摘要
为了明确杜梨叶绿体基因组密码子的使用偏性,以杜梨叶绿体基因组中的37条蛋白质编码序列为研究对象,利用Codon W 1.4.2和在线软件CUSP等对其密码子进行了中性绘图分析、ENC-plot和PR2-plot分析。结果表明:(1)杜梨叶绿体基因组密码子不同位置GC碱基含量为:GC(148.45%)>GC2(40.76%)>GC(328.66%),说明密码子末位碱基偏好以A/U结尾;(2)有效密码子数(ENC)取值范围是33.13~52.73,表明密码子偏性较弱;(3)相对同义密码子(RSCU)分析表明,其值>1的密码子有30个,其中以A、U结尾的有29个;(4)GC3和GC12无显著相关,相关系数和回归系数分别为-0.1434和0.2072;ENC-plot中大部分基因分布于曲线周围和下方,ENC比值分布在-0.05~0.05区间的有14个,说明密码子偏性主要受选择的影响;PR2-plot分析中,T的使用频率高于A,G的使用频率高于C,说明密码子偏性受多重因素影响;(5)最终筛选出UUU、UAA、AUU等18个密码子为最优密码子,多以A或U结尾。综上所述,杜梨叶绿体基因组密码子的使用主要受选择影响,研究结果可为杜梨乃至梨属植物叶绿体基因组学的研究提供理论依据。
In order to realize the usage bias of codons in Pyrus betulifolia chloroplast genome,37 CDS of P.betulifolia chloroplast genome were used as the research object,and the codons were analyzed by neutral plotting,ENC-plot and PR2-plot using Codon W 1.4.2 and online software CUSP.The results showed that:(1)the GC content at different locations of the codons in the chloroplast genome of P.betulifolia were GC1(48.45%)>GC2(40.76%)>GC3(28.66%),indicating that the codon terminal base preferred to end with A/U.(2)The value range of the effective codon number(ENC)was 33.13-52.73,indicating weak codon bias.(3)Relative synonymous codon(RSCU)analysis showed that there were 30 codons with the RSCU value>1,and 29 codons ending with A and U.(4)There was no significant correlation between GC3 and GC12,and the correlation coefficient and regression coefficient was-0.1434 and 0.2072,respectively.Most of the genes in ENC-plot were distributed around and below the curve,and 14 ENC ratios were distributed between-0.05 and 0.05,indicating that codon bias was mainly affected by selection.In PR2-plot analysis,the usage frequency of T was higher than that of A,and G was higher than C,so the preference of P.betulifolia chloroplast genome codon was affected by multiple factors.(5)Finally,18 codons such as UUU,UAA and AUU were selected as the optimal codons,most of which ended with A or U.In conclusion,the use of codons in chloroplast genomics of P.betulifolia is mainly influenced by selection.The theoretical basis is provided by this study for the research of chloroplast genomics of P.betulifolia and even Pyrus genus plants.
作者
辛雅萱
董章宏
瞿绍宏
刘成
叶鹏
辛培尧
XIN Yaxuan;DONG Zhanghong;QU Shaohong;LIU Cheng;YE Peng;XIN Peiyao(Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of Ministry of Education/Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China,Southwest Forestry University,Kunming 650224,China)
出处
《河北农业大学学报》
CAS
CSCD
北大核心
2020年第6期51-59,共9页
Journal of Hebei Agricultural University
基金
国家重点研发计划子课题项目(2017YFD060120204)
云南省科技厅科技计划项目(2018BB005).
