摘要
研究阿里山潜蝇茧蜂线粒体全基因组密码子的使用偏好性,探讨其偏好性形成的主要因素,为掌握该寄生蜂线粒体基因组的特性和进化方向提供理论依据.提取阿里山潜蝇茧蜂线粒体全基因组中的13个蛋白质基因序列,通过CondonW、CAIcal软件分析蛋白编码基因密码子各位点的GC百分比及有效密码子数(ENC);利用MEGA 11软件计算同义密码子使用频率,并利用中性绘图和ENC绘图揭示密码子使用偏好性形成的原因.结果表明,13条蛋白质基因序列的GC_(1)、GC_(2)和GC_(3)百分比平均值分别为20.65%、22.42%和6.42%,GC总百分比平均值为16.50%.由此可见,阿里山潜蝇茧蜂线粒体基因组蛋白质编码序列的AU百分比远大于GC百分比,且该寄生蜂线粒体基因组偏好使用第3位为A/U的密码子.综合高频与高表达密码子,共选出13个最优密码子,皆以A/U结尾,分别是UUU、UUA、AUU、GUA、UCU、AGA、CCA、ACU、GCU、GCA、AAA、CGA、GGA;ENC平均值为29.50,且中性绘图分析表明,密码子GC_(12)百分比与GC_(3)百分比相关性不显著(P=0.665),表明阿里山潜蝇茧蜂线粒体全基因组密码子偏好性形成主要受自然选择的影响.
To provide a theoretical foundation for understanding the characteristics and evolutionary direction of the mitochondrial genome of Fopius arisanus(Sonan),this study investigated the codon use bias of this para-sitoid’s entire mitochondrial genome and analyzed the factors influencing this bias.Thirteen protein-coding genes(PCGs)were studied by analyzing the GC content of three codon sites,effective number of codon(ENC)using CodonW and CAIcal,and relative synonymous codon usage(RSCU)using MEGA 11.The cause of codon usage bias was analyzed by neutrality plots and ENC-plot mapping.Results showed that the average GC con-tent of positions 1,2 and 3 among the 13 protein gene sequences was 20.65%,22.42%,and 6.42%,respec-tively.The overall average GC content was 16.50%.It revealed that the AU content of the protein coding se-quence was significantly higher than the GC content,and that the codons A/U were favoured by the mitochon-drial genome of F.arisanus at position 3.Thirteen optimal codons including UUU,UUA,AUU,GUA,UCU,AGA,CCA,ACU,GCU,GCA,AAA,CGA and GGA were screened based on their high frequency and expres-sion levels.The third site of these optimal codons preferred to use A/U.The average value of ENC was 29.50,and the neutral plot analysis showed that the correlation between the content of codon GC_(12) and GC_(3) was not sig-nificant(P=0.665).The results from the neutrality plots and ENC-plot both showed that natural selection was major influencing factor on codon usage bias in the mitochondrial genome of F.arisanus.
作者
林翔
宋蕴哲
聂传朋
李焰焰
孟李涛
蔡普默
LIN Xiang;SONG Yun-zhe;NIE Chuan-peng;LI Yan-yan;MENG Li-tao;CAI Pu-mo(College of Tea and Food Science,Wuyi University,Wuyishan,Fujian 354300,China)
出处
《宁德师范学院学报（自然科学版）》
2024年第1期57-64,共8页
Journal of Ningde Normal University(Natural Science)
基金
福建省技术创新重点攻关及产业化项目(2023XQ019)
国家级大学生创新创业项目(202110397011)
福建省一流专业(园艺)(SJZY2020002)
武夷学院服务产业专项(2021XJFWCY01)
武夷学院高级人才引进项目(YJ201910).
