title: In silico prediction of horizontal gene transfer in Streptococcus thermophilus.
abstract: A combination of gene loss and acquisition through horizontal gene transfer (HGT) is thought to drive Streptococcus thermophilus adaptation to its niche, i.e. milk. In this study, we describe an in silico analysis combining a stochastic data mining method, analysis of homologous gene distribution and the identification of features frequently associated with horizontally transferred genes to assess the proportion of the S. thermophilus genome that could originate from HGT. Our mining approach pointed out that about 17.7% of S. thermophilus genes (362 CDSs of 1,915) showed a composition bias; these genes were called 'atypical'. For 22% of them, their functional annotation strongly support their acquisition through HGT and consisted mainly in genes encoding mobile genetic recombinases, exopolysaccharide (EPS) biosynthesis enzymes or resistance mechanisms to bacteriophages. The distribution of the atypical genes in the Firmicutes phylum as well as in S. thermophilus species was sporadic and supported the HGT prediction for more than a half (52%, 189). Among them, 46 were found specific to S. thermophilus. Finally, by combining our method, gene annotation and sequence specific features, new genome islands were suggested in the S. thermophilus genome.
authors.affiliation: Génétique et Microbiologie, UMR UHP-INRA 1128, IFR 110 EFABA, Université de Lorraine, Faculté des Sciences et Technologies, BP 239, 54506, Vandœuvre-lès-Nancy, France, Catherine.Eng@scbiol.uhp-nancy.fr
authors.forename: Catherine
authors.initials: C
authors.lastname: Eng
authors.forename: Annabelle
authors.initials: A
authors.lastname: Thibessard
authors.forename: Morten
authors.initials: M
authors.lastname: Danielsen
authors.forename: Thomas Bovbjerg
authors.initials: TB
authors.lastname: Rasmussen
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Mari
authors.forename: Pierre
authors.initials: P
authors.lastname: Leblond
mesh_terms: D000465:Algorithms; D057225:Data Mining; D030541:Databases, Genetic; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D044404:Genomic Islands; D008390:Markov Chains; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D013269:Stochastic Processes; D048249:Streptococcus thermophilus / Q000235:genetics*