Département d'informatique et de recherche opérationnelle (DIRO), Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada.
Département de biochimie, Université de Montréal, CP 6128 succursale Centre-Ville, Montreal, QC, Canada.
Mol Biol Evol. 2015 Jun;32(6):1643-56. doi: 10.1093/molbev/msv029. Epub 2015 Feb 6.
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/.
介绍了一种针对基因排序比对问题（同源物比对）的算法 OrthoAlign，它考虑了大多数全基因组进化事件，如重复、丢失、重排和替换。在一个系统发育框架中，使用 OrthoAlign 推断了 50 个完全测序的芽孢杆菌属细菌的转移 RNA 库的进化。观察到基因重复和丢失的发生频率高于重排事件。在芽孢杆菌中推断的重复平均速率比在大肠杆菌中报告的速率低 24 倍，而丢失和倒位的平均速率分别低 12 倍。这些速率极低，表明在芽孢杆菌中，tRNA 基因库受到强烈的选择压力。提供了对进化事件的类型、位置、分布和长度的详尽分析，以及祖先结构。OrthoAlign 可以在以下网址下载：http://www.iro.umontreal.ca/~mabrouk/。
