Differential expression and co-localization of transcription factors during the indirect de novo shoot organogenesis in the fern Ceratopteris richardii

Background: Regeneration can be achieved through various approaches in flowering plants and different sets of transcription factors are involved in those processes. Ceratopteris richardii is one of the water ferns and can obtain intact plantlets from the callus, thus providing an opportunity for comprehensively understanding plant regeneration. Results: The callus could be induced from the aerial part and the putative embedded root primordia in emergent leaves within this fern, with formation of shoot pro-meristems and meristems verifying an indirect de novo shoot organogenesis. Differentially expressed genes identified by RNA-seq indicated that photosynthesis including both light and dark reaction, response to stimuli, and transmembrane signaling were immediately altered upon transition of the callus from proliferation to differentiation. Moreover, genes concerning hormones and transcription factors were up- or down-regulated, with a suggestion that mechanisms controlling this transition was partly conserved across green plants. Three STM -, ANT -, and ESE3 -like transcription factors differentially expressed were all localized at the presumptive vascular-initial-like cells but not in the other callus tissues as indicated by in situ hybridization, thus identifying a putative mechanism underlying callus development. Conclusions: This work provided a basis for studying regeneration in ferns and generated a hypothesis related to callus development.