ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2008
Differential selective constraints shaping codon usage pattern of housekeeping and tissue-specific homologous genes of rice and arabidopsis.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
14 citing papers in PubMed, 38 citations in OpenAlex.
- GC3 codons enhance protein production in diverse GC- and AT-rich plant species.bioRxiv : the preprint server for biology · 2025Article
- Codon usage bias.Molecular biology reports · 2022Review
- Article
- Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations.BMC genomics · 2020Article
- 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
- Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants.BMC genomics · 2015Article
- Article
- Synonymous codon usage bias is correlative to intron number and shows disequilibrium among exons in plants.BMC genomics · 2013Article
- The signatures of selection for translational accuracy in plant genes.Genome biology and evolution · 2013Article
- Article
- Mutational bias and translational selection shaping the codon usage pattern of tissue-specific genes in rice.PloS one · 2012Article
- Gene expression: sizing it all up.Frontiers in genetics · 2011Article
- Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Intra-genomic variation between housekeeping and tissue-specific genes has always been a study of interest in higher eukaryotes. To-date, however, no such investigation has been done in plants. Availability of whole genome expression data for both rice and Arabidopsis has made it possible to examine the evolutionary forces in shaping codon usage pattern in both housekeeping and tissue-specific genes in plants. In the present work, we have taken 4065 rice-Arabidopsis homologous gene pairs to study evolutionary forces responsible for codon usage divergence between housekeeping and tissue-specific genes. In both rice and Arabidopsis, it is mutational bias that regulates error minimization in highly expressed genes of both housekeeping and tissue-specific genes. Our results show that, in comparison to tissue-specific genes, housekeeping genes are under strong selective constraint in plants. However, in tissue-specific genes, lowly expressed genes are under stronger selective constraint compared with highly expressed genes. We demonstrated that constraint acting on mRNA secondary structure is responsible for modulating codon usage variations in rice tissue-specific genes. Thus, different evolutionary forces must underline the evolution of synonymous codon usage of highly expressed genes of housekeeping and tissue-specific genes in rice and Arabidopsis.
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