灭字脊虎天牛线粒体基因组密码子使用偏好性分析  

Analysis of Codon Usage Bias of Mitochondrial Genome in Xylotrechus quadripes

作　　者：付兴飞 李亚麒 程金焕[1] 李贵平[1] 李亚男[1] 黄家雄[1] 杨旸[1] 胡发广[1] FU Xing-fei;LI Ya-qi;CHENG Jin-huan;LI Gui-ping;LI Ya-nan;HUANG Jia-xiong;YANG Yang;HU Fa-guang(Institute of Tropical and Subtropical Cash Crops,Yunnan Academy of Agricultural Sciences,Baoshan 678000,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：《江西农业学报》2023年第6期101-107,共7页Acta Agriculturae Jiangxi

基　　金：云南省重大科技专项计划“咖啡产业提质增效关键技术研发与示范”(202202AE090002)。

摘　　要：以筛选的16条灭字脊虎天牛(Xylotrechus quadripes)线粒体的CDS蛋白编码序列为研究对象,通过Codon W和CUSP在线软件对灭字脊虎天牛密码子进行组成分析。结果表明:灭字脊虎天牛线粒体基因组密码子不同碱基位置的GC含量不同,排序为GC_(3)(47.14%)>GC_(1)(46.85%)>GC_(2)(33.98%),密码子偏好使用以碱基A/T结尾;中绘图分析显示GC12与GC3间无显著相关性(R=0.229,P=0.393),密码子第3位碱基可能与前2位碱基的构成不同;ENC-plot分析显示,16个基因离标准曲线一定距离,ENC的实际值与预测值有差异,密码子偏好性更多受到自然选择的影响;PR2-plot绘图分析,密码子第3位碱基使用具有偏好性,碱基使用频率表现为T高于A,C高于G;筛选出最优密码子17个,多以A/U结尾。灭字脊虎天牛线粒体基因组密码子偏好性较弱,对A/U碱基结尾的密码子具有偏好性,偏好性使用受突变动力、自然选择及基因表达等因素共同影响,但自然选择的影响更显著。The 16 selected CDS coding protein sequences of mitochondrial genome in Xylotrechus quadripes were used as the research object,and codon preference was analyzed by Codon W and CUSP online software.The results showed that the GC content of mitochondrial genome codon of X.quadripes was different at different base locations.The order was GC_(3)(47.14%)>GC_(1)(46.85%)>GC_(2)(33.98%),indicating that the X.quadripes codon usage bias ended with A/T.Neutral plot analysis showed that there was no significant correlation between GC12 and GC3(R=0.229,P=0.393).The third base of the codon may have a different composition from the first two.In the ENC-plot analysis,16 genes were at a certain distance from the standard curve,manifesting that there was a certain difference between the actual value of ENC and the expected value of ENC,indicating that the codon bias was more influenced by natural selection.The use of the third codon base was biased,and usage frequency of T was higher than that of A,and C was higher than G.17 codons were selected as the optimal codons,most of which ended with A/U.The mitochondrial genome codon of X.quadripes is weak,and prefers to use the A/U ending codon.Multiple factors associated with the codon usage bias,such as natural selection,mutation and gene expression level,among which natural selection is the major factor.

关 键 词：灭字脊虎天牛 线粒体基因组 密码子偏好性 自然选择 

分 类 号：S435.712[农业科学—农业昆虫与害虫防治]