江苏农业学报2025，Vol.41Issue(3)：468-476,9.DOI:10.3969/j.issn.1000-4440.2025.03.005
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
Codon usage bias analysis and influencing factors of the cassava expansin protein gene family
摘要
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 co-don usage bias.The ENC values showed highly significant correlations with the G+C contents at the first and third co-don positions,and showed significant correlation with ami-no 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 ana-lyses 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.关键词
木薯/扩展蛋白基因/密码子偏好性/最优密码子Key words
cassava/expansin genes/codon usage bias/optimal codon分类
农业科技引用本文复制引用
刘秦,蔡雨静,李锦兰,耿晓姗,卢恩科..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,2025,41(3):468-476,9.基金项目
国家自然科学基金项目(32101691) （32101691）
广西自然科学基金项目(2021GXNSFBA196077) （2021GXNSFBA196077）
国家级大学生创新创业训练计划项目(202310606031) （202310606031）
