河北科技大学学报2025，Vol.46Issue(1)：91-99,9.DOI:10.7535/hbkd.2025yx01010
紫叶苔(Pleurozia purpurea)线粒体基因组密码子偏好性分析
Analysis of codon usage bias in the mitochondrial genome of Pleurozia purpurea
摘要
Abstract
In order to enrich the understanding of the genetic basis of the genus Pleurozia purpurea,the codon usage bias(CUB)in the mitochondrial genome of Pleurozia purpurea and its main influencing factors were investigated.Firstly,protein-coding sequences were screened based on the complete mitochondrial genome of Pleurozia purpurea.Then,CodonW and EMBOSS explorer were utilized to calculate various metrics for each gene,including GC content,effective number of codons(ENC),codon adaptation index(CAI),and relative synonymous codon usage(RSCU).Finally,correlation analysis between parameters was analyzed and plotted using R software.The results show that:1)A total of 31 protein-coding sequences are identified from the mitochondrial genome of Pleurozia purpurea,with an average GC content of 38.17%and a GC content of 32.28%for the third base of codons,respectively.The average values for ENC and CAI are 50.29 and 0.17,indicating a preference for codons ending with A/U bases and a relatively weak CUB;2)ENC exhibits significantly positive correlations with GCall,GC3,and the length of amino acid encoding genes,indicating significant influences of GC content and gene length on CUB;3)Analyses including neutrality plot,ENC-plot and PR2-plot indicate that mutation pressure and natural selection jointly shaped the CUB,with mutation being the most important influencing factor;4)A total of 23 optimal codons are selected,most of which end with A/U.Therefore,the CUB in the mitochondrial genome of Pleurozia purpurea is relatively weak,influenced primarily by mutational pressure,and by factors such as natural selection,base composition,and gene length.The research results can provide reference for evolutionary studies of mitochondrial genomes in bryophytes.关键词
分子遗传学/紫叶苔属/密码子偏好性/线粒体基因组/最优密码子Key words
molecular genetics/the genus Pleurozia purpurea/codon usage bias/mitochondrial genomes/optimal codon分类
农业科技引用本文复制引用
杜梦雪,张鑫,高洁,毕胜,郝杰威,张莉娜..紫叶苔(Pleurozia purpurea)线粒体基因组密码子偏好性分析[J].河北科技大学学报,2025,46(1):91-99,9.基金项目
国家自然科学基金(32160315,31760054) （32160315,31760054）
海南大学科研启动项目(KYQD(ZR)-22105) （KYQD(ZR）
