摘要
密码子偏好性由突变、自然选择和遗传漂变进化而来,其对于理解物种的系统发育和分子进化具有重要参考意义。为了探索枳(Citrus trifoliata)叶绿体基因组密码子的偏好性特征及形成原因,本研究使用CodonW 1.4.2和CUSP软件分析了枳叶绿体基因组中53个候选基因的密码子偏好性指标。结果表明,相对同义密码子使用度(relative synonymous codon usage, RSCU)大于1的同义密码子有29个,其中28个以A或U结尾。有效密码子数(effective number of codon, ENC)分布在39.79~59.37,大于45的有43个。ENC与GC_(3)显著相关,GC_(all)与GC_(1)、 GC_(2)和GC_(3)均极显著相关,GC_(1)与GC_(2)极显著相关。中性绘图分析发现GC_(12)与GC_(3)相关系数为0.028 6,回归系数为0.171 1。ENC-plot分析发现多数基因偏离标准曲线。PR2-plot结果显示,枳叶绿体基因组密码子第三位碱基T的使用频率大于A的,G和C频率相当。此外,本研究通过分析高表达及低表达基因RSCU组成,筛选确定了13个最优密码子。本研究结果表明枳叶绿体基因组密码子偏好性主要由选择因素形成,为基于质体基因组编辑的枳的性状改良提供数据支撑。
Codon usage bias were evolved from mutation,natural selection,and genetic drift.Also,codon usage bias were important references for understand the phylogeny and molecular evolution relationships of species.To explore the formation reasons and chara-cteristics of codon usage bias,CodonW 1.4.2 and CUSP were used to analysis the detailed indexes of codon usage bias with 53 candidate genes in the chloroplast genome of Citrus trifoliata.Results indicated that the relative synonymous codon usage(RSCU)value of 29 synonymous codons greater than 1 with 28 codons ended in A or U.The distribution of effective number of codon(ENC)was ranged from 39.79 to 59.37 and the ENC value of 43 genes were greater than 45.Moreover,the ENC value and GC_(3),GC_(all)and GC_(1),GC_(2),GC_(3),GC_(1) and GC_(2) was significant relevant.Neutral plot analysis showed that the correlation coefficient of GC_(12)and GC_3 was 0.0286 and the regression coefficient was 0.1711.ENC-plot analysis indicated most genes deviated from the standard curve.PR2-plot analysis showed that the frequency of thymine is higher than adenine while cytosine is basically the same with guanine in the third codon position.In addition,13 optimal codons were determined in this study,through analyzing the RSCU of high expression and low expression genes.Results of the present study indicated the codon usage bias in the chloroplast genome of C.trifoliata were mainly influenced by natural selection which would provide scientific supports for plastid genome editing and traits improvement of C.trifoliata.
作者
王淘
陈烨
李竹
李瑞民
WANG Tao;CHEN Ye;LI Zhu;LI Ruimin(College of Life and Sciences,Gannan Normal University,Ganzhou,341000)
出处
《基因组学与应用生物学》
CAS
CSCD
北大核心
2023年第10期1050-1057,共8页
Genomics and Applied Biology
基金
国家自然科学基金项目(32260659)
国家级大学生创新创业训练计划(202110418008)共同资助。
关键词
枳
叶绿体基因组
密码子偏好性
选择压力
Citrus trifoliate
Chloroplast genome
Codon usage bias
Selection pressure
