title: Evolution of tRNA Repertoires in Bacillus Inferred with OrthoAlign.
abstract: OrthoAlign, an algorithm for the gene order alignment problem (alignment of orthologs), accounting for most genome-wide evolutionary events such as duplications, losses, rearrangements, and substitutions, was presented. OrthoAlign was used in a phylogenetic framework to infer the evolution of transfer RNA repertoires of 50 fully sequenced bacteria in the Bacillus genus. A prevalence of gene duplications and losses over rearrangement events was observed. The average rate of duplications inferred in Bacillus was 24 times lower than the one reported in Escherichia coli, whereas the average rates of losses and inversions were both 12 times lower. These rates were extremely low, suggesting a strong selective pressure acting on tRNA gene repertoires in Bacillus. An exhaustive analysis of the type, location, distribution, and length of evolutionary events was provided, together with ancestral configurations. OrthoAlign can be downloaded at: http://www.iro.umontreal.ca/~mabrouk/.
authors: Département d'informatique et de recherche opérationnelle (DIRO), Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada.
authors: Olivier
authors: O
authors: Tremblay-Savard
authors: Département d'informatique et de recherche opérationnelle (DIRO), Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada.
authors: Billel
authors: B
authors: Benzaid
authors: Département de biochimie, Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada.
authors: B Franz
authors: BF
authors: Lang
authors: Département d'informatique et de recherche opérationnelle (DIRO), Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada mabrouk@iro.umontreal.ca.
authors: Nadia
authors: N
authors: El-Mabrouk
mesh_terms: D000465:Algorithms; D001407:Bacillus / Q000145:classification / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D003198:Computer Simulation; D030541:Databases, Genetic; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D023061:Gene Order; D005798:Genes, Bacterial; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009876:Operon / Q000235:genetics; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics*; D015203:Reproducibility of Results; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012343:RNA, Transfer
keywords: Bacillus; alignment; duplications; gene order; orthology; phylogeny; rearrangements; transfer RNA