西南林业大学学报2025，Vol.45Issue(5)：82-92,11.DOI:10.11929/j.swfu.202406061
3种毛蕊花属植物叶绿体基因组密码子偏好性研究
Analysis of Codon Bias in the Chloroplast Genome of 3 Species of Verbascum
摘要
Abstract
To explore the codon usage bias and its main influencing factors in the chloroplast genome of Verbascum plants,the chloroplast genome protein-coding sequences(CDS)of Verbascum thapsus,V.phoeniceum and V.songaricum were downloaded from the NCBI database,and the complete sequence of CDS,excluding du-plicates and that less than 300 bp in length,was selected for further analyses using Geneious v.7.1.3 bioinformat-ics software.Codon W 1.4.2,CUSP and SPSS 26 were used to analyse the effective codon count(ENC),the relat-ive usage of synonymous codons(RSCU),the GC content of bases 1,2,and 3 of the gene codon(denoted as GC1,GC2,and GC3,respectively)and the average GC content(GCall).Multivariate statistics from neutral plot analysis,PR2-plot analysis,and ENC-plot analysis were employed to predict the codon usage preference patterns in the chloroplast genomes of 3 species of Verbascum and to screen the optimal codons.The results showed that the complete chloroplast genomes of the 3 species of Verbascum had sequence lengths of 153 338 bp,153 348 bp,and 153291 bp,respectively,and the ENC values of the protein-coding genes of the 3 species of Verbascum exceeded 35,indicating that the codon preference of the chloroplast genomes of the 3 species of Verbascum was weak;and the average GC content at each position of the codon(GCall)was 38.31％,38.00％,38.00％,respectively.In addi-tion,GC1(46.83％)＞GC2(39.63％)＞GC3(28.49％)in V.thapsus;similarly,GC1(46.12％)＞GC2(38.40％)＞GC3(29.50％)in V.phoeniceum;and GC1(46.07％)＞GC2(38.38％)＞GC3(29.56％)in V.songaricum,indicat-ing that the distribution of GC content was not uniform in different locations of different species.In brief,natural selection was the primary factor influencing codon preference in the chloroplast genomes of the 3 Verbascum spe-cies.Furthermore,the RSCU and ENC values were used to identify 11,15,and 11 optimal codons in V.thapsus,V.phoeniceum,V.songaricum,respectively,among which there were 9 common optimal codons,namely AUA,UCC,GCC,AAU,GAU,UGC,UGA,CGU,AGU,and most of codons preference ends with A/U.关键词
叶绿体/基因组/密码子/偏好性/毛蕊花/紫毛蕊花/准噶尔毛蕊花Key words
chloroplast/genome/codon/preference/Verbascum thapsus/Verbascum phoeniceum/Verbas-cum songaricum分类
农业科学引用本文复制引用
尹成龙,许灵杰,张玥,海永林,赵飞亚,陶爱恩..3种毛蕊花属植物叶绿体基因组密码子偏好性研究[J].西南林业大学学报,2025,45(5):82-92,11.基金项目
云南省科技厅基础研究计划面上项目(202101AT070001)资助 （202101AT070001）
云南省教育厅科学研究基金项目(2022J1214)资助 （2022J1214）
云南省大学生创新创业训练计划项目(SC20201332804、SC20211332803、SC202213328004)资助 （SC20201332804、SC20211332803、SC202213328004）
丽江市科技计划项目(2022LJSHFZ010)资助 （2022LJSHFZ010）
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. （）
