Evolution of tRNA Repertoires in Bacillus Inferred with OrthoAlign

Tremblay-Savard, Olivier; Benzaid, Billel; Lang, B. Franz; El-Mabrouk, Nadia

doi:10.1093/molbev/msv029

Cited by 17 publications

(34 citation statements)

References 28 publications

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“…As observed in a previous study of the Bacillus genus [16], inversions are mostly occurring around one of the axes of replication (origin or terminus) because this causes the genes to stay on the leading strand.…”

Section: Evolutionary Modelmentioning

confidence: 53%

“…Andreotti et al [15] then proposed a faster and more efficient linear programming algorithm for the duplication-loss model, and generalized it to the median of three genomes setting. More recently, OrthoAlign [16] and multiOrthoAlign [17] were developed to generalize the evolutionary model to account for rearrangements (inversions and transpositions) in addition to duplications and losses. The idea there was to use dynamic programming to align the rRNA and tRNA gene orders and identify orthologs, and then explain the mismatches and gaps in the alignment by inferring rearrangement events (inversions and transpositions) and content-modifying events (duplications and losses).…”

mentioning

confidence: 99%

“…Indeed, these operons tend to be more conserved in general, since rearrangement events mostly change their location inside the genome, but rarely modify their composition (e.g. a rearrangement event is unlikely to split an operon into two parts) [16]. Considering operons also allows our method to infer more realistic events by not considering events that would affect blocks of genes that are not part of the same operon, so technically not close to each other on the chromosome.…”

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confidence: 99%

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

et al. 2020

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Background: 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. 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: 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.

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Section: Evolutionary Modelmentioning

confidence: 53%

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confidence: 99%

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confidence: 99%

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

et al. 2020

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“…The mutational rates of bacterias (bacterial genomes are studied in Sec. Evaluation on biological data) are known to vary greatly between species and it is difficult to find indisputable reference points to evaluate them [31]. We thus approximate many generations in each step ( i.e level of the tree) by using as the mutation rate α three values: {1 % ,5 % ,10 % }.…”

Section: Resultsmentioning

confidence: 99%

Reconstruction of ancestral RNA sequences under multiple structural constraints

2016

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BackgroundSecondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors.MethodsIn this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families.ResultsWe test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database.ConclusionsOur results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3105-4) contains supplementary material, which is available to authorized users.

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“…This phylum presents three classes : Clostridia , Mollicutes and Bacilli [22]. Following the phylogeny published for Bacilli by Tremblay-Savard et al [26] we examined the genomes of 20 Bacilli belonging to strains of B. cereus , B. anthracis and B. thuringiensis , 4 strains of B. subtilis , and strains of B. weihenstephanensis , B. cytotoxicus and B. atrophaeus , and B. selenetireducens ; we added Staphylococcus aureus , Lactobacillus casei , Clostridium botulinum and Mycoplasma hominis ( Mollicutes ) which are non- Bacillus Firmicutes . Table 8 presents the periodicities found in the most deviated (from randomness) pair (first significance), in separations from 0 to 18.…”

Section: Main Textmentioning

confidence: 99%

Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses

Valenzuela

2017

Biol Res

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Direct tests of the random or non-random distribution of nucleotides on genomes have been devised to test the hypothesis of neutral, nearly-neutral or selective evolution. These tests are based on the direct base distribution and are independent of the functional (coding or non-coding) or structural (repeated or unique sequences) properties of the DNA. The first approach described the longitudinal distribution of bases in tandem repeats under the Bose–Einstein statistics. A huge deviation from randomness was found. A second approach was the study of the base distribution within dinucleotides whose bases were separated by 0, 1, 2… K nucleotides. Again an enormous difference from the random distribution was found with significances out of tables and programs. These test values were periodical and included the 16 dinucleotides. For example a high “positive” (more observed than expected dinucleotides) value, found in dinucleotides whose bases were separated by (3K + 2) sites, was preceded by two smaller “negative” (less observed than expected dinucleotides) values, whose bases were separated by (3K) or (3K + 1) sites. We examined mtDNAs, prokaryote genomes and some eukaryote chromosomes and found that the significant non-random interactions and periodicities were present up to 1000 or more sites of base separation and in human chromosome 21 until separations of more than 10 millions sites. Each nucleotide has its own significant value of its distance to neutrality; this yields 16 hierarchical significances. A three dimensional table with the number of sites of separation between the bases and the 16 significances (the third dimension is the dinucleotide, individual or taxon involved) gives directly an evolutionary state of the analyzed genome that can be used to obtain phylogenies. An example is provided.

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Evolution of tRNA Repertoires in Bacillus Inferred with OrthoAlign

Cited by 17 publications

References 28 publications

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

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

Reconstruction of ancestral RNA sequences under multiple structural constraints

Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses

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