基于全基因组的毛竹同义密码子使用偏好性分析

Synonymous codon bias of Phyllostachys edulis

密码子使用偏好性是物种在遗传信息传递过程中的一个重要特点,分析物种的密码子使用偏好性对于了解该物种遗传信息的传递规律具有重要意义。应用Codon W软件对毛竹Phyllostachys edulis基因组中的26 103个蛋白质编码基因序列进行了分析,计算了位于密码子3个位置的G+C含量、有效密码子数、同义密码子的使用频率等,确定了毛竹的最优密码子。结果显示:毛竹密码子第1位和第3位的G+C含量明显高于第2位,表现出对以G或C碱基开头和结尾的密码子发生强烈偏向使用,且确定的26种最优密码子均以G/C碱基结尾。与模式动植物酵母Saccharomys cerevisiae,大肠埃希菌Escherichia coli,果蝇Drosophila melanogaster,拟南芥Arabidopsis thaliana,烟草Nicotiana tabacum,水稻Oryza sativa,玉米Zea mays,小麦Triticum aestivum等8个代表性物种进行比较,结果显示:毛竹密码子偏好性与模式动植物存在不同程度的差异,与大肠埃希菌、酵母、果蝇、拟南芥、烟草和玉米的差异较大,差异分别为8个、11个、6个、7个、6个和6个,而与小麦的差异较小(1个),与水稻完全一致。密码子偏好性差异大小在一定程度上反映物种间的进化关系。

Analysis of codon usage bias for different species, an important characteristic of genetic information transfer in organisms, is important for understanding the rules of genetic information transfer. To better under-stand the characteristics of Phyllostachys edulis, coding DNA sequences （CDS） of 26 103 proteins in this species were analyzed. The content of G＋C at three positions of codons’ the Effective number of codons （ENC） and frequency of synonym codon usage for genes were calculated the “optimal codons”. were determined by Codon W, CHIPS and CUSP. Then, the frequency of codon usage for Ph. edulis with other organisms in-cluding five model value species （Drosophila melanogaster, Saccharomys cerevisiae, Escherichia coli, Ara- bidopsis thaliana, and Nicotiana tabacum） and three other Gramineae species （Oryza saliva, Zea mays, and Triticum aestivum） were compared. Results showed that the content of G＋C at the first and third position of codons was much higher than that of the second positions, and genes preferred codons with C or G in the syn-onymous position. Meanwhile, 26 codons, ending with G or C, were determined as the “optimal codons” . Fre-quency of codon usage also had fewer differences for the three Gramineae species than it did for the six model value species. To some extent, differences in the size of codon bias reflected the evolutionary relationships be-tween species. These results provided the useful information for understanding the evolution of Ph. edulis [Ch,1 fig. 4 tab. 29 ref.]