2013
DOI: 10.1093/dnares/dss039
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Evaluation of Codon Biology in Citrus and Poncirus trifoliata Based on Genomic Features and Frame Corrected Expressed Sequence Tags

Abstract: Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT ric… Show more

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Cited by 29 publications
(26 citation statements)
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“…1 A ). In the case of unimodal bell-shaped distribution, common to many plant and animal species, the extreme 5% of the genes from the tails of the distributions are denoted as “GC 3 -rich” and “GC 3 -poor” genes (Sablok et al 2011; Ahmad et al 2013). By contrast, for bimodal distributions that are common to grasses and homeotherm vertebrates (Elhaik et al 2009; Elhaik and Tatarinova 2012), the GC 3 cutoff is determined based on the position of the “valley” between the two peaks.…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…1 A ). In the case of unimodal bell-shaped distribution, common to many plant and animal species, the extreme 5% of the genes from the tails of the distributions are denoted as “GC 3 -rich” and “GC 3 -poor” genes (Sablok et al 2011; Ahmad et al 2013). By contrast, for bimodal distributions that are common to grasses and homeotherm vertebrates (Elhaik et al 2009; Elhaik and Tatarinova 2012), the GC 3 cutoff is determined based on the position of the “valley” between the two peaks.…”
Section: Methodsmentioning
confidence: 99%
“…Because mutations in this position lead primarily to synonymous substitutions, the selective pressures affecting its composition are different from those acting on the first two codon positions, making it a valuable tool to study evolution. To name a few, it has been previously shown (Tatarinova et al 2010; Sablok et al 2011; Ahmad et al 2013) that dicot and monocot plant genes with high GC 3 have distinctly different properties from genes with low GC 3 : they contain more targets for methylated GC 3 -rich genes, and also exhibit more variable expression, possess more upstream TATA boxes, are enriched for certain classes of genes (e.g., stress responsive genes), and have a GC 3 content that increases from 5′ to 3′ (Tatarinova et al 2010). GC 3 -rich genes were also shown to be inducible while the GC 3 -poor are ubiquitously active (Tatarinova et al 2010).…”
Section: Introductionmentioning
confidence: 98%
“…These seeds germinated normally and developed into diploid plants. In Citrus, recently, a rough draft of the genome was completed using the haploid Clementine mandarin and the doubled haploid sweet orange (Ollitrault et al, 2012;Xu et al, 2013). This genomic information has also been applied for the development of DNA markers, genetic analysis, and the production of new cultivars (Ahmad et al, 2013;Cuenca et al, 2013;Garcia-Lor et al, 2013).…”
Section: Resultsmentioning
confidence: 99%
“…In Citrus, a rough draft of the genome was recently completed using the haploid clementine mandarin and the DH sweet orange (Ollitrault et al 2012, Xu et al 2013). This genomic information has been applied in the development of DNA markers, genetic analysis, and the production of new cultivars (Ahmad et al 2013, Cuenca et al 2013, GarciaLor et al 2013.…”
Section: Conclusion and Prospectsmentioning
confidence: 99%