<Emphasis Type="Italic">In silico</Emphasis> prediction of horizontal gene transfer in <Emphasis Type="Italic">Streptococcus thermophilus</Emphasis> |
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Authors: | Catherine Eng Annabelle Thibessard Morten Danielsen Thomas Bovbjerg Rasmussen Jean-François Mari Pierre Leblond |
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Institution: | 1.Génétique et Microbiologie, UMR UHP-INRA 1128, IFR 110 EFABA, Université de Lorraine, Faculté des Sciences et Technologies,Vand?uvre-lès-Nancy,France;2.LORIA, UMR CNRS 7503 et INRIA Lorraine, Campus scientifique,Vand?uvre-lès-Nancy,France;3.Department of Assays,Chr. Hansen A/S,H?rsholm,Denmark;4.Department of Physiology, innovation,Chr. Hansen A/S,H?rsholm,Denmark |
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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. |
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