics, Yersinia/genetics
Pubmed
Web of science
Open Access
Yes
Create date
24/01/2008 15:07
Last modification date
25/09/2019 7:09
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