ArticleScientific reports2017
Comprehensive analysis of correlations among codon usage bias, gene expression, and substitution rate in Arachis duranensis and Arachis ipaënsis orthologs.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 57 citations in OpenAlex.
- Genetic factors explaining anthocyanin pigmentation differences.BMC plant biology · 2024Article
- Deciphering evolutionary dynamics of WRKY genes in Arachis species.BMC genomics · 2023Article
- Genome-wide identification, evolutionary and expression analysis of the cyclin-dependent kinase gene family in peanut.BMC plant biology · 2023Article
- Chloroplast gene expression level is negatively correlated with evolutionary rates and selective pressure while positively with codon usage bias in Ophioglossum vulgatum L.BMC plant biology · 2022Article
- Whole genome sequencing and comparative genomic analyses of Pseudomonas aeruginosa strain isolated from arable soil reveal novel insights into heavy metal resistance and codon biology.Current genetics · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- Article
- Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns.Genomics · 2021Article
- A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19.Journal of biomedical informatics · 2021Article
- Comparison of Brassica Genomes reveals asymmetrical gene retention between functional groups of genes in recurrent polyploidizations.Plant molecular biology · 2021Article
- Comprehensive analysis of coding sequence architecture features and gene expression inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants.Molecular biology and evolution · 2020Article
- Comparative analysis of codon usage betweenMitochondrial DNA. Part B, Resources · 2020Article
- A report on DNA sequence determinants in gene expression.Bioinformation · 2020Article
- Evolutionary balance between LRR domain loss and young NBS-LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner.BMC genomics · 2019Article
- Old and young duplicate genes reveal different responses to environmental changes in Arachis duranensis.Molecular genetics and genomics : MGG · 2019Article
- Evolutionary Rate Heterogeneity and Functional Divergence of Orthologous Genes inBiomolecules · 2019Article
- Evolvement of nutraceutical onion plants engineered for resveratrol biosynthetic pathway.Plant cell reports · 2019Article
- Gene flow signature in the S-allele region of cultivated buckwheat.BMC plant biology · 2019Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The relationship between evolutionary rates and gene expression in model plant orthologs is well documented. However, little is known about the relationships between gene expression and evolutionary trends in Arachis orthologs. We identified 7,435 one-to-one orthologs, including 925 single-copy and 6,510 multiple-copy sequences in Arachis duranensis and Arachis ipaënsis. Codon usage was stronger for shorter polypeptides, which were encoded by codons with higher GC contents. Highly expressed coding sequences had higher codon usage bias, GC content, and expression breadth. Additionally, expression breadth was positively correlated with polypeptide length, but there was no correlation between gene expression and polypeptide length. Inferred selective pressure was also negatively correlated with both gene expression and expression breadth in all one-to-one orthologs, while positively but non-significantly correlated with gene expression in sequences with signatures of positive selection. Gene expression levels and expression breadth were significantly higher for single-copy genes than for multiple-copy genes. Similarly, the gene expression and expression breadth in sequences with signatures of purifying selection were higher than those of sequences with positive selective signatures. These results indicated that gene expression differed between single-copy and multiple-copy genes as well as sequences with signatures of positive and purifying selection.
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