条斑紫菜叶绿体基因密码子偏爱性分析  

Analysis of Codon Bias of Chloroplast Genome in Porphyra yezoensis

作　　者：李国灵 潘宗莲 何雨阳 高诗晨 夏巧玉 靳燕 姚慧鹏[1] Li Guoling;Pan Zonglian;He Yuyang;Gao Shichen;Xia Qiaoyu;Jin Yan;Yao Huipeng(College of Life Science,Sichuan Agricultural University,Ya'an,625014)

机构地区：[1]四川农业大学生命科学学院,雅安625014

出　　处：《基因组学与应用生物学》2020年第12期5789-5795,共7页Genomics and Applied Biology

基　　金：四川省教育厅青年基金项目(13ZB0294);四川农业大学生命科学学院学科建设项目(2015HH0047)共同资助。

摘　　要：条斑紫菜是一种具有重要经济价值的藻类植物,广泛应用于医学、纺织和食品等领域。本研究通过Python、OGDRAW、CodonW、CUSP、DNAstar及SPSS20等软件进行多元统计和密码子偏爱性分析,并获得了56个条斑紫菜叶绿体基因序列的GC_(1)、GC_(2)、GC_(3)、ENC值和RSCU值,同时获得了条斑紫菜叶绿体基因组结构图和密码子使用热图。结果显示,条斑紫菜叶绿体基因的AT碱基含量高于GC碱基含量,说明其密码子偏爱于A/T碱基结尾。中性绘图分析、ENC绘图分析和PR2-plot分析结果表明影响条斑紫菜叶绿体基因密码子偏爱性的主要影响因素是自然选择。将高频密码子和高表达优越密码子结合,最终获得了9个条斑紫菜叶绿体基因的最优密码子,如UUU、UCA和CCU,均偏爱于A/U碱基结尾。研究结果为条斑紫菜的资源开发和培育利用,以及外源基因的稳定表达提供了重要的科学依据。Pyropia yezoensis is an algae plant with great economic value,which has been applicated widely in medicine,textile,food and etc.Our research conducted multivariate statistical and codon preference analysis by using Python,OGDRAW,Codonw,CUSP,DNA star,SPSS20 and other software,calculating the values of GC_(1),GC_(2),GC_(3),ENC and RSCU of 56 chloroplast gene sequences of P.yezoensis.Meanwhile,the maps of genome structure and codon usage of P.yezoensis were obtained.It is showed the AT-content in chloroplast gene of P.yezoensis was higher than that of GC-content,which indicates that its codon preferred ending with A/T.It is implied that natural selection is the main factor affecting codon preference of P.yezoensis’s chloroplast gene in neutral mapping analysis,ENC mapping analysis and PR2-plot analysis.The optimal codon analysis combined the high frequency codon with the high expression codon,getting nine optimal codons of P.yezoensis chloroplast genes finally,such as UUU,UCA and CCU,and they all preferred ending with A/U.The results furnish the resource development,cultivation and utilization of P.yezoensis and the stable expression of exogenous genes with an important scientific evidence.

关 键 词：条斑紫菜(Porphyra yezoensis) 叶绿体基因 密码子偏爱性 最优密码子 

分 类 号：S917.3[农业科学—水产科学]