Project description:To explore the role of auxin in Ceratopteris richardii root initiation, we carried out RNA-seq to analyze gene expression levels upon 2,4-D treatment.
Project description:To generate a de novo transcriptome assembly from three different parts of the Ceratopteris richardii young sporophyte (Hn-n cultivar). We then performed a differential gene expression analysis between the different plant segments, while trying to understand the expressed genes for each Ceratopteris part.
Project description:To study genes specially expressed in root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) of Ceratopteris richardii, we carried out an RNA-seq to analyze gene expression levels from these five tissues.
Project description:The fern Ceratopteris richardii has two distinct generations: the haploid gametophyte and diploid sporophyte, which resembles the difference between the major land plant clades of bryophytes and tracheophytes. We profiled the fast auxin-dependent phosphorylation response in both generations to identify the shared evolutionary targets and differences between the two generations
Project description:Background and Aims: Ferns are providing insight into fundamental biological processes, and spatial transcriptomics is a potent tool in unraveling complexes of plant development. This research is targeted at leaf development in the water fern Ceratopteris richardii with the use of spatial transcriptomics. Methods: A shoot tip of sporophytes under vegetative growth was investigated using spatial transcriptomics, which conducted spot clustering, marker gene identification, and functional enrichment. Ribosomal protein genes were queried using BLAST program and categorized based on multi-alignment produced by Clustalw2 program. RNA in situ tissue hybridization was performed on three ribosomal protein genes. Key Results: Leaves were mutually different at the level of transcriptome under various developmental stages. There were unexpected complexes in tissue structure for stems. A few transcription factors were identified characteristic of leaf development. Activities associated with translation were very different between tissues, and ribosomal protein genes were heterogeneous at the level of transcription. Ribosomal protein genes were specifically expressed in the shoot apical meristem, leaf primordia, and vasculature of various organs. Conclusions: Leaves are mutually different under various developmental stages in C. richardii, with contribution of transcription factors. Stems are unexpectedly complex in tissue structure. Organs/tissues are very different in translation activity from each other, partly due to transcription heterogeneity of ribosomal protein genes. Ribosomal protein genes are specifically expressed in the shoot apical meristem, leaf primordia, and vasculature.
Project description:Regeneration is common in plants and transcription factors greatly contribute to this versatility of flowering plants; however, the evolution of this capability has hardly been explored. The callus can be induced from an intact plant rather than an explant in the water fern Ceratopteris richardii and the employed media are very different. The callus was verified having resulted in indirect de novo shoot organogenesis (IDNSO). Hundreds of genes were differentially expressed between the proliferating and the differentiating callus, hinting at significant changes in photosynthesis and hormone response. Many transcription factors were also differentially expressed, providing cues on how the callus proliferated and differentiated. STM-, ANT-, and ESE3-like transcription factor were simultaneously expressed in the vascular-initial-like cells in the callus, thus identifying a key tissue in callus differentiation; furthermore, they might have undergone subfunctionalization or neofunctionalization during evolution. Therefore, IDNSO was considered both conserved and diversified throughout vascular plants.
