梓叶槭基因组密码子偏好性分析

Codon Usage Bias Analysis in the Acer amplum subsp.catalpifolium Genome

为确定槭属极小种群野生植物梓叶槭的基因组密码子使用模式和可能成因,以梓叶槭基因组中筛选的33034个编码基因为对象,利用Codon W 1.4.2、CUSP在线程序和R 4.1.1分别进行中性绘图、PR2-plot与ENC-plot分析,揭示梓叶槭基因组密码子使用偏好性及其影响因素,确定最优密码子。结果表明,1)梓叶槭基因组密码子GC含量在0.278~0.697,不同位置上的GC平均含量为GC_(1)(0.494)>GC_(3)(0.417)>GC_(2)(0.397),表明梓叶槭基因组密码子末位碱基偏好以A和U结尾;2)基因组中有效密码子数(ENC)在25.530~61.000,且大部分基因的ENC值>35,表明密码子偏好性较弱;3)PR2-plot与ENC-plot绘图分析结果显示,突变和选择等因素都在梓叶槭基因组密码子偏好性中起到了影响作用,但梓叶槭基因组受到突变压力的影响更大;4)最终确定UUU,UGU,CAA等29个密码子为梓叶槭基因组的最优密码子。研究结果为梓叶槭基因功能解析与后续利用基因工程技术改良槭属植物重要性状奠定了研究基础。

In order to determine the genomic codon usage patterns and possible causes of the minimal population of Acer amplum subsp.catalpifolium,33034 coding genes of the A.amplum subsp.catalpifolium genome were used for analysis.Codon W 1.4.2,CUSP online program,R 4.1.1 were used for the analysis of neutral plot,PR2-plot,and ENC-plot.The objectives of this study were to reveal the codon usage bias of the A.amplum subsp.catalpifolium genome and the potential causing factors,and to determine the optimal codons.The results showed that 1)the GC content in the codon genes of the genome ranged from 0.278 to 0.697,and the average GC content in different positions was GC_(1)(0.494)>GC_(3)(0.417)>GC_(2)(0.397),indicating that the third base of the genome codon prefers to end with A and U.2)ENC varied from 25.530 to 61.000.The ENC value of most genes was more than 35,indicating that codon usage bias is weak.3)PR2-plot and ENC-plot analysis showed that the mutation and selection both had contributions to the codon preference,but mutation stress may be a more important causing factor in the genome.4)The 29 optimal codons such as UUU,UGU,and CAA were determined.These results provide a basis for the further studies in the gene function of A.amplum subsp.catalpifolium and for the improvement of important traits in Acer species through genetic engineering.