Operon-based approach for the inference of rRNA and tRNA evolutionary histories in bacteria

Tomasz Pawliszak,Meghan Chua,Carson K Leung,Olivier Tremblay-Savard

doi:10.1186/s12864-020-6612-2

Abstract

BackgroundIn 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.ResultsWe 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.ConclusionsFrom 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.

Highlights

In bacterial genomes, ribosomal Ribonucleic acid (RNA) (rRNA) and transfer RNA (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
Instead of trying to find orthologous genes, which might not be located in the same region in both gene orders being compared, our method is based on identifying orthologous operons of rRNA and tRNA genes
Problem statement Input The algorithm we propose takes as input a phylogeny representing a bacterial genus, and annotated rRNA and tRNA gene orders, i.e. circular unichromosomal gene orders in which the locations of the origin and terminus of replication, the operons, the anticodons, and the signs of the genes have been identified

Summary

Results

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

Conclusions

Methods

Results and discussion

Conclusion