Journal ArticleDOI
Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species.
Qingpo Liu,Qingzhong Xue +1 more
TLDR
It is suggested that the chloroplast genome might display particular characteristics of codon usage that are different from its host nuclear genome, as pyrimidines were found more frequently than purines at the synonymous codon position of optimal codons.Abstract:
A detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm species Oryza sativa, Zea mays, Triticum aestivum and Arabidopsis thaliana. The average GC content of the entire genes, and at the three codon positions individually, was higher in nuclear than in chloroplast genes, suggesting different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots suggested that nucleotide compositional constraint had a large contribution to codon usage bias of nuclear genes in O. sativa, Z. mays, and T. aestivum, whereas natural selection was likely to be playing a large role in codon usage bias in chloroplast genomes. Correspondence analysis and chi-test showed that regardless of the genomic environment (species) of the host, the codon usage pattern of chloroplast genes differed from nuclear genes of their host species by their AU-richness. All the chloroplast genomes have predominantly A- and/or U-ending codons, whereas nuclear genomes have G-, C- or U-ending codons as their optimal codons. These findings suggest that the chloroplast genome might display particular characteristics of codon usage that are different from its host nuclear genome. However, one feature common to both chloroplast and nuclear genomes in this study was that pyrimidines were found more frequently than purines at the synonymous codon position of optimal codons.read more
Citations
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Journal ArticleDOI
Comparative chloroplast genomics: Analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus
Linda A. Raubeson,Rhiannon M. Peery,Timothy W. Chumley,Christopher Dziubek,H. Matthew Fourcade,Jeffrey L. Boore,Robert K. Jansen +6 more
TL;DR: Nymphaea and Ranunculus macranthus genomes were compared in this article to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.
Book ChapterDOI
Plastid Genomes of Seed Plants
TL;DR: A robust phylogenetic estimate provides an evolutionary framework for examining patterns and rates of change in plastid genomes across angiosperms and suggests aberrant DNA repair mechanisms may be involved in destabilizing these plastids.
Journal ArticleDOI
Production of heterologous proteins in plants: strategies for optimal expression.
TL;DR: The present review will evaluate the rate limiting steps of plant expression systems and suggest strategies to optimize protein expression at each of the steps: gene integration, transcription, translation and protein accumulation.
Journal ArticleDOI
Towards high-yield production of pharmaceutical proteins with plant cell suspension cultures
TL;DR: This review highlights the advantages and recent progress in plant cell culture technology and outlines viable strategies at both the biological and process engineering levels for advancing the economic feasibility of plant cell-based protein production.
Journal ArticleDOI
Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies
TL;DR: A broad coalescent-based species tree estimation of 45 seed plants is provided and it is suggested that the Amborella alone placement inferred using concatenation methods is likely misled by fast-evolving sites, which appear to be more robust to elevated substitution rates.
References
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Journal ArticleDOI
Theory and Applications of Correspondence Analysis
R. T. Clarke,Michael Greenacre +1 more
Journal ArticleDOI
The 'effective number of codons' used in a gene.
TL;DR: 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.
Journal ArticleDOI
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.
Journal ArticleDOI
Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes
TL;DR: Codon usage in the highly expressed group shows a higher correlation with tRNA abundance, a greater degree of third base pyrimidine bias, and a lesser tendency to the A+T richness which is characteristic of the yeast genome.
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The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
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