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Genes 2017, 8(9), 228; doi:10.3390/genes8090228

Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome

1
Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea
2
Department of Biology, Chungbuk National University, Cheongju 28644, Korea
3
TheragenEtex Bio Institute, Suwon 16229, Korea
4
Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Received: 3 July 2017 / Revised: 17 August 2017 / Accepted: 12 September 2017 / Published: 15 September 2017
(This article belongs to the Section Plant Genetics and Genomics)
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Abstract

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. View Full-Text
Keywords: isoform sequencing; Panax ginsing C.A. Meyer; transcriptomic profile; genomics isoform sequencing; Panax ginsing C.A. Meyer; transcriptomic profile; genomics
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Jo, I.-H.; Lee, J.; Hong, C.E.; Lee, D.J.; Bae, W.; Park, S.-G.; Ahn, Y.J.; Kim, Y.C.; Kim, J.U.; Lee, J.W.; Hyun, D.Y.; Rhee, S.-K.; Hong, C.P.; Bang, K.H.; Ryu, H. Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome. Genes 2017, 8, 228.

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