旱柳叶绿体基因组的密码子偏好性特征分析OA
Characterization of Codon Usage Bias in the Chloroplast Genome of Salix matsudana
旱柳是一种兼具生态与经济价值的植物,为揭示旱柳叶绿体基因组密码子偏好性及其驱动因素,利用CodonW和CUSP软件分析了筛选后的 51 条蛋白质编码序列的密码子使用特征.结果表明:旱柳叶绿体基因组密码子的第 1～3 位的GC含量以及总GC含量分别为 45.85%、37.77%、29.41%以及 37.67%;ENC值的范围为 33.59～57.39,平均值为 45.49.其中,有 33 个基因的ENC值超过 45,表明旱柳大部分基因编码序列的密码子使用偏性较弱;此外,共有 32 个密码子的RSCU值≥1,且这些密码子更倾向于以A或U结尾.进一步的中性绘图分析、ENC-plot分析和PR2-plot偏倚分析表明,旱柳叶绿体基因组密码子的使用偏好性受到自然选择压力和突变等因素的共同影响,其中自然选择为主要驱动因素;根据RSCU和ENC的评价最终在旱柳叶绿体基因组中确定了 13 个最优密码子.
Salix matsudanais is a plant of both ecological and economic value.To uncover the codon usage bias(CUB)and its driving factors in the chloroplast genome of S.matsudana,CodonW and CUSP software were used to analyze the codon usage patterns of 51 filtered protein-coding sequences.The results showed that the GC content of the GC1,GC2,GC3 and the GCall content of the codons in the chloroplast genome of S.matsudana were 45.85%,37.77%,29.41%,and 37.67%,respectively.The effective number of codons(ENC)values ranged from 33.59 to 57.39,with an average of 45.49,and 33 genes had ENC values exceeding 45,indicating weak codon us-age bias in most protein-coding sequences.Additionally,32 codons had relative synonymous codon usage(RSCU)values≥1,and these codons were more likely to end with A or U.Further neutrality plot,ENC-plot,and PR2-plot analyses suggested that mutation and natural selection commonly influenced codon usage bias,with natural selec-tion being the predominant factor.Through the analysis,13 optimal codons were identified in the chloroplast gen-ome of S.matsudana,providing theoretical support for its genetic improvement and gene engineering applications.
Zou Dajie;Guo Borui;Liu Jiaqian;Lu Xingxing;Sun Yuying;Wang Jiuli
College of Pharmacy,Qinghai Minzu University,Xining Qinghai 810007,ChinaCollege of Ecological Environment and Resources,Qinghai Minzu University,Xining Qinghai 810007,ChinaCollege of Ecological Environment and Resources,Qinghai Minzu University,Xining Qinghai 810007,ChinaCollege of Ecological Environment and Resources,Qinghai Minzu University,Xining Qinghai 810007,ChinaCollege of Ecological Environment and Resources,Qinghai Minzu University,Xining Qinghai 810007,ChinaCollege of Ecological Environment and Resources,Qinghai Minzu University,Xining Qinghai 810007,China
农业科技
旱柳密码子偏好性最优密码子叶绿体基因组
Salix matsudanacodon usage biasoptimal codonchloroplast genome
《西南林业大学学报》 2026 (1)
74-80,7
青海省科技重大专项项目(2023-SF-A5)资助.
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