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Springer (part of Springer Nature), Archives of Microbiology, 4(193), p. 287-297

DOI: 10.1007/s00203-010-0671-8

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In silico prediction of horizontal gene transfer in Streptococcus thermophilus

This paper was not found in any repository, but could be made available legally by the author.
This paper was not found in any repository, but could be made available legally by the author.

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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 com- bining 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 gen- ome 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. ; Une combinaison de perte / acquisition de gènes dans un processus de transfert horizontal (HGT) a conduit le Streptococcus thermophilus à s'adapter dans sa niche écologique, c-a-d le lait. Dans ce travail, nous décrivons une méthode de fouille de donnéeS fondée sur la modélisation stochastique, l'analyse de la distribution des gènes homologues et l'identification de traits fréquemment associés à des gènes transférés horizontalement afin d'évaluer quelle proportion du génome a été acquise par HGT. Nous approche montre que 17,7% approximativement des gènes de S. thermophilus (362 CDSs des 1915) ont un biais de composition; ces gènes sont dits "atypiques" . Pour 22% d'entre eux, leur annotation fonctionnelle laisse supposer fortement une acquisition par HGT.