Journal ArticleDOI
The 'effective number of codons' used in a gene.
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TLDR
A simple measure is presented that quantifies how far the codon usage of a gene departs from equal usage of synonymous codons, Nc, which provides an intuitively meaningful measure of the extent of codon preference in a gene.About:
This article is published in Gene.The article was published on 1990-03-01. It has received 1841 citations till now. The article focuses on the topics: Codon Adaptation Index & Codon usage bias.read more
Citations
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DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution
TL;DR: Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories.
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Evidence of perinatal transmission of Zika virus, French Polynesia, December 2013 and February 2014.
TL;DR: The clinical and laboratory features of two mothers and their newborns who had ZikAV infection as confirmed by ZIKAV RT-PCR performed on serum collected within four days post-delivery in date are described.
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Cross-species transmission of the newly identified coronavirus 2019-nCoV.
TL;DR: Comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019-nCoV sequence suggest that homologous recombination may occur and contribute to the 2019‐n coV cross‐species transmission.
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Selection in the evolution of gene duplications
TL;DR: It is hypothesized that gene duplications that persist in an evolving lineage are beneficial from the time of their origin, due primarily to a protein dosage effect in response to variable environmental conditions; duplications are likely to give rise to new functions at a later phase of their evolution once a higher level of divergence is reached.
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Solving the riddle of codon usage preferences: a test for translational selection
TL;DR: A model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms is proposed, which finally unifies the understanding of codon usage across prokaryotes and eukaryotes.
References
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Journal ArticleDOI
The Number of Alleles That Can Be Maintained in a Finite Population
Motoo Kimura,James F. Crow +1 more
TL;DR: This article proposes to examine some of the population consequences of a system of different isoalleles whose frequency in the population is determined by the mutation rate and by random drift, and considers three possibilities: A system of selectively neutral isoallels, a systemof mutually heterotic alleles, and a mixture of heterotic and harmful mutants.
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Codon usage and tRNA content in unicellular and multicellular organisms.
TL;DR: Examination of silent substitutions and tRNA populations in Enterobacteriaceae revealed that the evolutionary constraint imposed by tRNA content on codon usage decelerated rather than accelerated the silent-substitution rate, at least insofar as pairs of taxonomically related organisms were examined.
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Codon selection in yeast.
TL;DR: Extreme codon bias is seen for the Saccharomyces cerevisiae genes for the fermentative alcohol dehydrogenase isozyme I (ADH-I) and glyceraldehyde-3-phosphate dehydrogenased genes and a similar phenomenon is observed in the codon preferences of highly expressed genes in Escherichia coli.
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DNA Polymorphism Detectable by Restriction Endonucleases
Masatoshi Nei,Fumio Tajima +1 more
TL;DR: This application has suggested that the evolutionary change of mtDNA in higher animals occurs mainly by nucleotide substitution rather than by deletion and insertion, and the evolutionary distances among the three species have been estimated.
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Codon usage in bacteria: correlation with gene expressivity
Manolo Gouy,Christian Gautier +1 more
TL;DR: Analysis of genetic code usage in the 83 sequenced genes of the Escherichia coli genome is presented, taking into account new data on gene expressivity and regulation as well as iso-tRNA specificity and cellular concentration.
Related Papers (5)
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
Paul M. Sharp,Wen-Hsiung Li +1 more