September 22, 2019  |  

Isoform sequencing provides a more comprehensive view of the Panax ginseng transcriptome.

Authors: Jo, Ick-Hyun and Lee, Jinsu and Hong, Chi Eun and Lee, Dong Jin and Bae, Wonsil and Park, Sin-Gi and Ahn, Yong Ju and Kim, Young Chang and Kim, Jang Uk and Lee, Jung Woo and Hyun, Dong Yun and Rhee, Sung-Keun and Hong, Chang Pyo and Bang, Kyong Hwan and Ryu, Hojin

Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness. Of those unigenes, 67.5% were predicted to be complete full-length (FL) open reading frames (ORFs) and exhibited a high gene annotation rate. Furthermore, we successfully identified unique full-length genes involved in triterpenoid saponin synthesis and plant hormonal signaling pathways, including auxin and cytokinin. Studies on the functional genomics of P. ginseng seedlings have confirmed the rapid upregulation of negative feed-back loops by auxin and cytokinin signaling cues. The conserved evolutionary mechanisms in the auxin and cytokinin canonical signaling pathways of P. ginseng are more complex than those in Arabidopsis thaliana. Our analysis also revealed a more detailed view of transcriptome-wide alternative isoforms for 88 genes. Finally, transposable elements (TEs) were also identified, suggesting transcriptional activity of TEs in P. ginseng. In conclusion, our results suggest that long-read, full-length or partial-unigene data with high-quality assemblies are invaluable resources as transcriptomic references in P. ginseng and can be used for comparative analyses in closely related medicinal plants.

Journal: Genes
DOI: 10.3390/genes8090228
Year: 2017

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