Improved transcriptome assembly of Monarda citriodora reveals candidate HD-ZIP IV transcription factors involved in trichome development and secondary metabolism

Members of the HD-ZIP transcription factor family play an important role in plant processes, including growth, development, metabolism, and stress response regulation. Among these, the sub-family IV members regulate epidermal cell differentiation, trichome development, and secondary metabolism. Monarda citriodora, an aromatic plant, produces economically important essential oils enriched in thymol. Thymol and other related monoterpenes are primarily biosynthesized and stored in glandular trichomes. Despite its significant economic value, the comprehensive identification of the transcription factor families has not been studied in this plant species. Given the importance of HD-ZIP-IV members in regulating trichome development and secondary metabolism, we identified these members in M. citriodora in the present study. To this end, firstly, we carried out transcriptome sequencing of M. citriodora flowers, and the resulting reads, along with previously sequenced reads, were used to reconstruct a transcriptome assembly. The assembled transcripts represented all major plant parts. Using this improved assembly, HD-ZIP-IV members were identified. Their expression profiles and phylogenetic positions, in conjunction with those of known regulators, identified candidate genes involved in the secondary metabolism and/or trichome development in M. citriodora. Furthermore, through gene co-expression analysis, several McHD-ZIP-IV members were found to be co-expressed with McDXS and McTPS genes. These McHD-ZIP-IV members may serve as key candidate genes for functional analysis to determine the regulation of trichome development in M. citriodora. Taken together, the present study provides a resource for improving M. citriodora using molecular tools.