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王玥宁,张世杰,张志国,等. 萱草海水胁迫相关bZIP转录因子密码子偏向性分析[J]. 应用技术学报,2022,22(2):167-175.. DOI: 10.3969/j.issn.2096-3424.2022.02.010
引用本文: 王玥宁,张世杰,张志国,等. 萱草海水胁迫相关bZIP转录因子密码子偏向性分析[J]. 应用技术学报,2022,22(2):167-175.. DOI: 10.3969/j.issn.2096-3424.2022.02.010
WANG Yuening, ZHANG Shijie, ZHANG Zhiguo, NI Di’an, QIN Qiaoping, LIU Xiang. Analysis of Codon Usage Bias of bZIP Transcription Factors in Hemerocallis Fulva[J]. Journal of Technology, 2022, 22(2): 167-175. DOI: 10.3969/j.issn.2096-3424.2022.02.010
Citation: WANG Yuening, ZHANG Shijie, ZHANG Zhiguo, NI Di’an, QIN Qiaoping, LIU Xiang. Analysis of Codon Usage Bias of bZIP Transcription Factors in Hemerocallis Fulva[J]. Journal of Technology, 2022, 22(2): 167-175. DOI: 10.3969/j.issn.2096-3424.2022.02.010

萱草海水胁迫相关bZIP转录因子密码子偏向性分析

Analysis of Codon Usage Bias of bZIP Transcription Factors in Hemerocallis Fulva

  • 摘要: bZIP转录因子是普遍存在于动、植物及微生物中的一类蛋白,广泛参与胁迫响应、生长发育调节及能量代谢等多种生理过程。首次通过CodonW和Emboss对萱草海水胁迫相关bZIP基因家族的密码子构成特性及密码子使用模式进行分析,预测HfbZIP基因可能使用的最优密码子,为发掘萱草bZIP基因家族成员的潜在功能提供理论基础。结果表明,HfbZIP基因家族密码子平均GC含量为48.52%,GC3值为48.12%,略微偏向使用A/T结尾;ENC值所在范围为37.40~61.00,平均值为51.50,CAI值取值范围为0.14~0.21,均值为0.19,表明该家族密码子使用偏向性较弱且整体的表达水平不高;中性绘图分析,ENC-plot曲线分析及PR2-plot图表明HfbZIP家族基因密码子偏好性形成受碱基组成,突变与自然选择压力等多因素共同影响;根据RSCU分析筛选出7个最优密码子,可为萱草bZIP功能基因研究和序列设计中密码子优化和宿主选择提供理论支持。

     

    Abstract: As one type of protein, the bZIP transcription factor is widely found in animals, plants and microorganisms. It is widely involved in various physiological processes such as stress response, growth and development regulation, and energy metabolism. In this study, codon composition characteristics and codon usage patterns of HfbZIP gene family related to sea water stress in Hemerocallis fulva were analyzed by CodonW and Emboss for the first time to predict the optimal codon possible to be used by HfbZIP gene family, providing a theoretical basis for exploring the potential functions of Hemerocallis bZIP gene family members. The results showed that the average GC content of codon in the HfbZIP gene family was 48.52%, and the GC3 value was 48.12%, indicating a slight preference to use A/T ending. The ENC value ranges from 37.40 to 61.00, with an average of 51.50, and the CAI value ranges from 0.14 to 0.21, with an average of 0.19, indicating weak codon usage bias and low overall expression levels in this family. Neutrality plot analysis, ENC-plot analysis and PR2-plot analysis showed that codon preference of HfbZIP family gene was influenced by many factors, such as base composition, mutation and natural selection pressure. Seven optimal codons were selected on the basis of RSCU analysis, which could provide theoretical support for codon optimization and host selection in functional gene research or sequence design of bZIP in Hemerocallis fulva.

     

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