中国农业科技导报2025，Vol.27Issue(4)：87-98,12.DOI:10.13304/j.nykjdb.2024.0090
蓼属叶绿体基因组密码子偏好性分析及比较特征
Analysis and Comparative Characteristics of Codon Preference in Chloroplast Genome of Polygonum genus
摘要
Abstract
To explore the structure,function and evolutionary characteristics of chloroplast genome of Polygonum plants,the software of CodonW,SPSS and online programs Galaxy,Genepioneer Bioinformatics Cloud,mVISTA,GENE DENOVO and other tools were used to analyze the codon usage preferences and phylogenetic relationships of the chloroplast genomes of 28 Polygonum plants.The results showed that the codon adaptation index(CAI)and effective number of codon(ENC)in chloroplast genomes of 28 species of Polygonum plants were low,which indicated weak codon usage preference and being mainly influenced by natural selection.The third base of codon mainly ended in A/U,and 9 optimal codons of chloroplast genome all ended in A/U.The correlation analysis between the GC content at different positions of codon,ENC and GC3s,GC3,GC2 revealed that codon preference in chloroplast genome of Polygonum was weak and mainly influenced by the third base composition,while the length of the chloroplast gene sequence had less influence on base composition and codon preference.The phylogenetic tree based on the relative synonymous codon usage(RSCU)was consist with those besed on matk and rbcl gene sequences,28 species of Polygonum plants were classified into 3 groups,but there were differences in each group,such as P.maackiana was same group with P.tinctoria in phylogenetic tree based on matk gene,while was same group with P.posumbu in phylogenetic tree based on rbcl gene.Above results provided a reference for the utilization,phylogeny,and chloroplast genetic engineering of Polygonum plants.关键词
蓼属/叶绿体基因组/密码子偏好性/比较特征/系统发育Key words
Polygonum genus/chloroplast genome/codon preference/comparative features/phylogeny分类
农业科技引用本文复制引用
刘起麟,李金泽,丁佳渝,王烁理,程子铭,古康圆,冯光燕..蓼属叶绿体基因组密码子偏好性分析及比较特征[J].中国农业科技导报,2025,27(4):87-98,12.基金项目
国家重点研发计划项目((2021YFD1200105)) （(2021YFD1200105）
四川省饲草育种攻关项目(2021YFYZ0013) （2021YFYZ0013）
2024年大学生创新训练计划项目(202410626020). （202410626020）
