摘要
为明确复羽叶栾树叶绿体基因组密码子的使用模式,以筛选到的52条CDS蛋白质编码序列为研究对象,利用Codon W 1.4.2和在线软件CUSP等获取复羽叶栾树密码子的GC、RSCU、ENC等参数,并进行中性绘图、PR2-plot和最优密码子分析。结果表明:复羽叶栾树密码子不同位置上的GC含量表现为GC_(1)(47.27%)>GC_(2)(39.49%)>GC_(3)(29.84%),且有29个密码子RSCU>1,其中有28个以A/U结尾,表明密码子偏好以A/U结尾。有效密码子数ENC值在36~61之间,密码子使用偏性较弱。ENC与GC_(3)间具有极显著的相关关系,表明密码子第3位上的碱基组成影响密码子使用偏好性。中性分析结果显示,GC_(3)与GC_(12)间无显著的相关关系(r=0.198,P>0.05),回归系数为0.265 2,说明选择对密码子使用偏好性有重要影响。ENC-plot分析和奇偶偏好性分析表明,密码子偏性也受到其他因素影响。综合分析发现复羽叶栾树叶绿体基因组密码子偏好性较弱,选择为主要影响因素,同时受到其他因素的影响。最终确定CUU、GUU、AGU、GCA、CAA、CAU、AAA、GAU、CGU、CGA、GGU、GGA共12个为最优密码子。
In order to elucidate the codon usage pattern of the chloroplast genome of Koelreuteria bipinnata,we select 52 protein coding sequences as the research object.The GC,RSCU and ENC parameters of codons were obtained,and the neutral plot,PR2−plot and optimal codon analysis were performed using the Codon W 1.4.2 software,and online CUSP program.The results showed that the GC content at different locations of the codon is GC_(1)(47.27%)>GC_(2)(39.49%)>GC_(3)(29.84%).There were 29 codons with a relative synonymous codon usage RSCU>1,in which 28 ending with A/U,indicating that the codon preference ends with A/U.The effective codon number(ENC)of the chloroplast gene ranged from 36 to 61,suggesting that the codon usage bias is weak.There is a significant correlation between ENC and GC_(3),indicating that the base composition at the third codon position affects codon usage bias.Neutral analysis showed that there was no significant correlation between GC_(3) and GC_(12)(r=0.198,P>0.05),and the regression coefficient was 0.2652,indicating that selection had an important effect on codon usage bias.ENC−plot analysis and PR2−plot analysis showed that codon bias is also influenced by other factors.In conclusion,the codon bias in chloroplast genomes of K.bipinnata was weak,and the selection was the main influencing factor,while it was also impacted by other factors.Combined with the high expression codon and high frequency codon,we determine 12 optimal codon,including CUU,GUU,AGU,GCA,CAA,CAU,AAA,GAU,CGU,CGA,GGU and GGA.
作者
肖明昆
聂恺宏
沈绍斌
刘倩
段春芳
李月仙
张林辉
Xiao Mingkun;Nie Kaihong;Shen Shaobin;Liu Qian;Duan Chunfang;Li Yuexian;Zhang Linhui(Institute of Tropical and Subtropcal Cash Crops,Yunnan Academy of Agricultural Sciences,Baoshan Yunnan 678000,China;Forestry Bureau of Zhaohua District in Guangyuan City,Guangyuan Sichuan 628000,China)
出处
《西南林业大学学报（自然科学）》
CAS
北大核心
2023年第3期56-63,共8页
Journal of Southwest Forestry University：Natural Sciences
基金
国家中医药管理局全国中药资源普查项目(GZY-KJS-2018-004)资助。
