ArticleProceedings of the National Academy of Sciences of the United States of America1999
Strand asymmetry and codon usage bias in the chloroplast genome of Euglena gracilis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 60 citations in OpenAlex.
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- Molecular identification and phylogenetic analysis of Polygonatum Kingianum with different floral colors on the basis of chloroplast genomes.BMC plant biology · 2025Article
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- Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris.Scientific reports · 2022Article
- Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups.Journal of molecular evolution · 2022Article
- Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae).PloS one · 2021Article
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- ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication.Current genetics · 2016Article
- Codon Adaptation of Plastid Genes.PloS one · 2016Article
- Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC.BMC genomics · 2012Article
- The plastid genome of Eutreptiella provides a window into the process of secondary endosymbiosis of plastid in euglenids.PloS one · 2012Article
- Synonymous codon usage, GC(3), and evolutionary patterns across plastomes of three pooid model species: emerging grass genome models for monocots.Molecular biotechnology · 2011Article
- Factors affecting synonymous codon usage bias in chloroplast genome of oncidium gower ramsey.Evolutionary bioinformatics online · 2011Article
- The chloroplast genome of the green alga Schizomeris leibleinii (Chlorophyceae) provides evidence for bidirectional DNA replication from a single origin in the chaetophorales.Genome biology and evolution · 2011Article
- Analysis of synonymous codon usage patterns in different plant mitochondrial genomes.Molecular biology reports · 2009Article
- Study of codon bias perspective of fungal xylanase gene by multivariate analysis.Bioinformation · 2009Article
- A comparative approach to elucidate chloroplast genome replication.BMC genomics · 2009Article
- Analysis of the codon use frequency of AMPK family genes from different species.Molecular biology reports · 2009Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is shown that the two strands of the chloroplast genome from Euglena gracilis are asymmetric with regards to nucleotide composition. This asymmetry switches at both the origin of replication and a location that is halfway around the circular genome from the origin. In both halves of the genome the leading strand is G+T-rich, having a bias toward G over C and T over A, and the lagging strand is A+C-rich. This asymmetry is probably the result of a difference in mutation dynamics between the leading and lagging strands. In addition to composition asymmetry, the two strands differ with regards to coding content. In both halves of the genome the vast majority of genes are coded by the leading strand. These two aspects of strand asymmetry are then applied to a statistical test for selection on codon usage. The results indicate that selection on codon usage is limited to genes on the leading strand; no gene on the A+C-rich lagging strand shows evidence for selection, suggesting that highly expressed genes are coded predominantly on the strand of DNA that is the leading strand during replication. On the basis of these observations it is proposed that the coding strand bias is generated by selection to code highly expressed genes on the leading strand to coordinate the direction of replication and transcription, thereby increasing the potential rate of both reactions.
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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.