云南樟叶绿体基因组密码子偏好性分析  

Analysis of codon usage bias in the chloroplast genome of Cinnamomum glanduliferum

作　　者：肖明昆 严炜[1] 熊贤坤[1] 沈绍斌[1] 宋记明[1] 易怀锋[1] 张林辉[1] XIAO Mingkun;YAN Wei;XIONG Xiankun;SHEN Shaobin;SONG Jiming;YI Huaifeng;ZHANG Linhui(Tropical and Subtropical Cash Crops Research Institute,Yunnan Academy of Agriculture Sciences,Baoshan 678000,Yunnan,China)

机构地区：[1]云南省农业科学院热带亚热带经济作物研究所,云南保山678000

出　　处：《中南林业科技大学学报》2022年第6期127-134,共8页Journal of Central South University of Forestry & Technology

基　　金：国家中医药管理局全国中药资源普查项目(GZY-KJS-2018-004)。

摘　　要：【目的】为明确云南樟叶绿体基因组密码子使用模式及其成因,确定最优密码子并为其遗传改良提供理论基础。【方法】利用CodonW 1.4.2和在线软件CUSP等对云南樟叶绿体基因组中的52条基因编码子序列密码进行分析。【结果】云南樟的ENC值在36.82~57.85之间,表明云南樟叶绿体基因组的密码子偏好性较弱。密码子不同位置上的GC含量表现为GC1(47.61%)>GC2(40.28%)>GC3(30.67%),且RSCU>1的密码子有31个,其中有29个以A或U结尾,表明密码子偏好以A或U结尾。中性绘图分析结果显示,GC12与GC3的相关系数为0.040,表明两者相关性不显著。ENC-plot分析表明,基因ENC比值大多数分布在-0.05~0.05区间外,即大部分基因ENC值与预期值差距较大。说明密码子偏好性更多受到选择的影响。PR2-plot分析表明,云南樟叶绿体基因组中的绝大多数基因分布在PR2图的中心点偏右下位置,说明选择是云南樟叶绿体基因组密码子偏好性的关键影响因素。通过构建高低基因表达库,结合高频及高表达密码子最终确定云南樟叶绿体基因组最优密码子12个,分别为,UUA、UCU、ACA、UAU、GCU、UAG、CAA、AAA、GAU、GAA、CGA、AGA,其中,11个以A或U结尾。【结论】云南樟叶绿体基因组的密码子偏好性比较弱,偏好以A或U结尾的密码子。密码子的使用偏好性主要受到选择的影响。研究结果可为云南樟叶绿体基因工程、种源鉴定提供科学依据。【Objective】This article aimed to clarify the codon usage pattern of the chloroplast(cp)genome of Cinnamomum glanduliferum and its genesis,and determine the optimal codon,to provide a theoretical basis for the genetic improvement of C.glanduliferum.【Method】52 CDS(coding DNA sequences)were selected from the cp genome of C.glanduliferum and the codon usage pattern and bias were analyzed by using CodonW 1.4.2 and the online software CUSP.【Result】The bias of codons was weak as the ENC value of the cp gene ranged from 36.82 to 57.85.The GC content at different positions of codon was GC1(47.61%)>GC2(40.28%)>GC3(30.67%).There were 31 codons with RSCU values above 1,among which 29 codons were rich in A or U,indicating that the codon prefers A or U genetic bases.There was no significant correlation between GC12 and GC3,and the correlation coefficient was 0.040.Based on the ENCplot analysis,the ENC ratios of most genes were distributed outside the range of-0.05-0.05,the differences between the actual and expected NEC values were very large,indicating that the codon bias was more influenced by selection.The PR2-plot analysis showed that most of the genes in the cp genome of C.glanduliferum were distributed in the lower right center of the PR2 plane,indicating that the codon bias of the C.glanduliferum genome was mainly affected by natural selection.Through the construction of a high and low gene expression library,combined with high frequency and high expression codons,12 optimal codons were identified in the cp genome of C.glanduliferum,which were UUA,UCU,ACA,UAU,GCU,UAG,CAA,AAA,GAU,GAA,CGA and AGA,and 11 of them ended with A or U.【Conclusion】The codon preference of C.glanduliferum genes is relatively weak,the majority of codons prefer ending with A or U.The formation of C.glanduliferum codon preference may be mainly influenced by natural selection.The results of the study can be a scientific basis for C.glanduliferum cp genetic engineering and its provenance identification.

关 键 词：云南樟 叶绿体基因组 密码子偏好性 最优密码子 

分 类 号：S792.23[农业科学—林木遗传育种]