摘要
[目的]分析杓兰叶绿体基因组密码子的使用偏好性,探究影响杓兰叶绿体基因组密码子使用偏好性的主要因素,为兰科叶绿体基因组学研究提供参考。[方法]从NCBI数据库中下载完整的杓兰叶绿体基因组序列并进行蛋白编码序列筛选,利用EMBOSS在线程序计算各基因及密码子的GC含量,利用CodonW软件计算各基因的氨基酸长度(Laa)、有效密码子数(ENC)、同义密码子相对使用度(RSCU)、最优密码子使用频率(FOP)及各基因密码子的第3核苷酸碱基含量,利用SPSS软件分析各指标之间的相关性,利用Origin软件绘图。[结果]杓兰叶绿体基因组编码序列的密码子第3位碱基富含A和T,GC含量仅为29%,ENC值介于37.92~61.00之间,密码子偏好性不强,ENC与GC_(2)及GC_(3)均呈极显著相关。RSCU值大于1的密码子有34个,其中,29个以U或A结尾。ENC-plot分析、PR2-plot分析及中性绘图分析表明:影响杓兰叶绿体基因组密码子使用偏好性的主要因素为自然选择。对应性分析结果表明:编码光合系统蛋白基因的密码子具有相似的使用模式,编码其它类型基因的密码子则具有不同的使用模式,并最终筛选出最优密码子16个。[结论]本研究明确了自然选择是影响杓兰叶绿体基因组密码子使用偏好性的主要因素,并筛选出杓兰叶绿体基因的最优密码子,研究结果能够对兰科系统发育及叶绿体基因组密码子进化研究提供参考。
[Objective]To analyze the codon usage bias of Cypripedium calceolus chloroplast genome,and identify the main factors influencing codon usage bias of this species in order to provide reference for the chloroplast genomics research of Orchidaceae species.[Method]Downloading the complete chloroplast genome sequence of C.calceolus and screening the protein coding sequences,the EMBOSS online program was used to calculate the GC content of each gene and codon,and the software CondonW was used to calculate the length of amino acid(LAA),effective number of codon(ENC),relative synonymous codon usage(RSCU),frequency of optimal codons(FOP)and the acid base content of the third nucleoside of each gene codon.The software SPSS was used to analyze the correlation among each index,and software Origin was used to plot.[Result]The third codon position of C.calceolus chloroplast genome sequence was rich in A and T,and the GC_(3) content was only 29%.The ENC values varied from 37.92 to 61.00,indicating a relatively weak codon usage bias.The correlation between the number of effective codons and GC_(3) showed an extremely significant level.There were 34 codons with relative synonymous codon usage greater than 1 and 29 codons ending with A and U.Analysis of neutral plot,ENC-plot and PR2-plot showed that the preference of C.calceolus chloroplast genome codons was mainly influenced by natural selection.Correspondence analysis showed a similar pattern of codon usage bias of the genes encoding photosynthetic system proteins,while other types of genes were quite different.Sixteen codons were finally determined as the optimal codons.[Conclusion]This study confirms that natural selection is the main factor affecting codon usage bias of C.calceolus chloroplast genome.The optimal codon of this species is screened.The results can provide a reference for the phylogeny and chloroplast genome codon evolution of Orchidaceae.
作者
丁锐
胡兵
宗小雁
韩辰阳
张丽杰
陈旭辉
DING Rui;HU Bing;ZONG Xiao-yan;HAN Chen-yang;ZHANG Li-jie;CHEN Xu-hui(College of Land and Environment,Shenyang Agricultural University,Shenyang 110866,Liaoning,China;College of Bioscience and Biotechnology,Shenyang Agricultural University,Shenyang 110866,Liaoning,China;College of Forestry,Shenyang Agricultural University,Shenyang 110866,Liaoning,China)
出处
《林业科学研究》
CSCD
北大核心
2021年第5期177-185,共9页
Forest Research
基金
国家自然科学基金(31670378)
辽宁省“兴辽英才计划”项目(XLYC1807180)
沈阳农业大学大学生创新创业训练计划项目(2020-109)。
关键词
杓兰
叶绿体基因组
密码子偏好性
兰科
Cypripedium calceolus
chloroplast genome
codon usage bias
Orchidaceae
作者简介
并列第一作者:丁锐,博士,讲师。主要研究方向:植物生物技术与代谢工程。电话:15040207167。Email:mnidr7@syau.edu.cn;并列第一作者:胡兵,本科。专业:环境工程。电话:13842030986。Email:1735165327@qq.com;通讯作者:陈旭辉,博士,副教授。主要研究方向:兰科菌根生态学。电话:15040126208。Email:xhchen@syau.edu.cn。
