Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity
Paul M. Sharp,Elizabeth Cowe,Desmond G. Higgins,Denis C. Shields,Kenneth H. Wolfe,Frank Wright +5 more
Reads0
Chats0
TLDR
These trends for codon usage are illustrated for six species whereCodon usage has been examined in detail, by presenting the pooled codon used for the 10% of genes at either end of the major trend.Abstract:
The genetic code is degenerate, but alternative synonymous codons are generally not used with equal frequency. Since the pioneering work of Grantham's group it has been apparent that genes from one species often share similarities in codon frequency; under the "genome hypothesis" there is a species-specific pattern to codon usage. However, it has become clear that in most species there are also considerable differences among genes. Multivariate analyses have revealed that in each species so far examined there is a single major trend in codon usage among genes, usually from highly biased to more nearly even usage of synonymous codons. Thus, to represent the codon usage pattern of an organism it is not sufficient to sum over all genes as this conceals the underlying heterogeneity. Rather, it is necessary to describe the trend among genes seen in that species. We illustrate these trends for six species where codon usage has been examined in detail, by presenting the pooled codon usage for the 10% of genes at either end of the major trend. Closely-related organisms have similar patterns of codon usage, and so the six species in Table 1 are representative of wider groups. For example, with respect to codon usage, Salmonella typhimurium closely resembles E. coli, while all mammalian species so far examined (principally mouse, rat and cow) largely resemble humans.read more
Citations
More filters
Journal ArticleDOI
Comparative Analysis of Codon Bias in the Chloroplast Genomes of Theaceae Species
Zhanjun Wang,Qi-Liang Cai,Yue Wang,Minhui Li,Chenchen Wang,Zhaoxia Wang,Chunyan Jiao,Congcong Xu,Hongyan Wang,Zhaoliang Zhang +9 more
TL;DR: A systematic study on the CUB and expression of Theaceae species provides further evidence for their evolution and phylogeny and observed a positive correlation between the SCUO and MILC values, which indicated that CUB might affect gene expression.
Journal ArticleDOI
Exploring the codon patterns between CCD and NCED genes among different plant species.
R. Priya,P. Sneha,J. Febin Prabhu Dass,C. George Priya Doss,Markandan Manickavasagam,Ramamoorthy Siva +5 more
TL;DR: The result of this investigation indicates that CCD and NCED genes are under mutational pressure, which paves the way for increasing the production of apocarotenoids, which have a great significance in the industry.
Journal ArticleDOI
Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force.
Utsang Kumar,Rekha Khandia,Shailja Singhal,Nidhi Puranik,Meghna Tripathi,A. K. Pateriya,Raju Khan,Talha Bin Emran,Kuldeep Dhama,Ashok Munjal,Taha Alqahtani,Ali Alqahtani +11 more
TL;DR: In this article, the full-length sequences of the EPB41L3 gene for the human, brown rat, domesticated cattle, and Sumatran orangutan available at the NCBI were retrieved and utilized to analyze CUB patterns across the selected mammalian species.
Journal ArticleDOI
Sequence variation of mitochondrial DNA ND5 in captive South China tigers (Panthera tigris amoyensis)
Kun Wei,Zhihe Zhang,Wenping Zhang,Fujun Shen,Guangxin He,Rong Hou,Zhong Xie,Nong‐Lin Liu,Bisong Yue +8 more
TL;DR: The mtDNA ND5 variations detected in the present study could provide significant information to the studbook data of the South China tiger.
Journal ArticleDOI
Transcript free energy positively correlates with codon usage bias in mitochondrial genes of Calypogeia species (Calypogeiaceae, Marchantiophyta)
TL;DR: This study used bioinformatic tools to analyze the mitochondrial protein-coding sequences of four Calypogeia and found that natural selection might have played a major role over mutation pressure in shaping the CUB of mitochondrial genes in these four taxa.
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