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231 results for “codon”

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dryad28/100

Data from: Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias

Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea to resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino-acid data provide implicit support for the respective optimal topologies. By analyzing the nucleotide data, we found that the 3rd codon positions are more saturated than the 1st and 2nd codon positions, and excluding these from the analyses leads to a topology congruent with that obtained using amino-acid data. Further, we determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a non-stationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoids the effects of synonymous mutations that underlie codon-usage bias, again recovered liverworts being sister to the remaining land plants. These analyses indicate that the discrepancy between the nucleotide-based and the amino acid-based trees is caused by the lineage specific, parallel compositional bias, or synonymous mutations driving codon-usage bias, as well as saturation in the 3rd codon positions. While genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein coding gene data and their amino-acids translations, by analyzing data modeling compositional bias, and by excluding nucleotide noisy signals due to saturation or codon-usage bias. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even when analyzing large-scale data sets, no matter how well-supported, without fully exploring the effects of substitution models.

opencc-zeroDec 2013View details →

dryad28/100

Data from: A pair of nonoptimal codons are necessary for the correct biosynthesis of the Aspergillus nidulans urea transporter, UreA

Both in prokaryotic and eukaryotic genomes synonymous codons are unevenly used. Such differential usage of optimal or nonoptimal codons has been suggested to play a role in the control of translation initiation and elongation, as well as at the level of transcription and mRNA stability. In the case of membrane proteins codon usage has been proposed to assist in the establishment of a pause necessary for the correct targeting of the nascent chains to the translocon. In this work, using as model UreA, the Aspergillus nidulans urea transporter, we show that the synonymous mutation of a pair of nonoptimal codons coding for amino acids situated at the limit between the N-terminus and the first transmembrane segment are necessary for its proper biogenesis at 37ºC. This effect is less relevant at 25ºC. These codons presumably regulate translation rate in order to allow for the correct interaction of UreA-translating ribosomes with factors required for the targeting and/or folding of the protein, in a very early stage of the biosynthesis process. Whether this mechanism would affect other proteins, remains to be determined.

opencc-zeroNov 2019View details →

zenodo28/100

Variability in codon usage in Coronaviruses is mainly driven by mutational bias and selective constraints on CpG dinucleotide

Supplementary Figures and Tables for the article called: " Variability in codon usage in Coronaviruses is mainly driven by mutational bias and selective constraints on CpG dinucleotide"

opencc-by-4.0Jul 2021View details →

zenodo28/100

RSCU value for each codon of each analyzed species

RSCU value for each codon of each analyzed species

opencc-by-4.0Nov 2022View details →

ClinicalTrials.gov28/100

Erythromycin Treatment for Readthrough of APC Gene Stop Codon Mutation in Familial Adenomatous Polyposis-minors' Adjusted Version

ClinicalTrials.gov study NCT02354560. IPD Sharing: Not stated. Countries: 0. Publications: 11.

restrictedIPD-UNDECIDEDFeb 2026View details →

ClinicalTrials.gov28/100

Novel Therapeutic Approaches for Treatment of CF Patients With W1282X Premature Termination Codon Mutations

ClinicalTrials.gov study NCT03624101. IPD Sharing: NO. Countries: 1. Publications: 0.

closedIPD-NOFeb 2026View details →

dryad28/100