Cynara cardunculus (L.) transcriptome sequencing

Background: Substantial advancements in the investigation of transcriptome profiles in non-model organisms lacking of a high-quality genome annotation through conventional RNA-seq approach are hampered by the use of short reads which affect gene completeness reconstruction and isoform detection. The recent use of long-reads sequencing techniques, even though with a higher error rate, revealed a high capability to generate a complete assembly also when the reference genome is lacking. Cynara cardunculus var. altilis (DC) (cardoon) is a perennial hardy crop adapted to dry environments with many industrial and nutraceutical applications for the variety of compounds 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 flowering process remains still unexplored. Here we analysed the cardoon transcriptome in vegetative and flower tissues through a novel hybrid RNA-seq assembly approach utilizing both long and short RNA-seq reads.Results: The inclusion of a single Nanopore flow-cell output in a hybrid sequencing approach determined an increase of 15% complete assembled genes and 18% transcript isoforms respect to short reads alone. Among 25,463 assembled unigenes, we identified 578 novel genes and updated 13,039 gene models, 11,169 of which were alternatively spliced isoforms. During flower development, 3,424 genes were differentially expressed and approximately two-thirds were identified as transcription factors including bHLH, MYB, NAC, C2H2 and MADS-box which were highly expressed especially after capitulum opening. We also show the expression dynamics of key genes involved in the production of valuable secondary metabolites such as phenylpropanoids, flavonoids and sesquiterpene lactones. Most of their biosynthetic genes were strongly transcribed in the flowers with alternative isoforms exhibiting differentially expression levels across the tissues.Conclusions: This novel hybrid sequencing approach allowed to improve the transcriptome assembly, to update more than half of annotated genes and to identify many novel genes and different alternatively spliced isoforms. This study provides new insights on the flowering cycle in an Asteraceae plant, a valuable resource for plant biology and breeding in Cynara and an effective method for improving gene annotation.