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

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.