| Rice is the more important and stable crop for human consumption, and about half of the population on earth depends on rice for live. As the model plant of cereal, the genomic research of rice attracts to great interests of lots of scientists. Recently, the draft genome sequences of indica and japonica rice, even for the final fine genomic data of 93-11 were determined, which announced the opening of another new way to resolve the world food crisis. In the present study, taking the hot genomic research points into consideration, We used the complete genome sequences as materials, and performed detailed analysis on codon usage bias and the sequence patterns surrounding the translation initiation and termination codon in rice, which would be significative during investigation of the evolution mechanism of species, modification and transformation of special genes, shedding further lights on the molecular mechanisms of efficiency of translation initiation and translation termination as well as readthrough events. Furthermore, the above analysis could give some useful clues for further improvement of gene prediction software and functional genome annotation. Herein the main results were summarized as follows.1. The biased codon usage of rice was the results of nucleotide compositional bias, gene expression level, and CDS length as well as the hydrophobicity of each protein. However, nucleotide compositional bias was the major factor in accounting for the variation of codon usage in the rice nuclear genome. On the contrary, the codon usage of the japonica rice chloroplast and mitochondrion genomes were mainly attributable to the gene expression level. Moreover, the major codons of the three genomes were determined respectively.2. The codon usage pattern between nuclear and chloroplast genomes was significantlydifferent. Regardless of the host genomic environment, the four plant chloroplasts were all preferential for A or U-ending codons, and no clear heterogeneity existed among genes. The results of neutrality plot analysis suggested low mutation bias or high conservation of GC content throughout the whole chloroplast genome. In contrast, large discrepancies should be occurred among plant nuclear genomes during the evolution process. Therefore, the emergence of chloroplast must be earlier than the monocotyledon-dicotyledon divergence.3. Synonymous codon usage and gene function were strongly related in rice nuclear. genome. It was found that the selection for biased codons, the magnitude of codon bias, and the selection intensity for preferred codons differed greatly among functional categories.4. There was no clear relationship between mRNA abundance, codon usage bias and the effectivity of AUG context for translation initiation. However, the GC content of AUG context could significantly enhance the efficiency of translation initiation. The eight positions (-1, -2, -3, -5, -6, +4, +5, and +6) being significantly strictly conserved would be concerned with translation initiation. Notably, the magnitude of conservation of seven positions (-18, -16, -15, -9, -7, -1, and +6) should be strongly related with the expressivity of highly expressed genes.5. Among all the examined codon positions around the stop codons, the -1 and +1 codon positions showed strictly biases, at where AAC and ACA were used more frequently respectively. Clearly different base preferences were observed among the UAA, UAG and UGA gene groups, among which base appearances at the positions directly downstream of the stop codons were much stronger than other positions, like at the +4, +5 and +6 positions. It could be speculated that these highly conserved base positions proximal to the stop codons, such as -2, -1, +4, +5, and +6 would act as part of the extended stop signal in translation termination. Compared with weakly expressed genes, significantly biased nucleotide context, like CterGCC, was much preferred in genes with extremely high expression levels. One of the possible explanations for this discrepancy would be that highly expressed genes must have the mechanisms not only...
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