[1]刘秦,蔡雨静,李锦兰,等.木薯扩展蛋白基因家族密码子使用偏好性分析及影响因素[J].江苏农业学报,2025,(03):468-476.[doi:doi:10.3969/j.issn.1000-4440.2025.03.005]
　LIU Qin,CAI Yujing,LI Jinlan,et al.Codon usage bias analysis and influencing factors of the cassava expansin protein gene family[J].,2025,(03):468-476.[doi:doi:10.3969/j.issn.1000-4440.2025.03.005]
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木薯扩展蛋白基因家族密码子使用偏好性分析及影响因素()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2025年03期
页码:
468-476
栏目:
遗传育种·生理生化
出版日期:
2025-03-31

文章信息/Info

Title:
Codon usage bias analysis and influencing factors of the cassava expansin protein gene family
作者:
刘秦1; 蔡雨静1; 李锦兰1; 耿晓姗2; 卢恩科1
(1.玉林师范学院广西农产资源化学与生物技术重点实验室，广西玉林537000；2.广西农业职业技术大学农业工程学院,广西南宁530000)
Author(s):
LIU Qin1; CAI Yujing1; LI Jinlan1; GENG Xiaoshan2; LU Enke1
(1.Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin Normal University, Yulin 537000, China;2.College of Agricultural Engineering, Guangxi Vocational University of Agriculture, Nanning 530000, China)
关键词:
木薯; 扩展蛋白基因; 密码子偏好性; 最优密码子
Keywords:
cassava; expansin genes; codon usage bias; optimal codon
分类号:
S889+.5
DOI:
doi:10.3969/j.issn.1000-4440.2025.03.005
文献标志码:
A
摘要:
木薯(Manihot esculenta)是全球一种重要的粮食作物。扩展蛋白在植物生长发育中起关键作用,具有改良作物性状的潜力。本研究利用CodonW、R语言等软件对木薯基因组中的42个扩展蛋白基因进行密码子使用偏好(CUB)的系统分析。结果显示,木薯扩展蛋白基因的平均有效密码子数(ENC)为53.74,表明其密码子使用存在一定偏好性,但偏好程度较轻。ENC值与密码子第一、第三位置的G+C含量极显著相关，与氨基酸长度显著相关。相对同义密码子使用频率(RSCU)分析结果表明,木薯扩展蛋白基因倾向于选择以A/U结尾的密码子。中性绘图和ENC-plot分析结果显示,自然选择是影响木薯扩展蛋白基因CUB形成的主导力量,突变压力作用较小。PR2绘图进一步验证了自然选择在密码子使用偏好中的重要作用。通过比较高偏好基因和低偏好基因的RSCU差异,筛选出23个最优密码子。本研究结果揭示了木薯扩展蛋白基因CUB形成的分子机制,为利用密码子优化策略提高木薯产量和抗逆性提供了理论基础。
Abstract:
Cassava (Manihot esculenta) is a globally important food crop. Expansins （EXPs） play a crucial role in plant growth and development, holding the potential to improve crop traits. This study aimed to systematically analyze the codon usage bias (CUB) of 42 expansin genes in the cassava genome using softwares such as CodonW and R language. The results revealed that the average effective number of codons (ENC) for M.esculenta EXP genes (MeEXPs) was 53.74, indicating a moderate level of codon usage bias. The ENC values showed highly significant correlations with the G+C contents at the first and third codon positions, and showed significant correlation with amino acid length. Relative synonymous codon usage (RSCU) analysis demonstrated that MeEXPs tended to utilize codons ending with A/U. The results of neutral plot and ENC-plot analyses suggested that natural selection was the predominant force influencing the CUB shaping of MeEXPs, while mutational pressure played a relatively minor role. The PR2 plot further corroborated the pivotal role of natural selection in codon usage bias. By comparing the RSCU differences between high and low bias genes, a total of 23 optimal codons were identified. This study unraveled the molecular mechanisms underlying the formation of CUB in MeEXPs, and provided a theoretical foundation for using codon optimization strategies to enhance cassava yield and stress tolerance.

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备注/Memo

备注/Memo:
收稿日期:2024-06-05基金项目:国家自然科学基金项目(32101691)；广西自然科学基金项目(2021GXNSFBA196077)；国家级大学生创新创业训练计划项目(202310606031)作者简介:刘秦(1986-),男,湖北广水人,博士,副研究员,主要从事木薯块根发育研究。(Tel)18176600018；(E-mail)liuqin@ylu.edu.cn通讯作者:耿晓姗，(E-mail)gengxs@ylu.edu.cn；卢恩科,(E-mail)luek2823348@ylu.edu.cn
更新日期/Last Update: 2025-04-27