[1]朱艳,韩长志.普通核桃与深纹核桃中叶绿体基因组密码子使用特征对比[J].江苏农业学报,2024,(08):1507-1520.[doi:doi:10.3969/j.issn.1000-4440.2024.08.015]
　ZHU Yan,HAN Changzhi.Comparison of codon usage characteristics of chloroplast genomes in Juglans regia and Juglans sigillata[J].,2024,(08):1507-1520.[doi:doi:10.3969/j.issn.1000-4440.2024.08.015]
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普通核桃与深纹核桃中叶绿体基因组密码子使用特征对比()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2024年08期
页码:
1507-1520
栏目:
园艺
出版日期:
2024-08-30

文章信息/Info

Title:
Comparison of codon usage characteristics of chloroplast genomes in Juglans regia and Juglans sigillata
作者:
朱艳; 韩长志
(西南林业大学林学院/云南省森林灾害预警与控制重点实验室,云南昆明650224)
Author(s):
ZHU Yan; HAN Changzhi
(College of Forestry, Southwest Forestry University/Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Kunming 650224, China)
关键词:
普通核桃; 深纹核桃; 叶绿体; 基因组; 同义密码子; 偏好性
Keywords:
Juglans regia; Juglans sigillata; chloroplast; genome; synonymous codon; bias
分类号:
S664.1
DOI:
doi:10.3969/j.issn.1000-4440.2024.08.015
文献标志码:
A
摘要:
本研究旨在对比分析普通核桃与深纹核桃中叶绿体基因组密码子的使用偏好性,对普通核桃与深纹核桃中各53条蛋白质编码区序列开展预测分析,明确上述2种核桃叶绿体基因组中的最优密码子,为未来开展核桃物种的亲缘关系研究提供理论依据。利用Codon W 1.4.2和在线软件CUSP等分析普通核桃与深纹核桃中的叶绿体基因组密码子,获得相对同义密码子使用度(RSCU)、有效密码子数(ENC)、G+C含量等参数,再进行中性绘图分析、有效密码子数分析及奇偶偏好性分析。普通核桃与深纹核桃中叶绿体基因组的密码子适应指数均为0.167,ENC均在45.00以上,表明密码子偏好性弱。普通核桃与深纹核桃中叶绿体基因组密码子的G+C含量整体表现为：基因中所有密码子第1位碱基G+C的含量(GC1)＞基因中所有密码子第2位碱基G+C的含量(GC2)＞基因中所有密码子第3位碱基G+C的含量(GC3)。进一步分析发现,第3位碱基的使用频率表现为T大于A,G大于C。从普通核桃中筛选出14个最优密码子,从深纹核桃中筛选出17个最优密码子,其中共有23个最优密码子在第3个位置偏好以A/U结尾。总之,普通核桃和深纹核桃中叶绿体基因组密码子偏好性主要受到自然选择的影响,本研究结果可以为进一步探索核桃抗性遗传基因的改良和表达提供理论基础和数据支撑。
Abstract:
The aim of the study was to compare and analyze the usage preference of chloroplast genome codons in Juglans regia and Juglans sigillata, and to predict and analyze 53 protein coding sequences (CDS) in Juglans regia and Juglans sigillata, so as to clarify the optimal codons in the chloroplast genomes of the above two walnuts and provide a theoretical basis for the future research of the genetic relationship of walnut species. Codon W 1.4.2 and online software CUSP were used to analyze the chloroplast genome codons in Juglans regia and Juglans sigillata, and the relative synonymous codon usage (RSCU), effective number of codons (ENC), G+C content and other parameters were obtained. Neutrality plot analysis, effective number of codons analysis (ENC-plot), and parity preference analysis (PR2-plot) were performed. The codon adaptation index of chloroplast genomes in Juglans regia and Juglans sigillata was 0.167, and the ENC was above 45.00, indicating that the codon preference was weak. The G+C content of chloroplast genome codons in Juglans regia and Juglans sigillata was as follows: the content of G+C at the first base of all codons in the gene (GC1)＞the content of G+C at the second base of all codons in the gene (GC2)＞the content of G+C at the third base of all codons in the gene (GC3). Further analysis showed that the usage frequency of the third base was T＞A, G＞C. A total of 14 optimal codons were screened in Juglans regia, and 17 optimal codons were screened in Juglans sigillata. Among them, 23 optimal codons preferred the A/U end at the third position. In conclusion, the codon preference of chloroplast genome in Juglans regia and Juglans sigillata is mainly affected by natural selection, which provides theoretical basis and data support for further exploration of the improvement and expression of walnut resistance genes.

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备注/Memo

备注/Memo:
收稿日期：2023-09-06基金项目：云南省研究生导师团队建设项目(2022100)；云南省“兴滇英才支持计划”青年人才专项(YNWR-QNBJ-2020-188)作者简介：朱艳(2000-),女,云南昭通人,硕士研究生,主要从事森林保护相关研究。(E-mail)508034093@qq.com通讯作者：韩长志,(E-mail)swfuhcz@163.com
更新日期/Last Update: 2024-09-18