ArticlePlant molecular biology2006
Comparative analysis of expressed sequences reveals a conserved pattern of optimal codon usage in plants.
Article in Plant molecular biology, 2006. 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, 64 citations in OpenAlex.
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- Comparative analyses of plastomes in Allaeanthus and Malaisia: structure, evolution, and phylogeny.Scientific reports · 2024Article
- Insights into the conservation and diversification of the molecular functions of YTHDF proteins.PLoS genetics · 2023Article
- Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa.Microorganisms · 2023Article
- Decoding the complete chloroplast genome ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2023Article
- Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice.Plant communications · 2023Article
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- Genome-wide identification and comparative evolutionary analysis of sorbitol metabolism pathway genes in four Rosaceae species and three model plants.BMC plant biology · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- Analysis of codon usage bias of chloroplast genomes inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Codon usage by chloroplast gene is bias inJournal of genetics · 2020Article
- Characterization of bovine (Bos taurus) imprinted genes from genomic to amino acid attributes by data mining approaches.PloS one · 2019Article
- Large-Scale Synonymous Substitutions in Cucumber Mosaic Virus RNA 3 Facilitate Amino Acid Mutations in the Coat Protein.Journal of virology · 2018Article
- Codon usage and codon pair patterns in non-grass monocot genomes.Annals of botany · 2017Review
- The Evolutionary Basis of Translational Accuracy in Plants.G3 (Bethesda, Md.) · 2017Article
- Analysis of transcriptome data reveals multifactor constraint on codon usage in Taenia multiceps.BMC genomics · 2017Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon usage bias is a ubiquitous phenomenon, which may be caused by mutational bias, selection, or both. The patterns of codon usage in plants are not well understood. Datasets of expressed sequence tags (ESTs) available for many plant species provide the resources for large-scale comparative analysis of codon usage patterns. We developed a computational approach to translate EST or assembled contig sequences, and then used the coding information for comparative analysis of codon usage in 12 plant species, including 6 eudicots, 5 monocots and the green alga Chlamydomonas reinhardtii. While codon nucleotide composition is highly conserved within eudicots or monocots, there is a significant difference between these two major taxonomic groups of higher plants. The third nucleotide position of codons is AU-rich in the eudicot genomes (35-42% of G+C content), but GC-rich in the monocot genomes (59-61% of G+C content). To identify optimal codons in these species, we used EST counts to estimate gene transcript levels. It was demonstrated that codon usage bias is correlated positively with gene transcript levels. Interestingly, the use of optimal codons appears to be well conserved between eudicots and monocots, and to a lesser degree between the higher plants and C. reinhardtii. Most of the optimal codons end with a C or G base, regardless of the different nucleotide composition in these genomes. The results suggest that plant codon usage is affected by translational selection, and the selective pressure appears to be conserved in the plant kingdom.
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