2018 ASHS Annual Conference

Ligularia fischeri is a popular edible herb in Korea containing broad ranges of pharmacologically important compounds. It is used in traditional medicine for treating infectious and inflammatory diseases. Despite its importance as herbal medicine, there are no transcriptome/genome sequences available in the public database limiting its research at molecular level. To address this issue, a transcriptome analysis of L. fischeri was performed using Pacific Biosciences single molecule long-read isoform sequencing platform. We identified 60,646 polished, high-quality non-redundant full-length transcripts with a total length of 116.5Mb. Among these 27,453 transcripts were annotated to known genes in different species based on non-redundant and uniport database. Functional classification using Gene ontology identified 11,279 transcripts of which majority were associated with the cellular and metabolic process. The Kyoto Encyclopedia of Genes & Genomes pathway analysis identified 1332 transcripts encoding 160 enzymes related to secondary metabolism with a higher number of transcripts for biosynthesis of antibiotics. Furthermore, we observed alternate splicing, in a total of 1,030 transcripts covering a total of 2250 isoforms with a variable of 2-11 isoforms. This data led us to identify 117 transcripts containing 271 isoforms involved in various metabolic pathways along with 36 transcripts containing 84 isoforms involved in various stress responses. This is the first detailed transcriptome analysis of L. fischeri. The resulting transcriptome along with the identified alternative splicing events provides insights into the biological process including the genes related to biosynthesis of characteristic secondary metabolites. This data will be valuable resource as transcriptome reference for further studies in the genetics and breeding of L. fischeri.