Abstract
BackgroundCurrently, there is little data available regarding the role of gender-specific gene expression on synonymous codon usage (translational selection) in most organisms, and particularly plants. Using gender-specific EST libraries (with > 4000 ESTs) from Zea mays and Triticum aestivum, we assessed whether gender-specific gene expression per se and gender-specific gene expression level are associated with selection on codon usage.ResultsWe found clear evidence of a greater bias in codon usage for genes expressed in female than in male organs and gametes, based on the variation in GC content at third codon positions and the frequency of species-preferred codons. This finding holds true for both highly and for lowly expressed genes. In addition, we found that highly expressed genes have greater codon bias than lowly expressed genes for both female- and male-specific genes. Moreover, in both species, genes with female-specific expression show a greater usage of species-specific preferred codons for each of the 18 amino acids having synonymous codons. A supplemental analysis of Brassica napus suggests that bias in codon usage could also be higher in genes expressed in male gametophytic tissues than in heterogeneous (flower) tissues.ConclusionThis study reports gender-specific bias in codon usage in plants. The findings reported here, based on the analysis of 1 497 876 codons, are not caused either by differences in the biological functions of the genes or by differences in protein lengths, nor are they likely attributable to mutational bias. The data are best explained by gender-specific translational selection. Plausible explanations for these findings and the relevance to these and other organisms are discussed.
Highlights
There is little data available regarding the role of gender-specific gene expression on synonymous codon usage in most organisms, and plants
The data show, as described in detail below, http://www.biomedcentral.com/1471-2164/8/169 that genes specific to female tissues and gametes have a greater bias in codon usage in both Z. mays and T. aestivum than genes expressed in male tissues and gametes
The results show that female-specific genes consistently have higher values for relative synonymous codon usage (RSCU) for the preferred codons within each of these three protein length categories for Z. mays and T. aestivum (Table 3) [see Additional data file 1; Tables 1 to 3)] indicating that protein length variation does not explain the gender-specific bias observed for specific codons described in Table 2
Summary
There is little data available regarding the role of gender-specific gene expression on synonymous codon usage (translational selection) in most organisms, and plants. Tissue-specific gene expression has been associated with bias in codon usage in certain multicellular organisms including humans, Drosophila melanogaster, and Arabidopsis thaliana [1,2,3,4,5], very little data currently exists for most organisms, regarding the role of gender-specific tissues and gametes. BMC Genomics 2007, 8:169 http://www.biomedcentral.com/1471-2164/8/169 in female tissues/gametes [7] Such findings at the population level (short-term), suggest that gender could impact the selective processes that alter molecular evolution in plants, including the usage of synonymous codons. We focus on the evaluation of gender-specific codon usage in plants
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