BMC Genomics volume 21, Article number: 317 (2020)
The investigation of transcriptome profiles using short reads in non-model organisms, which lack of well-annotated genomes, is limited by partial gene reconstruction and isoform detection. In contrast, long-reads sequencing techniques revealed their potential to generate complete transcript assemblies even when a reference genome is lacking. Cynara cardunculus var. altilis (DC) (cultivated cardoon) is a perennial hardy crop adapted to dry environments with many industrial and nutraceutical applications due to the richness of secondary metabolites mostly produced in flower heads.
The investigation of this species benefited from the recent release of a draft genome, but the transcriptome profile during the capitula formation still remains unexplored. In the present study we show a transcriptome analysis of vegetative and inflorescence organs of cultivated cardoon through a novel hybrid RNA-seq assembly approach utilizing both long and short RNA-seq reads.
By Giuseppe D. Puglia, Andrey D. Prjibelski, Domenico Vitale, Elena Bushmanova, Karl J. Schmid & Salvatore A. Raccuia
Dr. Raccuia Salvatore Antonino, Italian National Research Council | CNR · Institute for Mediterranean Agriculture and Forest Systems ISAFoM
Dr. Puglia Giuseppe Diego, Italian National Research Council | CNR · Institute for Mediterranean Agriculture and Forest Systems ISAFoM