ArticlePloS one2016
Codon Adaptation of Plastid Genes.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 44 citations in OpenAlex.
- Complete assembly of Onobrychis viciifolia mitochondrial genome reveals evolutionary dynamics.Planta · 2026Article
- The Pan-Plastome of Walnuts (International journal of molecular sciences · 2026Article
- Plastome Evolution and Codon Usage Dynamics inEcology and evolution · 2026Article
- Phylogenomic discordance among plastid genes in endangered Maltese Limonium.Scientific reports · 2026Article
- New generic classification for Korean Peucedanum L. (Apiaceae) species based on deep phylogenomic study.BMC plant biology · 2026Article
- Comparative plastome analyses reveal life-form-associated selection signatures in Orchidaceae.BMC plant biology · 2026Article
- Comparative plastid genomics of Hippophae reveals phylogenetic relationships and provides candidate DNA markers for taxonomic identification.Scientific reports · 2026Article
- Organellar genome evolution in Camellia tianeensis (Theaceae): comparative insights into RNA editing, codon usage, and DNA transfer between chloroplast and mitochondrion.BMC genomics · 2026Article
- Plastome evidence repositionsFrontiers in plant science · 2026Article
- Plastome characterization of Embelia ribes Burm. f. (Myrsinoideae: Primulaceae): comparative analysis and phylogenetic inference.Journal of biosciences · 2026Article
- Comparative chloroplast genomics reveals codon usage bias, simple sequence repeat dynamics, and phylogenomic relationships in Urticaceae.Frontiers in plant science · 2026Article
- Characteristics of plastid genomes in the Saururaceae and their phylogenomic implications.BMC genomics · 2025Article
- Article
- Comparative chloroplast genomes of Dactylicapnos species: insights into phylogenetic relationships.BMC plant biology · 2024Article
- Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species.Functional & integrative genomics · 2024Article
- Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina.BMC genomic data · 2024Article
- Extreme plastomes in holoparasitic Balanophoraceae are not the norm.BMC genomics · 2023Article
- Article
- Article
- Do Noncoding and Coding Sites in Angiosperm Chloroplast DNA Have Different Mutation Processes?Genes · 2023Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon adaptation is codon usage bias that results from selective pressure to increase the translation efficiency of a gene. Codon adaptation has been studied across a wide range of genomes and some early analyses of plastids have shown evidence for codon adaptation in a limited set of highly expressed plastid genes. Here we study codon usage bias across all fully sequenced plastid genomes which includes representatives of the Rhodophyta, Alveolata, Cryptophyta, Euglenozoa, Glaucocystophyceae, Rhizaria, Stramenopiles and numerous lineages within the Viridiplantae, including Chlorophyta and Embryophyta. We show evidence that codon adaptation occurs in all genomes except for two, Theileria parva and Heicosporidium sp., both of which have highly reduced gene contents and no photosynthesis genes. We also show evidence that selection for codon adaptation increases the representation of the same set of codons, which we refer to as the adaptive codons, across this wide range of taxa, which is probably due to common features descended from the initial endosymbiont. We use various measures to estimate the relative strength of selection in the different lineages and show that it appears to be fairly strong in certain Stramenopiles and Chlorophyta lineages but relatively weak in many members of the Rhodophyta, Euglenozoa and Embryophyta. Given these results we propose that codon adaptation in plastids is widespread and displays the same general features as adaptation in eubacterial genomes.
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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.