Open AccessBOPAL 2.0 and a study of tRNA and rRNA gene evolution in Clostridium
Author(s) -
Meghan Chua,
Anthony Tan,
Olivier Tremblay-Savard
Publication year - 2021
Publication title -
journal of bioinformatics and computational biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.339
H-Index - 43
eISSN - 1757-6334
pISSN - 0219-7200
DOI - 10.1142/s0219720021400072
Subject(s) - biology , gene , genetics , transfer rna , genome , ribosomal rna , context (archaeology) , phylogenetics , computational biology , evolutionary biology , rna , paleontology
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 Clostridium genus, in which the organization of these genes is very divergent. Our results indicate that tRNA and rRNA genes in Clostridium have evolved through numerous duplications, losses, transpositions and substitutions, but very few inversions were inferred.