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萱草海水脅迫相關bZIP轉錄因子密碼子偏向性分析

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

  • 摘要: bZIP轉錄因子是普遍存在於動𓀔、植物及微生物中的一類蛋白📟,廣泛參與脅迫響應、生長發育調節及能量代謝等多種生理過程。首次通過CodonW和Emboss對萱草海水脅迫相關bZIP基因家族的密碼子構成特性及密碼子使用模式進行分析𓀔,預測HfbZIP基因可能使用的最優密碼子🎦,為發掘萱草bZIP基因家族成員的潛在功能提供理論基礎。結果表明,HfbZIP基因家族密碼子平均GC含量為48.52%,GC3值為48.12%🕵🏻,略微偏向使用A/T結尾;ENC值所在範圍為37.40~61.00🧑🏿‍🌾,平均值為51.50,CAI值取值範圍為0.14~0.21,均值為0.19,表明該家族密碼子使用偏向性較弱且整體的表達水平不高;中性繪圖分析🥡,ENC-plot曲線分析及PR2-plot圖表明HfbZIP家族基因密碼子偏好性形成受堿基組成,突變與自然選擇壓力等多因素共同影響🎽;根據RSCU分析篩選出7個最優密碼子,可為萱草bZIP功能基因研究和序列設計中密碼子優化和宿主選擇提供理論支持👩🏽‍✈️。

     

    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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