广东农业科学2026，Vol.53Issue(5)：63-70,8.DOI:10.16768/j.issn.1004-874X.2026.05.005
小花吊兰叶绿体基因组密码子偏好性分析
Analysis of Codon Bias in Chlorophytum laxum Chloroplast Genome
摘要
Abstract
[Objective]To clarify the codon usage bias in the chloroplast genome of the medicinal plant Chlorophytum laxum,analyze the impacts of natural selection and mutation pressure on the formation of codon bias,and screen the optimal codons,so as to provide a theoretical basis for subsequent chloroplast genetic engineering and phylogenetic studies.[Method]The complete chloroplast genome sequence of C.laxum(OR078538)was obtained from the NCBI database.After strict filtering to exclude short sequences(＜300 bp)and sequences containing internal stop codons,49 valid protein-coding sequences(CDS)were obtained.Bioinformatics programs including CUSP and CodonW 1.4.2 were used to calculate the GC content at different codon positions(GC1,GC2,GC3,and GCall),the effective number of codons(ENC),and the relative synonymous codon usage(RSCU).Subsequently,combined with correlation analysis models such as neutrality plot,ENC-plot,and PR2-plot,the relative contributions of mutation pressure and natural selection to the formation of codon usage bias were comprehensively evaluated.Finally,the optimal codons of this species were identified by constructing high-and low-expression gene libraries.[Result]The average overall GC content(GCall)of the 49 chloroplast CDSs of C.laxum was 38.10％,and the GC content at different codon positions exhibited significant imbalance:GC1(46.92％)＞GC2(39.21％)＞GC3(28.17％).The ENC values ranged from 37.26 to 60.01,with an average of 46.70(genes with ENC＞45 accounted for 65.31％),indicating a weak overall codon usage bias.Correlation and neutrality plot analyses revealed no significant correlation between GC12 and GC3(R2=-0.011).The ENC-plot and PR2-plot indicated that the vast majority of genes deviated from the standard expected curve,and the usage frequencies of G and T at the third base position were higher than those of C and A,respectively.Through comprehensive screening,17 optimal codons(e.g.,UUU,UUA,AUU)were identified,all of which end in A or U.[Conclusion]The overall codon usage bias of the C.laxum chloroplast genome is relatively weak,with a strong preference for synonymous codons ending in A or U.This bias pattern is primarily driven by natural selection pressure,while the influence of gene mutation pressure is relatively weak.The 17 identified optimal codons can provide a reference for codon modification in the chloroplast genetic engineering of C.laxum and related Liliaceae plants.关键词
小花吊兰/密码子偏好性/叶绿体基因组/最优密码子/有效密码子数/自然选择/同义密码子/南药资源Key words
Chlorophytum laxum/codon usage bias/chloroplast genome/optimal codon/effective number of codons/natural selection/synonymous codon/southern medicinal resources分类
农业科技引用本文复制引用
李静宇,戴亦亨,顾艳,罗栩强,麦启健,蔡时可,王继华..小花吊兰叶绿体基因组密码子偏好性分析[J].广东农业科学,2026,53(5):63-70,8.基金项目
广东省农业科学院作物研究所-圭润南药联合实验室、汕尾市科技局重点项目(2021B007) （2021B007）
广东省农业科学院作物研究所所长基金(202602) （202602）
以农产品为单元的广东省现代农业产业技术体系创新团队建设项目(南药产业技术体系)(2026CXTD24) （南药产业技术体系）
南雄南药产业园科技支撑项目(2022) （2022）
乳源瑶药产业园科技支撑项目(2022) （2022）
