Journal Article

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

Jayakodi, Murukarthick, Lee, Sang-Choon, Choi, Beom-Soon, Lee, Dong-Yup, Mohan, Shobhana V. G., Yang, Tae-Jin, Lakshmanan, Meiyappan, Kim, Nam-Hoon, Park, Jee Young, Jang, Woojong

2018

Overview

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 /.

• Publisher: BioMed Central,BioMed Central Ltd,BMC
• Subject: Agriculture / Anopheles / Biomedical and Life Sciences / breeding / cultivars / data collection / Databases, Genetic / developmental stages / gene expression / Gene Expression Regulation, Plant - genetics / Gene Expression Regulation, Plant - physiology / Gene Ontology / Genes / Genome database / Genome, Plant - genetics / Genomes / Genomics / Genomics and evolution / Ginseng annotation / Ginseng genome browser / ginsenosides / Ginsenosides - metabolism / Health aspects / herbaceous plants / human health / humans / Life Sciences / nucleotide sequences / Oriental traditional medicine / Panax - genetics / Panax - metabolism / Panax ginseng / Plant Sciences / tissues / transcriptome / Tree Biology / Visualization (Computers)