【摘要】 本研究以银杏基因组数据为基础,利用HMMER软件对银杏WRKY家族进行预测,用保守域分析软件进行确认,再以密码子分析的序列筛选原则对序列进行筛选,共计筛选出34条基因编码序列作为研究对象,对其密码子使用偏向性进行分析。结果显示,银杏WRKY家族基因密码子GC含量范围在40.51%～52.07%,平均含量为45.60%,GC3平均含量为41.75%,说明该家族偏向使用以A或U结尾的密码子;ENC值在49.58～60.45之间,说明其密码子偏向性较弱;相对同义密码子使用度分析显示RSCU值大于1的密码子有23个,其中以A和U为结尾20个;中性绘图分析和ENC-plot曲线分析显示银杏WRKY家族基因GC3与GC12相关性并不显著,并且大部分基因ENC值偏离了理论值。综合分析发现突变和选择压力等诸多因素共同决定着银杏WRKY家族基因的密码子偏向性。银杏WRKY家族基因的最优密码子的确定是结合了高表达优越密码子分析法和高频密码子分析法,并最终确定出UUA、UUG、CCU等7个密码子为银杏WRKY家族基因的最优密码子。研究结果为银杏WRKY家族基因的密码子优化及其转基因研究中载体的选择提供理论依据。更多还原

【Abstract】 Based on ginkgo genom e data, HMMER software was used to predict ginkgo WRKY family, and conservative domain analysis software were used to confirm these predicted genes. Later, the sequences were screened based on the screen principle of codon analysis. 34 genes coding sequences were filtered as research object for codon usage bias analyzing. The results showed that the GC content in gene codon of ginkgo WRKY family ranged from 40.51% to 52.07%, and the average content was 45.60%, as well as the average GC3 content was 41.75%, suggesting that genes of this family favored the codons end with A or U. The effective number of codons(ENC) value ranged from 49.58 to 60.45, indicating that these genes had low codon bias. The relative synonymous codon usage(RSCU) analysis showed that the number of codons with RSCU value above 1 was 23,and 20 of them ended with ’ A’ and ’ U’. Neutral plot and ENC-plot curve analysis found that there was no significant correlation between GC3 and GC12 of ginkgo WRKY family genes, and most ENC value had deviated from the theoretical value. Comprehensive analysis suggested that many factors such as mutation and selective pressure jointly determined the codon bias of ginkgo WRKY family genes. The determination of the optimal codon of ginkgo WRKY family genes was on the basis of the combination of high expression superior codon analysis method and high-frequency codon analysis method, and seven codons including UUA, UUG, CUU and other codons were determined as the optimal codon of ginkgo WRKY family genes. These results might provide theoretical references for codon optimization of ginkgo WRKY family genes and the selection of vector in transgenic research.更多还原