世界竹藤通讯2025，Vol.23Issue(6)：17-29,13.DOI:10.12168/sjzttx.2025.09.02.002
牡竹叶绿体基因组密码子偏好性分析
Codon Bias in Chloroplast Genome of Dendrocalamus strictus
摘要
Abstract
The codon usage bias in the chloroplast genome of Dendrocalamus strictus is analyzed to identify the major factors shaping its codon usage pattern and to determine the optimal codons,thereby providing a molecular basis for taxonomic and phylogenetic studies of the genus Dendrocalamus.The complete chloroplast genome sequence is retrieved from the NCBI database.Following data filtering,codon usage bias is analyzed using CodonW and EMBOSS,while correlation analyzes and visualization of gene feature parameters are performed using SPSS and R.The results reveal that:1)The chloroplast genome of D.strictus contains 50 effective protein-coding genes,with an overall GC content of 39.34%,where GC1(47.72%)>GC2(39.36%)>GC3(30.05%),indicating a strong bias toward A/U-ending codons.The mean values of ENC(50.38),CAI(0.17),CBI(-0.09),and FOP(0.36)suggest low expression levels of chloroplast genes and a weak codon usage bias;2)Neutral plot,ENC-plot,and PR2-plot analyzes collectively indicate that natural selection is the dominant force shaping codon usage bias in the chloroplast genome;3)Eighteen optimal codons(GCA,GCU,GAU,GGU,AAA,GUU,UUA,CCU,CAA,CGA,CGU,AGU,UCC,UCU,ACA,ACU,GUA,GUU)are identified,and 4)Phylogenetic analysis reveals that D.strictus forms a highly supported monophyletic clade with D.latiflorus and D.giganteus,suggesting a close genetic relationship.This indicates that codon usage patterns exhibit significant phylogenetic signal at the genus level.These findings provide new molecular evidence for phylogenetic reconstruction and offer valuable insights for future taxonomic and evolutionary studies of Dendrocalamus species.关键词
牡竹/密码子偏好性/叶绿体基因组/系统进化Key words
Dendrocalamus strictus/codon bias/chloroplast genome/system evolution引用本文复制引用
包豪峰,辉朝茂,李建伟,张朝行,李皓婷,张颖,刘蔚漪..牡竹叶绿体基因组密码子偏好性分析[J].世界竹藤通讯,2025,23(6):17-29,13.基金项目
云南省农业联合专项项目(202301BD070001-123) （202301BD070001-123）
国家重点研发计划项目(2021YFD2200501) （2021YFD2200501）
西南特色笋用林高效培育技术项目(2023YFD220120302) （2023YFD220120302）
云南省基础研究项目(202201AT070053). （202201AT070053）
