Identification and analysis of ARF gene family in Huperzia serrata based on full-length transcriptome

Abstract

Auxin response factor (ARF) is a transcription factor family that mediates auxin signaling and regulates various biological processes. To investigate the ARF gene family members and their roles in response to high temperature and drought stress, the phylogenetic and expression patterns of the ARF gene family members in Huperzia serrata were analyzed using full-length transcriptome and RNA-seq data. Based on bioinformatics analysis, the physicochemical properties, domains, conserved motifs, phylogeny, tissue expression patterns, and expression patterns of the ARF gene family under high temperature and drought stress were analyzed. The results were as follows:(1) A total of 24 ARF family members were screened in the full-length transcriptome of H. serrata, all of which were acidic proteins and hydrophilic proteins. (2) Subcellular localization prediction revealed that 24 HsARF were all localized in nucleus. (3) Phylogenetic analysis revealed that HsARF had a distant genetic relationship with angiosperms Arabidopsis and rice, and only share two common ARF ancestors with higher flowering plants. (4) Domain analysis revealed that, except for HsARF18/23/24, most HsARF had B3 domains. Analysis of secondary structure found that the highest proportion of HsARF protein was random curling, followed by elongated chains and α-helix. Three-dimensional (3D) protein structure prediction model used in the 24 HsARF proteins was only four. (5) RNA-seq analysis showed that the expression levels of 7 HsARF were high in all detected organs. The expression levels of 10 HsARF in stems were higher than those in roots and leaves. Otherwise, the expression levels of HsARF13 and HsARF14 in leaves were lower than those in roots and stems. (6) The expression levels of HsARF undergo significant changes under high temperature and drought stress, with 18 HsARF being induced to varying degrees by high temperature stress, 7 HsARF responded to drought stress, with 3 HsARF induced by drought, while 4 HsARF inhibited by drought. The results provide theoretical references for the functional and biological breeding study of ARF gene family in H. serrata.

Keywords

• huperzia serrata
• auxin response factor (arf)
• phylogenetic analysis
• full-length transcriptome
• abiotic stress