葫芦茶叶绿体基因组密码子偏好性分析

Analysis of Codon Usage Bias in the Chloroplast Genome of Tadehagi triquetrum

  • 摘要: 为探究葫芦茶叶绿体基因组密码子的使用模式及其成因,利用Illumina NovaSeq 6000平台进行建库测序,组装、注释获得了葫芦茶叶绿体的全基因组,并利用Codon W、CUSP、OriginPro等工具对筛选到的52条蛋白编码序列进行密码子偏好性分析。结果表明:葫芦茶叶绿体基因组密码子GC平均含量为GC1(45.64%) > GC2(38.17%) > GC3(25.56%),编码氨基酸的同义密码子中T3S和A3S的含量明显高于C3S和G3S;ENC值为38.43~55.04,平均值为45.64;CAI值为0.1~0.18,平均值为0.16;说明其密码子偏好性弱。相关性、中性绘图、ENC‒plot以及PR2‒plot分析表明,突变和选择共同影响葫芦茶叶绿体基因组密码子的使用偏好性。通过RSCU值和ENC值筛选出CUU、AUU、AUA、GUU、GAU、UCA、GGA共7个密码子,为葫芦茶叶绿体基因组的最优密码子,均偏向以A/U结尾。

     

    Abstract: To investigate the patterns and causes of the codon usage in the chloroplast genome of Tadehagi triquetrum, the complete chloroplast genome of T. triquetrum was sequenced using the Illumina NovaSeq 6000 platform, assembled and annotated, with the analysis of codon usage of the 52 screened CDS was performed by Codon W, CUSP and OriginPro. The results showed that the average GC content of T. triquetrum chloroplast genome codons was GC1(45.64%) > GC2(38.17%) > GC3(25.56%), and the content of T3S and A3S in the synonymous codons encoding amino acids was significantly higher than that of C3S and G3S. The ENC values ranged from 38.43 to 55.04 with an average of 45.64, and the CAI values ranged from 0.1 to 0.18 with an average of 0.16, indicating that their codon bias was weak. Analysis of correlation, neutral plotting, ENC‒plot, and PR2‒plot, indicating that mutation and selection jointly affect codon usage bias in the chloroplast genome of T. triquetrum. The optimal 7 codons(CUU, AUU, AUA, GUU, GAU, UCA, GGA) were selected of T. triquetrum by RSCU and ENC values, which were biased to end in A/U.

     

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