3种栗属植物NAC基因家族的鉴定及密码子偏好性分析
Identification of NAC gene families and analysis of codon usage bias in three Castanea plants
付丽枝 1杨涌 1郭江辉 1刘静 2王萌 2王旋 2王东升 2于立洋 2张海娥2
作者信息
- 1. 河北科技师范学院园艺科技学院,河北秦皇岛 066004;板栗产业技术教育部工程研究中心,河北秦皇岛 066004;河北省特色园艺种质挖掘与创新利用重点实验室,河北秦皇岛 066004
- 2. 板栗产业技术教育部工程研究中心,河北秦皇岛 066004;河北省特色园艺种质挖掘与创新利用重点实验室,河北秦皇岛 066004;河北省板栗产业协同创新中心,河北秦皇岛 066004
- 折叠
摘要
[目的]鉴定3种栗属植物NAC基因家族,同时分析其密码子偏好性,为进一步探究栗属植物NAC基因家族功能提供重要理论依据.[方法]使用生物信息学方法,对3种栗属植物的染色体位置、系统进化关系、蛋白基序、所受选择压力、密码子偏好性等方面进行分析.[结果]共鉴定到333个栗属植物NAC基因家族成员,其不均等分布在各个染色体上;进化树分析显示其分为5个小组;蛋白基序分析显示5个小组都包含保守的Motif 1～Motif 7;共线性分析显示其在基因组内与组间包含极强的共线性关系且多数共线性基因对都在经历纯化选择压力;密码子偏好性分析显示其密码子偏好性较弱;中性绘图分析与ENCplot绘图分析显示其密码子偏好性受自然选择压力更大;最优密码子分析显示3种栗属植物的NAC基因家族共同包含11个最优密码子,例如CAU、UAA、GUU等;与模式植物比较密码子使用频率发现拟南芥、烟草、番茄均为3种栗属植物合适的外源受体.[结论]本研究探索栗属植物NAC基因家族成员的进化关系、选择压力、密码子偏好性等,为今后通过分子生物学手段提高栗属植物NAC基因表达效率奠定理论基础.
Abstract
[Objective]The study aimed to identify three NAC gene families of Castanea plants while analyzing codon usage bias.It provided an important theoretical basis for further exploring the function of NAC gene family in chestnut plants.[Method]Using bioinformatics meth-ods,the chromosome position,phyloevolutionary relationships,protein motif,selective pressure,codon usage bias were analyzed in the three Castanea plants.[Result]In the study,333 Castanea NAC gene family members were identified with unequal distribution across different chromosomes.The evolutionary tree analysis revealed that it could be divided into five groups.Protein motif analysis revealed that the five groups all contained the conserved Motif 1-Motif 7.Collinearity analysis showed that it contained strong collinearity within and between the genomes,and most of the collinear gene pairs were undergoing purifying selection pressure.The codon usage bias analysis showed a weak co-don usage bias.Neutral mapping analysis and ENC-plot mapping analysis showed that their codon usage bias was more under natural selective pressure.The optimal codon analysis revealed that the NAC gene families of three Castanea plants together contained 11 optimal codons.For example,CAU,UAA,GUU,etc.Comparing the codon usage frequency with the comparative model plants,Arabidopsis thaliana,Nicotiana tabacum and Solanum lycopersicum were all suitable exogenous receptors for the three Castanea plants.[Conclusion]The study provides a comprehensive understanding of the evolutionary relationships,selection pressures,codon preference of NAC gene family members of Castanea plants.The study lays a theoretical foundation for the later use of molecular biological means to improve the efficiency of NAC gene expression in Castanea plants.
关键词
栗属植物/NAC基因家族/选择压力/密码子偏好性Key words
Castanea plants/NAC gene family/Selection pressure/Codon usage bias引用本文复制引用
基金项目
国家重点研发计划项目(2022YFD2200400)
河北科技师范学院博士启动基金项目(2023YB026)
河北省重点研发计划项目(21326304D)
出版年
2024
国家科技期刊平台
NSTL
万方数据