种子2025，Vol.44Issue(6)：58-67,10.DOI:10.16590/j.cnki.1001-4705.2025.06.058
紫金牛属12种植物叶绿体基因组密码子使用模式与系统发育分析
Codon Usage Patterns and Phylogenetic Analysis on the Chloroplast Genomes of 12 Plant Species of Ardisia
摘要
Abstract
To explore the preference of chloroplast genome codon usage and its influencing factors in plants of the genus Ardisia,Codonw 1.4.2,CUSP,Genepioneer and other software were used to ana-lyze the codon usage patterns of chloroplast genomes and the main factors affecting codon usage pref-erence of 12 species of plants,and phylogenetic trees were constructed based on chloroplast genome coding regions(CDS).Nucleotide composition analysis indicated that the codon usage patterns in the chloroplast genomes of 12 species of Ardisia were similar,with codons enriched in A/U bases and more inclined to end with A and U.The analysis results of ENC-Plot,PR2-Plot and Neutrality plot indicated that natural selection was the main factor influencing the preference of cryptography for spe-cies of Ardisia.Based on the usage degree of the paired key codons(RSCU)and the difference be-tween high and low RSCU(ΔRSCU),a total of 29 high-frequency codons and 8 optimal codons were screened out.Codon usage frequency analysis revealed that Arabidopsis thaliana and Nicotiana taba-cum L.could be given priority as gene expression receptor systems for plants of Ardisia species.This study for the first time described the codon usage patterns and characteristics of the chloroplast ge-nomes of plants of the Ardisia species,and constructed a phylogenetic tree based on the coding re-gions of the chloroplast genomes,providing new insights into the evolution of plants of this genus.At the same time,it offerred references for the protection of medicinal plant resources of the Ardisia species,the screening of high-quality germplasm,and genetic engineering research.关键词
密码子偏好性/紫金牛属/叶绿体基因组/系统发育Key words
codon preference/Ardisia Swartz/chloroplast genome/phylogeny分类
农业科技引用本文复制引用
周永鑫,王悦云,魏升华,吴之坤,李顺珍,严福林..紫金牛属12种植物叶绿体基因组密码子使用模式与系统发育分析[J].种子,2025,44(6):58-67,10.基金项目
国家重点研发计划项目(2018YFC1708101) （2018YFC1708101）
贵州省科技计划项目(黔科中引地[2022]4016) （黔科中引地[2022]4016）
贵州省中药材现代产业技术体系建设项目(GZCYTX2025) （GZCYTX2025）
贵州中医药大学科研项目:朱砂根、红花龙胆、淫羊藿三种贵州民族药材栽培关键技术研究 （）
