3个茶树品种WOX基因家族的进化及密码子偏好性比较

王占军; 吴子琦; 王朝霞; 欧祖兰; 李杰; 蔡倩文; 徐忠东; 张照亮

doi:10.12302/j.issn.1000-2006.202108049

3个茶树品种WOX基因家族的进化及密码子偏好性比较

王占军, 吴子琦, 王朝霞, 欧祖兰, 李杰, 蔡倩文, 徐忠东, 张照亮

南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (2) : 71-80.

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南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (2) : 71-80. DOI: 10.12302/j.issn.1000-2006.202108049

研究论文

3个茶树品种WOX基因家族的进化及密码子偏好性比较

王占军 ¹^,²^,△ ,
吴子琦 ¹^,△ ,
王朝霞 ¹ ,
欧祖兰 ¹ ,
李杰 ¹ ,
蔡倩文 ¹ ,
徐忠东 ¹ ,
张照亮 ²^,^*

作者信息 +

A comparative study of the evolution and codon usage bias in WOX gene family of three Camellia sinensis cultivars

WANG Zhanjun ¹^,² ,
WU Ziqi ¹ ,
WANG Zhaoxia ¹ ,
OU Zulan ¹ ,
LI Jie ¹ ,
CAI Qianwen ¹ ,
XU Zhongdong ¹ ,
ZHANG Zhaoliang ²^,^*

Author information +

文章历史 +

摘要

【目的】WOX基因家族在模式植物组织培养中扮演着重要的分子调控角色。非模式植物WOX基因家族的系统发育和密码子使用偏好性研究有助于探索遗传进化规律和基因表达特征,进而为其转基因体系构建提供指导。【方法】利用生物信息学方法在3个茶树品种全基因组数据中鉴定WOX基因;通过ClustalX 2.1和MEGA X软件探索它们的进化规律。运用Perl语言、Codon W 1.4.2程序和SPSS 23.0等软件分析3个茶树品种WOX基因编码序列,探究它们的密码子使用偏好模式;基于ENc-GC_3s、PR2分析和中性分析结果解析影响密码子偏好的主要因素。【结果】共鉴定出42个WOX成员,其中‘云抗10号’(CSA)11个,‘舒茶早’(CSS)18个,‘云南野生古茶DASZ’(DASZ)13个,系统发育揭示3个茶树品种WOX基因在进化上存在较强的保守性。密码子偏好性分析揭示,3个茶树品种WOX基因密码子都偏好使用A/T和以A/T结尾;CSA和DASZ的WOX基因密码子使用模式相似,表明两者亲缘关系较近;以CSA和CSS作为转基因受体时,3个茶树品种WOX基因中个别密码子需优化;烟草是3个茶树品种WOX基因的最佳异源表达受体;ENc-GC_3s绘图、PR2分析和中性分析表明自然选择是影响3个茶树品种WOX基因密码子使用偏倚的主要因素。【结论】3个茶树品种WOX基因进化上较保守,密码子偏好使用A/T和以A/T结尾,且密码子偏好原因主要是自然选择;揭示出转茶树时密码子的优化信息和烟草为最佳异源表达受体的结果。

Abstract

【Objective】The WOX gene family plays an important molecular regulatory role in model plant tissue culture. Phylogeny studies and research on the codon usage bias in the WOX gene family in non-model plants are helpful for exploring genetic evolution and gene expression characteristics, which serve as a guideline for establishing a transgenic system.【Method】In this study, bioinformatics were used to identify the WOX genes among all coding sequences of three Camellia sinensis cultivars. The evolutionary patterns were analyzed using ClustalX 2.1 and MEGA X software. The codon usage index of the coding sequence of the WOX gene was analyzed, and the codon usage pattern and the source of codon variation were explored using Perl language, Codon W1.4.2, and SPSS 23.0. The main factors affecting codon usage bias were analyzed based on the results of ENc-GC_3s, a PR2-plot analysis, and a neutral analysis.【Result】A total of 42 WOX members were identified in this study, of which 11 were CSA, 18 were CSS and 13 were DASZ. The phylogenetic analysis revealed that the evolution of WOX genes of the three Camellia sinensis cultivars is highly conserved. The codon bias analysis revealed that the codons of WOX genes preferred to use A/T and end with A/T in the three Camellia sinensis cultivars; the codon usage patterns of WOX genes in CSA and DASZ are similar, indicating that they are closely related. When CSA and CSS are used as transgenic receptors, individual codons in WOX genes of three Camellia sinensis cultivars need to be optimized. Nicotiana tabacum is the best heterologous expression receptor for WOX genes of three Camellia sinensis cultivars. ENc-GC_3s mapping the PR2 analysis, and the neutrality analysis indicate that the natural selection is the main reason for the codon usage bias of WOX genes in the three Camellia sinensis cultivars.【Conclusion】This study showed that WOX genes of three Camellia sinensis cultivars are evolutionarily conserved, codons prefer to use A/T and end with A/T, and the codon usage bias is mainly due to the natural selection. The results reveal the optimization information of codons when transforming tea plants, and tobacco is the best heterologous expression receptor.

导出引用

王占军, 吴子琦, 王朝霞, 等. 3个茶树品种WOX基因家族的进化及密码子偏好性比较[J]. 南京林业大学学报（自然科学版）. 2022, 46(2): 71-80 https://doi.org/10.12302/j.issn.1000-2006.202108049

WANG Zhanjun, WU Ziqi, WANG Zhaoxia, et al. A comparative study of the evolution and codon usage bias in WOX gene family of three Camellia sinensis cultivars[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2022, 46(2): 71-80 https://doi.org/10.12302/j.issn.1000-2006.202108049

中图分类号： Q786;S794.4

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