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. 2018 Apr 12;18(1):62.
doi: 10.1186/s12870-018-1282-9.

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng

Murukarthick Jayakodi  1 , Beom-Soon Choi  2 , Sang-Choon Lee  1 , Nam-Hoon Kim  1 , Jee Young Park  1 , Woojong Jang  1 , Meiyappan Lakshmanan  3 , Shobhana V G Mohan  4 , Dong-Yup Lee  3   5 , Tae-Jin Yang  6   7
Affiliations

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng

Murukarthick Jayakodi et al. BMC Plant Biol. .

Abstract

Background: The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb.

Description: The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page.

Conclusion: This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.

Keywords: Genome database; Ginseng annotation; Ginseng genome browser; Panax ginseng.

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Figures

Fig. 1
Fig. 1
Overview of the architecture of the Ginseng Genome Database
Fig. 2
Fig. 2
Query interface to retrieve information on gene annotations and transcription factors
Fig. 3
Fig. 3
A detailed snapshot of the structural and functional annotations of a queried gene
See this image and copyright information in PMC

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