Abstract
Ruta chalepensis L. is among the most spread and important medicinal plant of the Ruta genus. Rutin is the major flavonoid found in R. chalepensis with a wide range of pharmacological activities. RNA-sequencing (RNA-Seq) facilitates the study of the transcriptome landscape in different organs/tissues of a plant The current study was aimed to de novo assemble and functionally annotate the whole transcriptome of R. chalepensis based on data obtained from different organs to identify genes involved in mtin biosynthesis. Assembled R. chalepensis transcriptome contained 145,018 genes (unigenes) represented by 254,685 transcripts (isoforms) with average length of assembled contigs of 1,183 base pair (bp) and contig N50 of 2,280 bp. A total of 202,961 transcripts were functionally annotated as protein-producing transcripts in either UniRef90 or SwissProt databases. The closest organisms to R. chalepensis based on the presence of protein homologues in each organism were Arabidopsis thaliana based on SwissProt database and Citrus sinensis based on Uniref90 database. In R. chalepensis transcriptome, potential 143,262 protein conserved domains, 45,367 simple sequence repeats (SSRs) and 46,213 lncRNAs were identified. Several GO terms and pathways were found to be enriched in the de novo assembled R. chalepensis transcriptome including those in relation to flavonoid, flavone, and flavonol biosynthesis and metabolism. The obtained results in the current study lay the foundation for further transcriptomic and genetic engineering studies on R. chalepensis. (C) 2020 Friends Science Publishers