Abstract
Background: Dryopteris fragrans, which is densely covered with glandular trichomes, is considered to be one of the ferns with the most medicinal potential. The transcriptomes from selected tissues of D. fragrans were collected and analyzed for functional and comparative genomic studies. The aim of this study was to determine the transcriptomic characteristics of wild D. fragrans sporangium in tissues from the SR (root), SL (sporophyll), and TRL (sporophyll with glandular trichomes removed). Results: Cluster analysis identified genes that were highly expressed in an organ-specific manner according to read mapping, feature counting, and normalization. The functional map identified gene clusters that can uniquely describe the function of each tissue. We identified a group of three tissue-specific transcription factors targeting the SL, SR, and TRL. In addition, highly expressed transcription factors (TFs) were found in each tissue-specific gene cluster, where ERF and bHLH transcription factors were the two types showing the most distinct expression patterns between the three different tissues. The specific expression of transcription factor genes varied between the different types of tissues. The numbers of transcription factors specifically expressed in the roots and sporophylls were 60 and 30, respectively, while only seven were found for the sporophylls with glandular trichomes removed. The expression of genes known to be associated with the development of glandular trichomes in flowering plants, including MIXTA, ATML1, and MYB106, were also validated and are discussed. In particular, a unigene encoding MIXTA was identified and exhibited the highest expression level in SL in D. fragrans. Conclusions: This study is the first report of global transcriptomic analysis in different tissues of D. fragrans, and the first to discuss these findings in the context of the development of homologous glandular trichomes. These results set the stage for further research on the development, stress resistance, and secondary metabolism of D. fragrans glandular trichomes.
Highlights
The regulation of gene expression is one of the most significant and complicated of the various biological processes, especially in eukaryotic species, due to their large genomes and complexity in tissue organization [1,2]
Dryopteris fragrans is a member of the Dryopteridaceae family that is mainly located in the temperate regions of North America, Europe, and Asia [3,4]
The entire plant is densely covered with glandular trichomes, there have so far been no reports on transcription factors (TFs) genes involved in regulating their formation in D. fragrans
Summary
The regulation of gene expression is one of the most significant and complicated of the various biological processes, especially in eukaryotic species, due to their large genomes and complexity in tissue organization [1,2]. Some aspects of fern morphological development have been reported, but little is known regarding the fern transcriptome It is well-known that transcription factors (TFs) regulate gene expression by binding to specific nucleotide sequences of their target genes, and control a range of biological pathways. Conclusions: This study is the first report of global transcriptomic analysis in different tissues of D. fragrans, and the first to discuss these findings in the context of the development of homologous glandular trichomes. These results set the stage for further research on the development, stress resistance, and secondary metabolism of D. fragrans glandular trichomes
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