西南农业学报2025，Vol.38Issue(4)：673-682,10.DOI:10.16213/j.cnki.scjas.2025.4.001
巨龙竹叶绿体基因组密码子偏好性分析
Condon usage bias in chloroplast genome of Dendrocalamus sinicus
摘要
Abstract
[Objective]The study aimed to investigate the use pattern of codons in the chloroplast genome of Dendrocalamus sinicus and its in-fluencing factors,and provide references molecula based research and species conservation for D.sinicus.[Method]The relevant sequences were downloaded from the NCBI database using GenBank accession number MK962316.1.The software Codon W,CUSP,SPSS and Excel were used to analyze the 52 genomic sequences of D.sinicus.[Result]The average GC content of the chloroplast genome was 39.4％,indica-ting a GC bias below 50％.The GC content exhibited the trend GC1(47.75％)＞GC2(39.55％)＞GC3(31.47％),suggesting an une-ven distribution and a preference for codons ending in A or U,particularly at the third codon position.The average ENC value was 50.51,with an 86.54％percentage,and the mean values of CAI,CBI and FOP were 0.167,-0.086 and 0.359,respectively,all indicating a weak codon usage bias.Correlation analysis showed that base composition significantly influenced codon usage,with the third codon base having the most substantial impact.Further analyses,including neutral mapping,ENC-plot and PR2-plot,suggested that natural selection was the primary factor driving codon usage preference in D.sinicus.Thirteen optimal codons(GCA,GCU,GAU,UUU,GGU,AAA,UUA,CAA,CGU,AGU,ACU,GUA,GUU)were identified as all of them were ending in A or U.[Conclusion]The codon preference of the chloroplast genome of the D.sinicus of them grouped is weak,with a preference for the use of A or U endings,which is mainly affected by base composition and mutation pressure in addition to natural selection pressure.A total of 13 optimal codons have been screened out,which can be used for research in the fields of D.sinicus germplasm improvement and genetic innovation.关键词
巨龙竹/叶绿体基因组/密码子偏好性/最优密码子Key words
Dendrocalamus sinicus/Chloroplast genome/Codon usage bias/Optimal codons分类
农业科技引用本文复制引用
曹建杰,辉朝茂,向自乾,蔡霖,胡梦茹,张寻梦,刘蔚漪..巨龙竹叶绿体基因组密码子偏好性分析[J].西南农业学报,2025,38(4):673-682,10.基金项目
国家重点研发计划项目(2021YFD2200501) （2021YFD2200501）
云南省基础研究项目(202201AT070053) （202201AT070053）
云南省农业联合专项项目(202301BD070001-123) （202301BD070001-123）
昌宁、澜沧农民院士科技服务站项目 （）
