西南林业大学学报2026，Vol.46Issue(3)：66-73,8.DOI:10.11929/j.swfu.202502025
3种扁核木属植物叶绿体基因组序列及密码子偏好性分析
Analysis of Chloroplast Genome Sequences and Codon Preferences in 3 Species of Prinsepia Plants
摘要
Abstract
This study aims to analyze the codon usage bias and its main influencing factors in the chloroplast genomes of 3 Prinsepia species,providing a scientific basis for understanding their codon optimization mechan-isms,preference patterns.The chloroplast genome sequences of P.utilis obtained through sampling and sequen-cing,along with those of P.sinensis and P.uniflora downloaded from the NCBI database,were processed in the Geneious bioinformatics software to filter and remove duplicate and CDS sequences shorter than 300 bp.Sub-sequently,CodonW 1.4.2 was employed to perform codon usage bias analysis on the screened CDS sequences and identify optimal codons.The findings revealed that the GCall content of the three species was 38.45％-39.08％,the effective codon number(ENC)of the chloroplast coding sequence of the genome was distributed between 35.60 and 61.00,the ENC value of protein coding genes was greater than 35,and their codon preference was weak.The 3 optimal codons shared by three species,the third base is mostly A/U.PR2-Plot analysis showed un-even distribution of genes in 4 regions.ENC-Plot analysis showed that most genes were distributed below the standard curve,and all genes were above the diagonal.In summary,natural selection is the primary factor influen-cing codon bias in the chloroplast genomes of three species of Prinsepia plants.Codon bases of the chloroplast genome from 3 Prinsepia plants species are mostly ended with A/U.The preference is weak and the main influen-cing factor is natural selection.Three optimal codons,including AAU,GAU,AGU are identified in this study.关键词
扁核木/东北扁核木/蕤核/叶绿体基因组/密码子偏好性/最优密码子Key words
Prinsepia utilis/Prinsepia sinensis/Prinsepia uniflora/chloroplast genome/codon preference/optimal codon分类
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赵飞亚,张捷,尹成龙,王婷,海永林,陶爱恩..3种扁核木属植物叶绿体基因组序列及密码子偏好性分析[J].西南林业大学学报,2026,46(3):66-73,8.基金项目
云南省2024年本科高校教育教学改革研究项目(JG2024096)资助 （JG2024096）
云南省教育厅科学研究基金项目(2022J1214)资助 （2022J1214）
丽江市中青年学术和技术带头人后备人才项目资助 （）
校级中青年学术和技术带头人后备人才项目资助. （）
