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Codon usage

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Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues

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Par- ticularly, the selected models generate random sequence by shuffling of synonymous codons, without affecting the codon usage bias and the protein structure. Relative synonymous codon usage (RSCU) and effective number of codons (Nc). This statistic, indicative of codon bias, is calculated based on the count of a particular codon, relative to the number of times that the codon would be observed as- suming a uniform synonymous codon usage.

Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes

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Rapid evolution of ovarian-biased genes in the yellow fever mosquito (Aedes aegypti). tRNA gene number and codon usage in the C. Genome-wide selection on codon usage at the population level in the fungal model organism Neurospora crassa.. Gene expression levels are correlated with synonymous codon usage, amino acid composition, and gene architecture in the red flour beetle, Tribolium castaneum. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees.

Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes

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The synonym- ous codon usage, relative synonymous codon usage values (RSCU) and codon usage of the complete plastid genomes were analyzed using MEGA 6.0 PREP suit [78]. with cut off values of 8.0 was used to predict the RNA editing sites in the plastome.. MUMmer was used to pair sequence alignment of the chloroplast genome [81]. The chloroplast genome of P.. unguiculata (NC_018051) in the Leguminosae tribe by mVISTA with the shuffle-LAGAN. The number of genes in the P.

Gene expression of functionally-related genes coevolves across fungal species: Detecting coevolution of gene expression using phylogenetic comparative methods

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CAI and similar codon usage metrics often show moderate to strong correlations with empir- ical gene expression estimates .

The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

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Similar to other angiosperm chloroplast gen- ome, codon usage in the Stauntonia chinensis chloro- plast genome was biased towards A and U at the third codon position, according to RSCU values (with a threshold of RSCU >. Further, the pattern of codon usage bias in the subfamily Lardizabaloideae and other species in Ranunculales were investigated (Fig.

Comparative genomic analysis of eutherian fibroblast growth factor genes

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Using MEGA 6.06, the rela- tive synonymous codon usage statistics were calculated as ratios between observed and expected amino acid codon counts (R = Counts / Expected counts). The protocol then described 20 amino acid codons including R ≤ 0,7 as not preferable amino acid codons, viz.: TTA, TTG, CTT, CTA, ATA, GTT, GTA, TCA, TCG, CCG, ACG, GCG, TAT, CAT, CAA, GAT, TGT, CGT, CGA, GGT (Fig.

Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

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The distributions of codon usage in four cp genomes showed that RSCU values of the 37 codons were identical in the three Chinese teas, but dif- ferent from those in Indian tea (Table 4)..

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): Insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

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Table 3 Codon Usage in this chloroplast genome. persica cp genome with the cp genome of related species. persica cp genome was compared with other eleven cp genomes (A. per- sica cp genome coding region and related species. persica cp genome about 153 SSRs were Table 3 Codon Usage in this chloroplast genome (Continued). persica chloroplast genome and compared it with 11 others cp genome genomes (Fig. persica and related cp genomes (a) Analysis of simple sequence repeats in the twelve chloroplast

Complete chloroplast genomes of all six Hosta species occurring in Korea: Molecular structures, comparative, and phylogenetic analyses

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According to the codon usage analysis, overall 64 codons were present across of the six Korean Hosta species en- coding 20 amino acids (AAs). Alanine was the least frequent AA in the Korean Hosta, which is encoded only by 309 codons (1.2. The codon usage based on relative synonymous codon usage values (RSCU) did not vary among the six Korean Hosta species except for some de- creases found in three AAs of H. Of the six Hosta species, H.

Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations

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Biased gene conversion affects patterns of codon usage and amino acid usage in the Saccharomyces sensu stricto Group of Yeasts

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

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This nucleotide bias is accompanied by strong codon bias in the predicted genes, meaning that within the possible codons for each amino acid, the two genomes are almost universally skewed towards the codon(s) with the lowest GC content (measured as Relative Synonymous Codon Usage, RSCU, Fig.

Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae

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The result of the analysis show that there is low codon usage bias in the plastome sequence of B.prionitis (Table 4).. The prediction of RNA editing sites present in the plastome sequence of B. The results as shown in (Table 5) showed that most of the conversions in the codon posi- tions are from Serine to Leucine. Generally, the editing sites observed in the plastome were 61 which are distrib- uted between the 19 protein-coding genes.

Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha

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Table 2 Codon usage in the 13 PCG for each of the six Ophryotrocha species investigated RSCU. In the remaining Ophryotrocha species, Valine and Glu- tamate were not found, while Aspartate was missing only in O.

Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history

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For plasmidions [62, 63] and viruses, additional constraints linked to packaging or structure can be imagined, in re- lation to but not limited to the properties of the extra- cellular environment.. [35] mentioned that the difference in codon usage between chromosomes I and II of Haloarcula marismortui must be linked to the more recent acquisition of the second chromo- some.

Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae

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Codon distribution (A) and relative synonymous codon usage (B) of PCGs in the 58 Cobitinae mitogenomes.. mitogenome: Mitochondrial genome. This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000) and the China Agriculture Research System (CARS-45-07).. macrostigma analyzed in this study was caught from the Yangtze River in Yibin City, Sichuan Province, China and reared in the National Aquatic Biological Resource Center (NABRC).

Sexual dimorphism and sex-biased gene expression in an egg parasitoid species, Anastatus disparis

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Patterns of synonymous codon usage in Drosophila melanogaster genes with sex-biased expression. Molecular evolution of sex-biased genes in Drosophila. Protein evolution in the context of Drosophila development. Sexual dimorphism and the evolution of sex-biased gene expression in the brown alga ectocarpus. Sex-biased gene expression and evolution of the x chromosome in nematodes.. Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata.

Massively parallel gene expression variation measurement of a synonymous codon library

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Codon usage is an important determinant of gene expression levels largely through its effects on transcription. Codon Bias as a means to fine-tune gene expression. Codon usage of highly expressed genes affects proteome-wide translation efficiency. Predicting gene expression level from relative codon usage bias: An application to escherichia coli genome. Codon usage influences the local rate of translation elongation to regulate co- translational protein folding.

Comprehensive analysis of genetic and evolutionary features of the hepatitis E virus

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Codon usage adaptation of the HEV ORFs to different hosts. The CAI values range from 0 to 1, being 1 if the fre- quency of codon usage by the virus equals the frequency of codon usage of the reference set.

Activity 5.3: Creating Usage Scenarios

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In this activity, you will develop usage scenarios for six of the use cases that you identified in Activity 5.2.. Create usage scenarios.. 34 Activity 5.3: Creating Usage Scenarios. Exercise 1: Creating Usage Scenarios. You will create a total of six usage scenarios from the use cases that you identified in Activity 5.2.. Create usage scenarios for the consultants and administrative assistants 1. 36 Activity 5.3: Creating Usage Scenarios

SWIFT UCP 600 Usage Guidelines

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Please refer to the usage guidelines section of field 77B of the MT 734 for further details