独脚金叶绿体基因组密码子偏好性分析  

Codon Usage Bias Analysis of Chloroplast Genome in Striga asiatica

作　　者：杨秀玲 许春梅 耿晓珊 甘静梅 刘秦 胡小虎 Yang Xiuling;Xu Chunmei;Geng Xiaoshann;Gan Jingmei;Liu Qin;Hu Xiaohu(Key Laboratory for Conservation and Utilization of Subtropical Bio-Resources,Education Department of Guangxi Zhuang Autonomous Region,College of Biology and Pharmaceuticals,Yulin Normal University,Yulin,537000)

机构地区：[1]玉林师范学院生物与制药学院,广西高校亚热带生物资源保护与利用重点实验室,玉林537000

出　　处：《分子植物育种》2023年第12期3889-3897,共9页Molecular Plant Breeding

基　　金：广西科技基地和人才专项(桂科AD20159013);广西自然科学基金青年科学基金项目(2019GXNSFBA245038);玉林师范学院博士科研启动项目(G2019ZK32)共同资助。

摘　　要：为明确独脚金叶绿体基因组密码子的使用模式及成因,本研究以筛选到的46条基因的CDS区为研究对象,利用CodonW 1.4.2、CUSP、SPSS 26.0等软件对独脚金叶绿体基因组密码子偏好性进行分析。结果表明:独脚金叶绿体基因组密码子3个位置的GC含量平均值依次为46.92%(GC_1)、39.78%(GC_2)、30.19%(GC_3),GC_1与GC_2呈极显著相关,二者与GC_3相关性不显著;ENC值分布于35.68~58.50,平均值为46.83,且ENC与GC_1、GC_2、GC_3、GC_(all)、Laa均无显著相关性,密码子偏好性较弱且受GC含量和基因长度的影响较小;RSCU>1的密码子共29个,偏好以A/U结尾(28个)。中性绘图分析显示,GC_(12)与GC_3回归系数为-0.0436,相关系数为-0.035,二者无显著相关性;ENC-plot分析显示,基因多分布于曲线的下方,仅有21.7%的ENC比值分布于-0.05~0.05;PR2-plot分析显示,基因分布不均匀,位于右下方的基因数量最多(占50%),密码子第3位碱基的使用频率表现为G>C,T>A。中性绘图、ENC-plot和PR2-plot 3种作图分析均表明,自然选择是独脚金叶绿体基因组密码子偏好性的主要成因。通过高频和高表达密码子筛选出15个最优密码子,分别为UAA、GCU、UGU、GGU、AUU、CUU、UUG、CCA、CCU、CGA、CGU、UCU、ACU、GUA和GUU。本研究为独脚金的分子进化与系统发生研究以及叶绿体基因工程研究提供了参考信息。In order to clarify the codon usage pattern of Striga asiatica chloroplast genome and its contributing factors,the codon usage bias of the 46 screened CDS region was analyzed using CodonW 1.4.2,CUSP,SPSS 26.0 and other software.The results showed that the average GC contents at the three positions of the codon in the chloroplast genome were 46.92%(GC_(1)),39.78%(GC_(2)),and 30.19%(GC_(3)),respectively.The value ranges of ENC was 35.68~58.50 with an average value of 46.83,and ENC was not significantly with GC_(1),GC_(2),GC_(3),GC_(all),and Laa,indicating that codon usage bias was weaker and less affected by GC content and gene length.There were 29 codons with RSCU>1,of which 28 ended with A/U,indicating that the codon preference ends with A/U(28).Neutral plot analysis showed that there was no significant correlation between GC_(12)and GC_(3)with regression coefficient of-0.0436 and correlation coefficient of-0.035.ENC plot analysis showed that most genes were distributed below the standard curve,and only 21.7%of the ENC ratios were distributed in the range of-0.05~0.05.PR2-plot analysis showed that the genes were mainly located in the lower right of the PR2 plan(accounting for 50%of the total),distributed unevenly.And the base usage frequency at the third position of the codon was expressed as G>C,T>A.Analysis of neutral plot,ENC-plot and PR2-plot showed that natural selection was the main factor affect the codon usage bias of Striga asiatica chloroplast genome.Finally,fifteen optimal codons were screened,namely UAA,GCU,UGU,GGU,AUU,CUU,UUG,CCA,CCU,CGA,CGU,UCU,ACU,GUA,and GUU.The results will provide reference information for the molecular evolution and phylogenetic research and chloroplast genetic engineering researchof Striga asiatica.

关 键 词：独脚金 叶绿体基因组 密码子偏好性 最优密码子 

分 类 号：S567.219[农业科学—中草药栽培]