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08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Bacterial phylogenetic tree construction based on genomic translation stop signals
Lijing Xu1, Jimmy Kuo2, Jong-Kang Liu3
1Department of Biological Sciences, Bioinformatics Program, The University of Memphis, Memphis, TN, USA.
Microbial Informatics and Experimentation
|June 2, 2012
Summary
Bacterial genomes exhibit biases in translation stop signals (TSS) and premature stop codons (PSC). Genomic-TSSR analysis, reflecting TSS distribution across reading frames, accurately resolves bacterial phylogeny and strain-level differences, offering a novel biomarker for bacterial natural history.
Area of Science:
- Genomics
- Bioinformatics
- Microbial Phylogeny
Background:
- Stop codon efficiencies (TAA, TAG, TGA) vary, potentially regulating gene expression.
- Premature stop codons (PSC) are nucleotide trimers in alternative reading frames, exhibiting genomic biases similar to stop codons.
- Understanding the relationship between stop codon and PSC usage biases can illuminate bacterial phylogeny and natural history.
Purpose of the Study:
- To investigate the relationship between selective forces influencing stop codon and PSC usage biases in bacterial genomes.
- To determine how these biases correlate with the natural history and phylogeny of bacteria.
- To evaluate the potential of translation stop signal ratios (TSSR) as a biomarker for bacterial classification.
Main Methods:
- Analysis of sixty-one bacterial genomes from α-, β-, and γ-Proteobacteria subphyla.
- Calculation of Translation Stop Signals Ratios (TSSR), including frame-specific (TSSR-1, TSSR-2, TSSR-3) and overall genomic (Genomic-TSSR) distributions.
- Phylogenetic analysis using a 16S rRNA gene alignment tree as a reference and comparison with Genomic-TSSR clustering.
Main Results:
- Frame-specific TSSR values partially resolved bacterial phylogeny.
- Genomic-TSSR values generated phylogenetic clusters identical to the 16S rRNA reference tree, with higher resolution for closely related species/strains.
- Genes near the replication origin (Ori) showed more similar Genic-TSSR values than those near the terminus (Ter), suggesting localized recombination influences.
Conclusions:
- Interrelated translation stop signals across reading frames are likely due to translational-associated recombination (TSR).
- Localized recombination near the Ori region, driven by polymerase collisions and homologous recombination, explains similar TSSR values in these genes.
- Genomic-TSSR serves as a robust biomarker reflecting a bacterium's phyletic status and natural history.
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