ArticleJournal of genetics2005
Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species.
Article in Journal of genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
77 citing papers in PubMed, 168 citations in OpenAlex.
- Comparative Chloroplast Genomics, Codon Usage Bias, and Phylogenetic Placement ofCurrent issues in molecular biology · 2026Article
- Comprehensive Codon Usage Analysis Across Diverse Plant Lineages.Biochemical genetics · 2026Article
- Comprehensive analysis of chloroplast genome evolution in Poaceae: codon usage patterns, selection pressures, and phylogenomic relationships.BMC genomics · 2026Article
- First Plastome Sequences of Two Endemic Taxa ofBiology · 2026Article
- The Complete Mitochondrial Genome of theBiology · 2026Article
- Comparative analysis of complete mitochondrial genomes fromFrontiers in plant science · 2026Article
- Integrating Morphology and Chloroplast Genomics: A New East Asian Species ofEcology and evolution · 2026Article
- Codon Usage Pattern and its Influencing Factors for Mitochondrial CO Genes Among Different Subfamilies of Cerambycidae.Biochemical genetics · 2025Article
- Plastomic insights into the genetic variation and phylogenetic relationships of Macadamia.Scientific reports · 2025Article
- Comparative Genomics ofInternational journal of molecular sciences · 2025Article
- Chloroplast Genome Diversity and Marker Potentials of DiverseInternational journal of molecular sciences · 2025Article
- Comprehensive analysis of complete Chloroplast genome sequence of Cardiospermum halicacabum L. (Sapindaceae).Scientific reports · 2025Article
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- Pan-Chloroplast Genomes Reveal the Accession-Specific Marker forInternational journal of molecular sciences · 2024Article
- Expression analysis of the apple HSP70 gene family in abiotic stress and phytohormones and expression validation of candidate MdHSP70 genes.Scientific reports · 2024Article
- Phylogenomics and plastome evolution of Lithospermeae (Boraginaceae).BMC plant biology · 2024Article
- Comparative analysis of 12 water lily plastid genomes reveals genomic divergence and evolutionary relationships in early flowering plants.Marine life science & technology · 2024Article
- Chloroplast genome analysis and evolutionary insights in the versatile medicinal plant Calendula officinalis L.Scientific reports · 2024Article
- Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae.BMC genomics · 2024Article
- Comprehensive analysis of complete chloroplast genome sequence ofPlant signaling & behavior · 2023Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.