摘要
为分析滇楸(Catalpa fargesii)叶绿体基因组密码子的使用模式,本研究以滇楸叶绿体基因组密码子为研究对象,筛选出了38条蛋白编码序列,并利用CodonW和CUSP在线软件对其进行了中性绘图分析、ENC-plot和PR2-plot分析。结果表明:滇楸叶绿体基因组密码子平均GC含量为39.03%,不同位置上的GC含量依次是GC_(1)(47.51%)>GC_(2)(40.80%)>GC_(3)(28.78%),说明叶绿体基因组密码子末位碱基偏好以A和U结尾;其有效密码子数(effective number of codons,ENC)的范围为34.93~55.78,平均值为46.61,有25个ENC值大于45,表明其密码子的偏好性较弱;同义密码子相对使用度(relative synonymous codon usage,RSCU)分析表明,RSCU>1的密码子中有30个以A或U作为结尾,说明其密码子偏好以A和U结尾;中性绘图分析显示,GC_(12)和GC_(3)的相关性不显著,GC_(12)和GC_(3)的相关系数和回归系数分别为-0.0230和-0.0255,说明选择对密码子使用偏好性有重要影响;ENC-plot分析显示大部分基因分布于标准曲线下方,且ENC频数比值在-0.05~0.05的有13个,表明其密码子偏好性主要受选择的影响;在PR2-plot分析中,滇楸叶绿体基因组中大部分基因分布于平面图的右下方,即T>A和G>C,表明除核苷酸组成外还有其他因素影响其密码子使用偏好。进一步对应性分析发现第一轴的贡献率为15.21%,第二轴的贡献率为13.20%,第三轴、第四轴的贡献率分别为8.82%和7.35%,累计前四轴的贡献率为44.58%,与ENC的相关性达到显著水平,上述分析结果表明滇楸的叶绿体基因密码子偏好受到选择和突变因素的影响。最终UUU,UUA,CUU等15个密码子被确定为滇楸叶绿体基因组的最优密码子,显示出强烈的偏向于NNA和NNU密码子的高代表性。本研究为今后开展滇楸叶绿体基因工程、遗传多样性分析、种源鉴定等研究提供参考依据,同时也为梓属叶绿体基因组进化机制研究提供理论基础。
To analyze the codon usage pattern of chloroplast genome in Catalpa fargesii,C.fargesii chloroplast genome codons were taken as the research object and 38 protein coding sequences were screened out in this study.CodonW and CUSP online software were used to carry out the neutral plotting,ENC-plot and PR2-plot analyses.The results showed that the average GC content of codons in the chloroplast genome of C.fargesii was 39.03%,and the GC content at different positions was GC_(1)(47.51%)>GC_(2)(40.80%)>GC_(3)(28.78%).The base preference ended in A and U of the chloroplast genome.The effective codon number ENC ranged from 34.93 to 55.78,with an average value of 46.61.There were 25 ENC values greater than 45,indicated that the codon preference was weak.The relative synonymous codon usage(RSCU)analysis showed that there were 30 codons terminated as A or U when RSCU>1,indicated that their codon preference ends in A/U.The neutral drawing analysis showed that the correlation between GC_(12) and GC_(3) was not significant and the correlation coefficient and regression coefficient of GC_(12) and GC_(3) were-0.0230 and-0.0255,respectively,indicated that selection had an important influence on codon usage preference.ENC-plot analysis showed that most of the genes were distributed under the standard curve.There were 13 for ENC frequency ratio in the range of-0.05 to 0.05,indicated that the codon bias was mainly affected by the selection.Most of the genes in the chloroplast genome of C.fargesii were distributed in the lower right of the plan by the PR2-plot analysis,that was,T>A,G>C,indicated that there were other factors that affect its codon usage preference in addition to the nucleotide composition.Further correspondence analyses found that the contribution rate of the first axis was 15.21%,the contribution rate of the second axis was 13.20%,the contribution rates of the 3 rd and 4 th axes were 8.82% and 7.35%,respectively,and the cumulative contribution rate of the first 4 axes was 44.58%,the correlation with ENC had reached
作者
李江飞
李熙颜
王瑜
颜廷雨
孙继伟
蔡年辉
陈诗
许玉兰
Li Jiangfei;Li Xiyan;Wang Yu;Yan Tingyu;Sun Jiwei;Cai Nianhui;Chen Shi;Xu Yulan(Key Laboratory for Forest Genetic and Tree Improvement&Propagation in Universities of Yunnan Province,Southwest Forestry University,Kunming 650224;Key Laboratory of Ministry of Education for Conservation and Utilization of Mountain Forest Resources in Southwest China,Southwest Forestry University,Kunming,650224)
出处
《基因组学与应用生物学》
CAS
CSCD
北大核心
2022年第4期843-853,共11页
Genomics and Applied Biology
基金
国家自然科学基金项目(31860203,31760204)
云南省万人计划青年拔尖人才项目(09901-80201441)
西南林业大学高值木本油料新种质创制与产业化创新团队项目(2019HC007)共同资助。
关键词
滇楸
叶绿体
基因组
密码子偏好性
最优密码子
Catalpa fargesii
Chloroplast
Genome
Codon usage bias
Optimal codons
