Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis

Centaurium erythraea Rafn. (common centaury, Gentianaceae) is a medicinal plant with great regeneration potential and developmental plasticity in vitro. Centaury can be regenerated from leaf explants by both somatic embryogenesis (SE) and shoot development (SD). We believe that its regeneration potential and developmental plasticity rest on high activity of certain genes, which may not be active or present in species recalcitrant to in vitro regeneration. However, there are no sequenced Gentianaceae genomes to support investigation of the molecular events during SE or SD. To this end, we have sequenced six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of in vitro grown plants) and de novo assembled centaury referent transcriptome comprising 105.726 genes. The high quality and completeness transcriptome was functionally annotated against NCBI nt, Swissprot and PFAM databases with KOG and GO enrichment. In addition, 11 housekeeping and functional genes were validated for expression stability in 27 tissue samples representing the processes of SE and SD, plants from nature and wounded tissues using GeNorm and NormFinder. The most stable genes that can be used for expression studies during SE, SD and in vitro manipulations are Ribosomal protein L2 (RPL2) and TATA binding protein 1 (TBP1) in combination with RAS (Rat Sarcoma)-related Nuclear protein (RAN) or Adenosine kinase (AK). These results comprise a complete framework for the search for genes involved in SE and SD, but may also be useful in identifying genes involved in biosynthesis of C. erythraea secondary metabolites. De novo assembled and fully annotated Centaurim erythraea transcriptome is publically available along with validated housekeeping genes with stable expression during in vitro development and mechanical injury.