细基江蓠线粒体基因组密码子偏好性分析  

Analysis of Codon Bias in Mitochondrial Genome of Gracilaria tenuistipitata

作　　者：邱春桃 梁芳梅 吕颖 王鹏良 朱鹏 张虹 许尤厚 Qiu Chuntao;Liang Fangmei;Lü Ying;Wang Pengliang;Zhu Peng;Zhang Hong;Xu Youhou(Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation,Beibu Gulf University,Qinzhou,535011)

机构地区：[1]北部湾大学,广西北部湾海洋生物多样性养护重点实验室,钦州535011

出　　处：《分子植物育种》2024年第8期2555-2563,共9页Molecular Plant Breeding

基　　金：钦州市科学研究与技术开发项目(No.2015270602);广西北部湾海洋生物多样性养护重点实验室项目(2018ZB02)共同资助。

摘　　要：以细基江蓠为研究对象,选取其线粒体基因组序列中以AUG为起始密码子且长度大于300 bp的22条非重复序列来进行密码子偏好性分析。结果表明:密码子第3位的平均GC含量为14.60%;ENC的分布范围为28.48~43.36,平均值为36.51;RSCU值>1的密码子共有29个,且密码子全部是以A或U结尾。中性绘图分析显示,GC_(12)与GC_(3)之间的相关系数为0.297,相关性未达到显著水平;ENC-plot分析发现,大部分基因位于标准曲线的附近;PR2-plot绘图分析显示,密码子第3位碱基含量T>A、G>C;对应性分析表明,第1、第2、第3、第4向量轴的贡献率分别为23.96%、11.15%、9.95%和6.38%,第1向量轴与GC、CAI、ENC、GC_(3s)均无显著相关,最终把AUA、CUU、CCA、ACU、GCU、GAA、UGA、CGA、AGU和AGA 10个密码子确定为最优密码子。研究结果为今后优化细基江蓠线粒体基因组密码子,提高表达效率和改良细基江蓠目标性状提供理论基础。Taking Gracilaria tenuistipitata as the research object,22 non-repetitive sequences of the mitochondrial genome sequence longer than 300 bp with AUG as the start codon were selected for codon bias analysis.The results showed that the average GC content at position 3 of the codon was 14.60%;the range of ENC is 28.48~43.36,the average value is 36.51;there are 29 codons with RSCU value>1,and all codons are End with A or U.Neutrality plot analysis shows the correlation coefficient between GC_(12) and GC_(3)was 0.297,and the correlation did not reach a significant level.ENC-plot analysis found that most genes are located near the standard curve.PR2-plot analysis showed that the content of the third base in the codon was T>A,G>C.Correspondence analysis shows that the contribution rates of the first,second,third,and fourth vector axes are 23.96%,11.15%,9.95%,and 6.38%,respectively.The first vector axis has no significant correlation with GC,CAI,ENC,and GC_(3s).Finally,AUA,CUU,CCA,ACU,GCU,GAA,UGA,CGA,AGU and AGA were selected as the optimal codons.The results of this study provide theoretical basis for optimizing the codons of the mitochondrial genome of Gracilaria tenuistipitata in the future,improving the expression efficiency,and improving the target traits of Gracilaria tenuistipitata.

关 键 词：细基江蓠 线粒体基因组 密码子偏好性 最优密码子 

分 类 号：S917.3[农业科学—水产科学]