南方农业学报2025，Vol.56Issue(2)：573-582,10.DOI:10.3969/j.issn.2095-1191.2025.02.021
鳄梨属3种油梨叶绿体基因组密码子偏好性分析
Codon bias analysis in chloroplast genomes of 3 avocado species in Persea
摘要
Abstract
[Objective]To study the codon bias in chloroplast genome of 3 avocado species in Persea,which could provide theoretical basis for improving the expression of exogenous genes in genetic engineering of avocado and molecu-lar breeding of avocado.[Method]The 49 coding region(CDS)sequences in chloroplast genomes of 3 avocado species in Persea(P.americana var.drymifolia,P.americana var.guatemalensis,P.americana var.americana)were selected as the study object.Using Excel 2010,Origin 2021,TBtools,CodonW 1.4.2,Chiplot online website and CUSP software,codon composition analysis,parameter correlation analysis,neutral mapping analysis,ENC-plot analysis,PR2-plot analysis and optimal codon analysis of chloroplast genomes codons of 3 avocado species were carried out.[Result]The se-quence of GC content at the first,second and third bases of the chloroplast genome codons of 3 avocado species was GC1>GC2>GC3,indicating that the distribution of GC at different codon locations was uneven.GC1 was positively correlated with GC2,GC3,GC and ENC,and the correlation coefficient between GC1 and GC was the highest(0.80).GC2 was negatively correlated with GC3 and ENC respectively.The results of neutral mapping analysis showed that the regression coefficients between the chloroplast genome GC3 and GC12 of P.americana var.drymifolia,P.americana var.guatemalensis and P.americana var.americana were 0.0956,0.0869 and 0.0872,and the correlation coefficients were 0.0050,0.0042 and 0.0043 respectively.It showed that codon bias was mainly influenced by natural selection.The results of ENC-plot analysis showed that most genes deviated from the standard curve and were scattered below the standard curve,while a few genes were distributed above or close to the standard curve,indicating that different genes were af-fected differently by mutation pressure and natural selection.The chloroplast codon preference of 3 avocado species were greatly affected by natural selection.PR2-plot analysis results showed that the usage bias of base T at the third position of the codon was higher than that of A,while that of G was higher than that of C,indicating that the usage bias of the codon was affected not only by mutation pressure,but also by natural selection and other factors.A total of 15 optimal codons were screened from 3 avocado species in Persea:UUU,UUA,UUG,CUU,AUU,GUU,UCU,CCU,CCC,ACU,ACC,GCU,UAA,UGU and AGA.[Conclusion]The codon bias in the chloroplast genomes of 3 avocado species in Persea are mainly influenced by natural selection,but also influenced by multiple factors such as mutation pressure,and most of the third bases of the 15 optimal codons screened ended in A/U.关键词
鳄梨属/叶绿体基因组/密码子偏好性/最优密码子Key words
Persea/chloroplast genome/codon usage bias/optimal codon分类
农业科技引用本文复制引用
杞美军,葛宇,张振伟,董诗浪,张镕麒,张秋燕,段雨婷,王凯,吕志鹏,黄文龙..鳄梨属3种油梨叶绿体基因组密码子偏好性分析[J].南方农业学报,2025,56(2):573-582,10.基金项目
国家自然科学基金项目(32260735) （32260735）
云南省"兴滇英才支持计划"青年人才项目(XDYC-QNRC-2022-0711) （XDYC-QNRC-2022-0711）
云南省专家基层科研工作站项目(2021RYZJGZZ004) （2021RYZJGZZ004）
云南农业大学本科实践教学、劳动教育和耕读教育教学改革研究与实践项目(2024SJJX036) National Natural Science Foundation of China(32260735) （2024SJJX036）
Young Talent Project of Yunnan Re-vitalization Talent Support Project(XDYC-QNRC-2022-0711) （XDYC-QNRC-2022-0711）
Yunnan Expert Basic Scientific Research Station Project(2021RYZJGZZ004) （2021RYZJGZZ004）
Yunnan Agricultural University Undergraduate Practical Teaching,Labor Education and Rural Edu-cation Teaching Reform Research and Practice Project(2024SJJX036) （2024SJJX036）
