Department of Computer Science, University of Manitoba, 103 Dafoe Rd W, Winnipeg, Manitoba, Canada R3T 5V6, Canada.
J Bioinform Comput Biol. 2021 Dec;19(6):2140007. doi: 10.1142/S0219720021400072. Epub 2021 Nov 13.
We present BOPAL 2.0, an improved version of the BOPAL algorithm for the evolutionary history inference of tRNA and rRNA genes in bacterial genomes. Our approach can infer complete evolutionary scenarios and ancestral gene orders on a phylogeny and considers a wide range of events such as duplications, deletions, substitutions, inversions and transpositions. It is based on the fact that tRNA and rRNA genes are often organized in operons/clusters in bacteria, and this information is used to help identify orthologous genes for each genome comparison. BOPAL 2.0 introduces new features, such as a triple-wise alignment step, context-aware singleton matching and a second pass of the algorithm. Evaluation on simulated datasets shows that BOPAL 2.0 outperforms the original BOPAL in terms of the accuracy of inferred events and ancestral genomes. We also present a study of the tRNA/rRNA gene evolution in the genus, in which the organization of these genes is very divergent. Our results indicate that tRNA and rRNA genes in have evolved through numerous duplications, losses, transpositions and substitutions, but very few inversions were inferred.
我们提出了 BOPAL 2.0，这是一种用于细菌基因组中 tRNA 和 rRNA 基因进化历史推断的 BOPAL 算法的改进版本。我们的方法可以在系统发育树上推断完整的进化场景和祖先基因顺序，并考虑了多种事件，如复制、缺失、替换、倒位和转座。这是基于这样一个事实，即 tRNA 和 rRNA 基因通常在细菌中组织成操纵子/簇，并且该信息用于帮助为每个基因组比较识别同源基因。BOPAL 2.0 引入了新的功能，例如三向比对步骤、上下文感知单例匹配和算法的第二次通过。在模拟数据集上的评估表明，BOPAL 2.0 在推断事件和祖先基因组的准确性方面优于原始 BOPAL。我们还对属中的 tRNA/rRNA 基因进化进行了研究，其中这些基因的组织非常多样化。我们的结果表明，属中的 tRNA 和 rRNA 基因通过多次复制、丢失、转座和替换进化而来，但推断出的倒位很少。
