扁蓿豆叶绿体基因组密码子偏好性分析

doi:10.11733/j.issn.1007-0435.2021.12.006

草地学报 ›› 2021, Vol. 29 ›› Issue (12): 2678-2684.DOI: 10.11733/j.issn.1007-0435.2021.12.006

扁蓿豆叶绿体基因组密码子偏好性分析

田春育^1,2, 武自念¹, 李贤松¹, 李志勇¹

1. 中国农业科学院草原研究所, 内蒙古呼和浩特 010010;
2. 内蒙古大学生态与环境学院, 内蒙古呼和浩特 010021

收稿日期:2021-06-15 修回日期:2021-07-26 出版日期:2021-12-15 发布日期:2022-01-06
作者简介:田春育(1993-)，女，汉族，内蒙古乌兰察布市人，博士研究生，主要从事草种质资源与育种研究，E-mail：tiancy2021@163.com
基金资助:
内蒙古自治区科技重大专项（2021ZD0031）；内蒙古自治区科技计划（2019GG006）；2020-科技兴蒙-草种业技术创新中心-2；科技基础资源调查专项-草原区生物多样性综合考察（2019FY102003）资助

Codon Usage Bias of Chloroplast Genome in Medicago ruthenica

TIAN Chun-yu^1,2, WU Zi-nian¹, LI Xian-song¹, LI Zhi-yong¹

1. Institute of Grassland Research of CAAS, Hohhot, Inner Mongolia 010010, China;
2. School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia 010021, China

Received:2021-06-15 Revised:2021-07-26 Online:2021-12-15 Published:2022-01-06
Contact: 李志勇,E-mail:zhiyongli1216@126.com

摘要/Abstract

摘要： 为阐明扁蓿豆（Medicago ruthenica）叶绿体基因组密码子使用模式，以其50条蛋白编码序列（CDS）为对象，利用软件CodonW 1.4.2、Excel以及在线程序对其ENC，RSCU，GC含量、中性绘图、PR2-plot、最优密码子等进行分析得到以下结果：基因组平均GC含量为40.58%，其中GC1>GC2>GC3；ENC的取值介于35.77～56.62之间，表明密码子使用偏好性较弱；基因组中共有30个密码子RSCU>1，其中29个以A/U结尾；ENC-plot绘图分析结果中多数基因分布于标准曲线下方，22个基因ENC比值在—0.05～0.05之间，密码子偏好性主要受选择影响；PR2-plot分析表明碱基T的使用频率大于A，G大于C，说明密码子偏好性还受其他因素影响；该基因组中共有UUU，UUA，ACU等11个最优密码子并均以A/U结尾。以上研究结果可为扁蓿豆叶绿体基因组优良基因利用提供理论与基础。

关键词: 扁蓿豆, 叶绿体基因组, 密码子偏好性, 选择影响, 最优密码子

Abstract: In order to elucidate the codon usage pattern of the chloroplast genome of Medicago ruthenica,a series of analyses such as the value range of the ENC,RSCU,GC content,neutral mapping,PR2-plot,and optimal codon were performed using the software CodonW 1.4.2,Excel,and online programs 50 protein-coding sequences (CDS). The results showed that the average GC content of the genome was 40.58%,with GC1 > GC2 > GC3;the values of ENC ranged from 35.77～56.62,indicating a weak preference for codon usage in M ruthenica;The correlation analysis showed that the correlation coefficient between GC₁₂ and GC₃ was 0.1685,which was not significant;the analysis showed that there were 30 codons in the chloroplast genome in M ruthenica with RSCU>1,29 of which ended in A/U;the ENC-plot analysis showed that most of the genes were distributed below the standard curve,and the ENC ratios of 22 genes were between —0.05 and 0.05,indicating that the codon M ruthenica of lucerne was mainly influenced by selection. PR2-plot analysis showed that base T was used more frequently than A,and G was used more frequently than C,indicating that the codon preference of the chloroplast genome was also influenced by other factors;11 optimal codons,including UUU,UUA,CUU,and ACU,were analyzed in the chloroplast genome and all ended with A/U. The results of the above study can provide some theory and basis for the utilization of excellent genes in the chloroplast genome of M ruthenica.

Key words: Medicago ruthenica, Chloroplast genome, Codon usage bisa, Selecion, Optimal codons

中图分类号:

S349+.55

田春育, 武自念, 李贤松, 李志勇. 扁蓿豆叶绿体基因组密码子偏好性分析[J]. 草地学报, 2021, 29(12): 2678-2684.

TIAN Chun-yu, WU Zi-nian, LI Xian-song, LI Zhi-yong. Codon Usage Bias of Chloroplast Genome in Medicago ruthenica[J]. Acta Agrestia Sinica, 2021, 29(12): 2678-2684.

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扁蓿豆叶绿体基因组密码子偏好性分析

Codon Usage Bias of Chloroplast Genome in Medicago ruthenica

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