西南林业大学学报2026，Vol.46Issue(3)：74-81,8.DOI:10.11929/j.swfu.202503052
南川梅花草叶绿体基因组密码子偏好性分析
Analysis of Codon Usage Bias in Chloroplast Genome of Parnassia amoena
摘要
Abstract
To investigate the codon usage pattern and major influencing factors in the chloroplast genome of Parnassia amoena,the complete chloroplast genome of P.amoena was used as the research object.Through screening and removing duplicate genes,a total of 44 coding DNA sequences(CDS)were ultimately obtained.These sequences were analyzed using Codon W 1.4.2 and CUSP programs,including assessments of codon base composition,neutral plot analysis,ENC-plot analysis,PR2-plot analysis,and optimal codon identification.The results showed that the GC content at the three positions of codons in the chloroplast genome of P.amoena was GC]＞GC2＞GC3,indicating a preference for A/T(U)at the end of codons.The average effective number of codons(ENC)in the genome was 48.05,indicating a relatively weak codon usage bias in P.amoena.A highly significant positive correlation was observed between ENC and GC3,suggesting that the nucleotide composition at the third codon position influences codon usage bias.The neutral plot results showed the codon usage bias is influenced by 48.15％mutation pressure and 51.85％selection pressure.Combined with ENC-plot and PR2-plot analyses,it fur-ther indicates that both base mutation and natural selection jointly influence the codon usage pattern in the chloro-plast genome of this species,with natural selection playing a dominant role.Furthermore,optimal codon analysis identified 19 optimal codons(including UUA,AUU,and GUA)in the P.amoena chloroplast genome,most of which terminate with U,while the remainder end with A.关键词
南川梅花草/叶绿体/基因组/密码子/偏好性/遗传密码Key words
Parnassia amoena/chloroplast/genome/codon/usage bias/genetic code分类
生物科学引用本文复制引用
雷智淋,王世琪,舒渝民..南川梅花草叶绿体基因组密码子偏好性分析[J].西南林业大学学报,2026,46(3):74-81,8.基金项目
西华师范大学校级科研项目(20A002)资助. （20A002）
