The DOI matches its Crossref record; 94 of the 94 references it cites were found in a registry or an index.
The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes
Open accessAbstract
Many cases of nonstandard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The "gain" represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The "loss" represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is codon disappearance (CD), where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the unassigned codon mechanism, the loss occurs first, whereas in the ambiguous intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. CD is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense-to-sense reassignments cannot be explained by CD. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the unassigned codon and the ambiguous intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.
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“There is no evidence that any modern code modifications are adaptive. Most likely, these change evolved neutrally, through genetic drift and mutational pressure that drives small genomes toward high AT-content.”
From Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code (2017) · cites this paper as [24]
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“于初步探索,有待于进一步研究。 在真核生物系统进化研究中,多数学者采用mtDNA作为研究对象,并且获得了丰富的研究成果,但它 们并不是分子进化研究中的金钥匙,也存在着一些缺陷和特例([19]),例如在物种亲缘关系较远的情况下, mtDNA不能真实反映物种间亲缘关系变化的问题。因此必须采用基于多个独立进化(不连锁)的基因组信息,”
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ResultObservations and perspectives on the prebiotic sequence evolutionPreprint
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Eukaryotic Mitogenomes and Their Key Insights: Architecture, Evolution, and Mitonuclear Coevolution
Mehrotra, A., Sood, A., & Kartavtsev, Y. P. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27209010
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Metadata
- Authors
- Sengupta, S., Yang, X., & Higgs, P. G.
- Affiliations
- McMaster University (CA)
- Corresponding author
- Higgs, Paul G.
- Venue
- Journal of Molecular Evolution
- Published
- 2007-05-29
- Volume
- 64
- Issue
- 6
- Pages
- 662-688
- ISSN
- 0022-2844 (ISSN-L)
- 1432-1432
- PMC
- PMC1894752
- OpenAlex
- W2171069213
- Cited by
- 121
- References
- 94
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 4 · 2023: 4 · 2022: 2 · 2021: 3 · 2020: 7 · 2019: 4 · 2018: 4 · 2017: 12 · 2016: 9 · 2015: 9 · 2014: 5 · 2013: 7 · 2012: 5
- FWCI
- 3.57
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Molecular Evolution (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- arXiv (Cornell University)
- Funders
- Canada Research Chairs
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
- Keywords
- codon reassignment, mitochondrial genetic code, codon usage, tRNA, stop codon reassignment, mitochondrial genome, phylogeny
- MeSH terms
- Animals, Codon, Cytoplasm, DNA, Mitochondrial, Fungi, Genetic Code, Introns, Phylogeny, Plants, RNA, Transfer, Ile, Open Reading Frames, Codon, Terminator, Mitochondrial Proteins, Eukaryota
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