Department of Computer Science, University of Manitoba, Winnipeg, Canada.
BMC Genomics. 2020 Apr 16;21(Suppl 2):252. doi: 10.1186/s12864-020-6612-2.
In bacterial genomes, rRNA and tRNA genes are often organized into operons, i.e. segments of closely located genes that share a single promoter and are transcribed as a single unit. Analyzing how these genes and operons evolve can help us understand what are the most common evolutionary events affecting them and give us a better picture of ancestral codon usage and protein synthesis.
We introduce BOPAL, a new approach for the inference of evolutionary histories of rRNA and tRNA genes in bacteria, which is based on the identification of orthologous operons. Since operons can move around in the genome but are rarely transformed (e.g. rarely broken into different parts), this approach allows for a better inference of orthologous genes in genomes that have been affected by many rearrangements, which in turn helps with the inference of more realistic evolutionary scenarios and ancestors.
From our comparisons of BOPAL with other gene order alignment programs using simulated data, we have found that BOPAL infers evolutionary events and ancestral gene orders more accurately than other methods based on alignments. An analysis of 12 Bacillus genomes also showed that BOPAL performs just as well as other programs at building ancestral histories in a minimal amount of events.
在细菌基因组中，rRNA 和 tRNA 基因通常组织成操纵子，即紧密相邻的基因片段，它们共享一个单一的启动子，并作为一个单元转录。分析这些基因和操纵子的进化方式可以帮助我们了解影响它们的最常见的进化事件，并更好地了解祖先的密码子使用和蛋白质合成。
我们引入了 BOPAL，这是一种用于推断细菌中 rRNA 和 tRNA 基因进化历史的新方法，它基于同源操纵子的识别。由于操纵子可以在基因组中移动，但很少发生转变（例如，很少被分成不同的部分），因此这种方法可以更好地推断出受许多重排影响的基因组中的同源基因，从而有助于推断出更现实的进化场景和祖先。
通过使用模拟数据对 BOPAL 与其他基因顺序比对程序进行比较，我们发现 BOPAL 在推断进化事件和祖先基因顺序方面比其他基于比对的方法更准确。对 12 个芽孢杆菌基因组的分析也表明，BOPAL 在以最少的事件构建祖先历史方面与其他程序一样有效。
