Comparative transcriptome reconstruction of four Hypericum species focused on hypericin biosynthesis

• Main Authors: Miroslav Soták, Odeta Czeranková, Daniel Klein, Zuzana Jurčacková, Ling Li, Eva Čellárová
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2016-07-01
• Series: Frontiers in Plant Science
• Subjects: RNA-Seq; hypericin; de novo assembly; differential expression analysis; Hypericum spp.
• Online Access: http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01039/full

Next generation sequencing technology (NGS) rapidly developed research applications in thefield of plant functional genomics. Several Hypericum spp. with an aim to generate andenhance gene annotations especially for genes coding the enzymes supposedly included inbiosynthesis of valuable bioactive compounds were analyzed. The first de novo transcriptomeprofiling of H. annulatum Moris, H. tomentosum L., H. kalmianum L. and H. androsaemumL. leaves cultivated in vitro was accomplished. All four species with only limited genomicinformation were selected on the basis of differences in ability to synthesize hypericins andpresence of dark nodules accumulating these metabolites with purpose to enrich genomicbackground of Hypericum spp. H. annulatum was chosen because of high number of the darknodules and high content of hypericin. H. tomentosum leaves are typical for the presence ofonly 1-2 dark nodules localized in the apical part. Both H. kalmianum and H. androsaemumlack hypericin and have no dark nodules. Four separated datasets of the pair-end reads weregathered and used for de novo assembly by Trinity program. Assembled transcriptomes wereannotated to the public databases Swiss-Prot and non-redundant protein database (NCBI-nr).Gene ontology analysis was performed. Differences of expression levels in the marginaltissues with dark nodules and inner part of leaves lacking these nodules indicate a potentialgenetic background for hypericin formation as the presumed site of hypericin biosynthesis isin the cells adjacent to these structures. Altogether 165 contigs in H. annulatum and 100contigs in H. tomentosum were detected as significantly differentially expressed (P<0.05) andupregulated in the leaf rim tissues containing the dark nodules. The new sequenceshomologous to octaketide synthase and enzymes catalyzing phenolic oxidative couplingreactions indispensable for hypericin biosynthesis were discovered. The presentedtranscriptomic sequence data will improve current knowledge about the selected Hypericumspp. with proposed relation to hypericin biosynthesis and will provide a useful resource ofgenomic information for consequential studies in the field of functional genomics, proteomicsand metabolomics.