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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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Shifting the genomic gold standard for the prokaryotic species definition
Richter, M., & Rossello-Mora, R. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906412106 · Cited by 6,343
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Wu, Y., Tang, Y.-H., Tringe, S. G., Simmons, B. A., & Singer, S. W. (2014) · Microbiome · doi:10.1186/2049-2618-2-26 · Cited by 725
Improved metagenome binning and assembly using deep variational autoencoders
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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
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