Codon usage and gene function are related in sequences of Arabidopsis thaliana

Chiapello, Hélène; Lisacek, Frédérique; Caboche, Michel; Hénaut, Alain

doi:10.1016/s0378-1119(97)00671-9

Cited by 158 publications

(114 citation statements)

References 25 publications

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“…As these authors point out, mRNA abundance estimates may be error prone because of biases in the tissues sampled, biases in cloning of mRNAs and the normalization of cDNA libraries prior to sequencing, that is, adjustment toward uniform concentrations of cDNAs from different genes, causing an underestimation of highly expressed genes. Nevertheless, broad-scale positive associations between mRNA abundance and codon bias are in concordance with results from experimental studies (Shields et al, 1988;Stenico et al, 1994;Chiapello et al, 1998;Akashi, 2001). Moreover, the imprecise estimates of gene expression and underestimation of highly expressed genes yield conservative tests of statistical association.…”

Section: Hk Stenøiensupporting

confidence: 72%

“…Most optimal codons in A. thaliana end in G or C (Chiapello et al, 1998;Duret and Mouchiroud, 1999), and this trend also seems to be present in P. patens. There is a strong positive correlation between GC content in N3 and Fop (Pearson's coefficient 0.541, Po0.001).…”

Section: Resultsmentioning

confidence: 80%

“…In order to investigate whether this sample of P. patens genes represented the whole genome, a similar analysis was conducted on the orthologous A. thaliana genes. Gene expression levels, codon biases and GC content measures were estimated for the homologous A. thaliana genes in a similar way to the P. patens genes (see above), except that Fop was calculated from previously determined optimal codons (Chiapello et al (1998); the A. thaliana data set can be accessed at http://www. vaxtbio.uu.se/resfold/stenoien/physcomitrella/).…”

Section: Methodsmentioning

confidence: 99%

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Adaptive basis of codon usage in the haploid moss Physcomitrella patens

Stenøien

2004

Heredity

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Patterns of codon usage bias were studied in the moss model species Physcomitrella patens. A total of 92 nuclear, protein coding genes were employed, and estimated levels of gene expression were tested for association with two measures of codon usage bias and other variables hypothesized to be associated with gene expression. Codon bias was found to be positively associated both with estimated levels of gene expression and GC content in the coding parts of studied genes. However, GC content in noncoding parts, that is, introns and 5 0 and 3 0 untranslated regions (UTRs), was not associated with estimated levels of gene expression. It is argued that codon bias is not shaped by mutational bias, but rather by weak natural selection for translational efficiency in P. patens. The possible role of life history characteristics in shaping patterns of codon usage in this species is discussed. Heredity (2005) 94, 87-93.

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Section: Hk Stenøiensupporting

confidence: 72%

Section: Resultsmentioning

confidence: 80%

Section: Methodsmentioning

confidence: 99%

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Adaptive basis of codon usage in the haploid moss Physcomitrella patens

Stenøien

2004

Heredity

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“…Previous studies have shown that many factors -for instance, base composition, expression level, structure of encoded protein -affect codon usage bias (Chiapello et al, 1998;Mukhopadhyay et al, 2007a). Many hypotheses have been put forward to explain the origin of codon usage bias.…”

Section: Discussionmentioning

confidence: 99%

Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon

Liu

Huang²,

Du³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Brachypodium distachyon has been proposed as a new model for the temperate grass because it is related to the major cereal grain species (such as wheat, barley, oat, maize, rice, and sorghum) and many forage and turf species. In this study, a multivariate statistical analysis was performed to investigate the characteristics of codon bias and the main factors affecting synonymous codon usage in Brachypodium. We found that lowand high-GC content genes with different codon usage occur frequently in the genome. The results of neutrality, correspondence, and correlation analyses indicated that mutational pressure and selective constraint were the main factors in shaping codon usage. Coding sequence length and the hydrophobicity of each protein were also identified as influences on codon usage bias, although their effect was minor. In addition, 27 codons, defined as "optimal codons", might provide useful information for gene engineering, gene prediction, and molecular evolution studies.

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“…The formation of codon bias is due to complex factors that lead to gene mutation and selection (Wong et al, 2002). Proteinencoded gene structure, function, and expression are closely linked and affected by a variety of evolutionary factors (Chiapello et al, 1998).…”

Section: Codon Usagementioning

confidence: 99%

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Gao

Zhang

et al. 2016

Front. Ecol. Evol.

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Zizania latifolia (Griseb.) Turcz. ex Stapf was once utilized as an important grain in ancient China and has been cultivated as an aquatic vegetable. Here, we report the complete Z. latifolia chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads generated by directly purified chloroplast (cp) DNA genome sequencing. The Z. latifolia cp genome is 136,501 bp in length, comprising a pair of 20,878-bp inverted repeat regions (IR) separated by small and large single copy regions (SSC and LSC) of 12,590 and 82,155 bp, respectively. The Z. latifolia cp genome encodes 110 unique genes (77 protein-coding genes, 29 tRNA genes, and 4 rRNA genes), of which 15 encompass introns. Sequence analysis identified a total of 39 direct/inverted repeats and 63 simple sequence repeats (SSR) with an average rate of 0.46 SSRs/kb. Our results revealed that the Z. latifolia cp genome is AT-rich (61.02%) and gene codon usage may be largely affected by a low GC content and codon usage bias for A, T-ending codons. We predicted 33 RNA editing sites in the chloroplast of Z. latifolia, all for C-to-U transitions. Comparative analyses with other available Oryzeae plastid genomes showed that the coding and IR sequences were more conserved than the single-copy and non-coding regions, suggesting that the indels should be cautiously employed in phylogenetic studies. Phylogenetic analysis of 52 complete grass chloroplast genomes including the reported Z. latifolia cp genome in this study yielded an identical tree topology as previous plastid-based trees, providing strong support for a sister relationship between Bambusoideae+Pooideae and Ehrhartoideae in the BEP (Bambusoideae, Ehrhartoideae, Pooideae) clade of the grass family.

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Codon usage and gene function are related in sequences of Arabidopsis thaliana

Cited by 158 publications

References 25 publications

Adaptive basis of codon usage in the haploid moss Physcomitrella patens

Adaptive basis of codon usage in the haploid moss Physcomitrella patens

Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

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