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Evolutionary Implications of Microbial Genome Tetranucleotide Frequency Biases
Open accessAbstract
We compared nucleotide usage pattern conservation for related prokaryotes by examining the representation of DNA tetranucleotide combinations in 27 representative microbial genomes. For each of the organisms studied, tetranucleotide usage departures from expectations (TUD) were shared between related organisms using both Markov chain analysis and a zero-order Markov method. Individual strains, multiple chromosomes, plasmids, and bacteriophages share TUDs within a species. TUDs varied between coding and noncoding DNA. Grouping prokaryotes based on TUD profiles resulted in relationships with important differences from those based on 16S rRNA phylogenies, which may reflect unequal rates of evolution of nucleotide usage patterns following divergence of particular organisms from a common ancestor. By both symmetrical tree distance and likelihood analysis, phylogenetic trees based on TUD profiles demonstrate a level of congruence with 16S rRNA trees similar to that of both RpoA and RecA trees. Congruence of these trees indicates that there exists phylogenetic signal in TUD patterns, most prominent in coding region DNA. Because relationships demonstrated in TUD-based analyses utilize whole genomes, they should be considered complementary to phylogenies based on single genetic elements, such as 16S rRNA.
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“we calculated tetranucleotide usage deviations (TUDs), a strong indicator metric of phylogenetic relatedness (78).”
From Sequence modeling and design from molecular to genome scale with Evo (2024) · cites this paper as [78]
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Additional file 21 of MetaDecoder: a novel method for clustering metagenomic contigs
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Additional file 5 of MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis
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Additional file 12 of MetaDecoder: a novel method for clustering metagenomic contigs
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Additional file 8 of MetaDecoder: a novel method for clustering metagenomic contigs
Liu, C.-C., Dong, S.-S., Chen, J.-B., Wang, C., Ning, P., Guo, Y., & Yang, T.-L. (2022) · Figshare · doi:10.6084/m9.figshare.19343002
Additional file 7 of MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis
Steinke, K., Pamp, S. J., & Munk, P. (2024) · Figshare · doi:10.6084/m9.figshare.26666785
Additional file 1 of MetaDecoder: a novel method for clustering metagenomic contigs
Liu, C.-C., Dong, S.-S., Chen, J.-B., Wang, C., Ning, P., Guo, Y., & Yang, T.-L. (2022) · Figshare · doi:10.6084/m9.figshare.19342963
Additional file 4 of MetaDecoder: a novel method for clustering metagenomic contigs
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Additional file 10 of MetaDecoder: a novel method for clustering metagenomic contigs
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Additional file 3 of MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis
Steinke, K., Pamp, S. J., & Munk, P. (2024) · Figshare · doi:10.6084/m9.figshare.26666773
Bize, A., Midoux, C., Mariadassou, M., Schbath, S., Forterre, P., & Cunha, V. D. (2021) · Figshare · doi:10.6084/m9.figshare.14228116
Additional file 2 of MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis
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Additional file 2 of MetaDecoder: a novel method for clustering metagenomic contigs
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Additional file 9 of MetaDecoder: a novel method for clustering metagenomic contigs
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Additional file 7 of MetaDecoder: a novel method for clustering metagenomic contigs
Liu, C.-C., Dong, S.-S., Chen, J.-B., Wang, C., Ning, P., Guo, Y., & Yang, T.-L. (2022) · Figshare · doi:10.6084/m9.figshare.19342999
Metadata
- Authors
- Pride, D. T., Meinersmann, R. J., Wassenaar, T. M., & Blaser, M. J.
- Affiliations
- Agricultural Research Service (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2003-01-14
- Volume
- 13
- Issue
- 2
- Pages
- 145-158
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC420360
- OpenAlex
- W2082521980
- Cited by
- 289
- References
- 49
- Citations by year
- 2026: 1 · 2025: 7 · 2024: 9 · 2023: 4 · 2022: 31 · 2021: 10 · 2020: 9 · 2019: 11 · 2018: 7 · 2017: 12 · 2016: 11 · 2015: 27 · 2014: 11 · 2013: 21 · 2012: 11
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Rutgers University Community Repository (Rutgers University) (submittedVersion)
- Funders
- National Institutes of Health (5r01dk053707-06, CA68485)
- National Cancer Institute (CA68485, P30CA068485)
- National Institute of General Medical Sciences (R01 GM 63270, R01GM063270)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK 53707)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- prokaryotic genomes, phylogenetic signal, phylogenetic incongruence, 16S rRNA phylogeny, Markov chain analysis, bacterial evolution, genome-based phylogeny
- MeSH terms
- Chromosome Mapping, Chromosomes, Bacterial, DNA, Bacterial, Gram-Negative Bacteria, Gram-Positive Bacteria, Phylogeny, Plasmids, RNA, Bacterial, RNA, Ribosomal, 16S, Spirochaeta, Cluster Analysis, Genome, Bacterial, Microsatellite Repeats, DNA, Archaeal, RNA, Archaeal, Chromosomes, Archaeal, Genome, Archaeal, Gene Transfer, Horizontal
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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