ArticleGenes & genomics2019
Analysis of synonymous codon usage of chloroplast genome in Porphyra umbilicalis.
Article in Genes & genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 75 citations in OpenAlex.
- Analysis and comparison of chloroplast genome codon usage patterns in five accessions of Toxicodendron vernicifluum.BMC genomics · 2026Article
- Insights into the chloroplast genome diversity of the genus Isatis in China.BMC plant biology · 2026Article
- Comparative analysis of complete chloroplast genomes reveals the phylogenetic relationships of Lygodium Sw. (Lygodiaceae) species in China.BMC genomics · 2026Article
- Codon Usage Bias of the Polyphenol Oxidase Genes inPlants (Basel, Switzerland) · 2025Article
- The First Complete Chloroplast Genome Sequence of theCurrent issues in molecular biology · 2025Article
- Genome-Wide Identification, Evolution and Expression Analysis ofPlants (Basel, Switzerland) · 2025Article
- Codon usage patterns and genomic variation analysis of chloroplast genomes provides new insights into the evolution of Aroideae.Scientific reports · 2025Article
- Genome-Wide Analysis ofInternational journal of molecular sciences · 2024Article
- Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species.Functional & integrative genomics · 2024Article
- Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species.Plants (Basel, Switzerland) · 2024Article
- Complete chloroplast genomes of 13 species of sect. Tuberculata Chang (Camellia L.): genomic features, comparative analysis, and phylogenetic relationships.BMC genomics · 2024Article
- Chloroplast genomes in sevenFrontiers in genetics · 2024Article
- New Insights into Phylogenetic Relationship ofInternational journal of molecular sciences · 2023Article
- Analysis of codon usage patterns inChinese herbal medicines · 2023Article
- Article
- Codon usage bias and genetic diversity in chloroplast genomes ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2023Article
- Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species.BMC genomic data · 2023Article
- Molecular characterizations of genes in chloroplast genomes of the genus Arachis L. (Fabaceae) based on the codon usage divergence.PloS one · 2023Article
- The pattern of coding sequences in the chloroplast genome of Atropa belladonna and a comparative analysis with other related genomes in the nightshade family.Genomics & informatics · 2022Article
- Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species.BMC plant biology · 2022Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSynonymous codon usage bias is noticed in the genome of every organism, influenced by mutation pressure and natural selection. The analysis of codon usage pattern in Porphyra umbilicalis chloroplast genome are inferred while previous study focused on codon bias in nuclear genome.
objectiveTo develop a better understanding of the factors affecting synonymous codon usage, codon usage patterns and nucleotide composition of 150 genes in P. umbilicalis cp genome, and provide a theoretical basis for genetic modification of chloroplast genome.
methodsIn this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS and Microsoft Excel.
resultsIt shows that codon usage models are mainly influenced by compositional constraints under mutational pressure and synonymous codon prefers to use codons ending with A/T, comparing to C/G. The ENC value is slight low which shows the weak codon bias. For all coding genes of P. umbilicalis chloroplast genome except Photosystem I genes, a weak correlation between GC
conclusionThe codon usage bias in P. umbilicalis cp genome is low and in some way or other, influenced by natural selection, mutation pressure, nucleotide composition. Our results can provide a theoretical basis for codon modification of exogenous genes, accuracy of prediction about new members of chloroplast gene family and identification of unknown genome.
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