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. 2022 May 25:13:883818.
doi: 10.3389/fpls.2022.883818. eCollection 2022.

PanaxGDB: A Comprehensive Platform for Panax

Yuan Lin  1   2   3 , Bing Hao  1   2 , Ying Chun Lu  1   2 , Yang Dong  1   2   4 , Ying Li  1   2 , Guang Hui Zhang  1   2 , Zi Jiang Yang  1   2   3 , Gui Sheng Xiang  1   2 , Guan Ze Liu  1   2 , Xue Jiao Li  1   2 , Qin Zhu  1   2   3 , Qing Hui Yang  3 , Xu Zhen Li  1   4 , Sheng Chao Yang  1   2
Affiliations

PanaxGDB: A Comprehensive Platform for Panax

Yuan Lin et al. Front Plant Sci. .

Abstract

The genus Panax is a valuable natural medicinal source used worldwide that contains high levels of triterpenoid saponins with extensive pharmacological activities. In past decades, molecular biotechnology and breeding techniques have been respectively used to generate omics data and information on cultivars primarily from Panax ginseng (ginseng), Panax quinquefolium (American ginseng), and Panax notoginseng (Sanqi) to biosynthesize valuable saponins, improve product quality, and conduct cost-controlled cultivation. Although much data have been produced, there are concerns that redundant data might be generated and that relatively scattered data might be overlooked. Therefore, many scientists desire a reliable, comprehensive omics database of the Panax genus that could save time and promote integrated analysis. Therefore, to provide all-inclusive, reliable, and valuable information on the Panax genus, PanaxGDB, an open comprehensive database that integrates data on omics and information on varieties, was established. The database contains information on nearly 600 compounds from 12 Panax species, draft genomic sequences with annotations and gene expression levels, single nucleotide polymorphisms, genome-wide association analysis based on agronomic traits, globally collected germplasm information, summaries, omics data of the Panax genus, and online versatile analytic tools. The Panax genus database will be updated when new data are released to continue serving as a central portal to boost research on the biology and functions of Panax. PanaxGDB is available at: http://panaxGDB.ynau.edu.cn.

Keywords: Panax; cultivars; database; genome; saponins.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
A schematic diagram of the architecture of the PanaxGDB.
Figure 2
Figure 2
Query interface to retrieve information on germplasm, genomic application, and compounds. (A) Species page.16 species information on this page. (B) Cultivars page.62 cultivars information on this page. (C) Gene page. Search for genetic information including functional annotation, CDS, and protein sequence, etc. JBrowse (D) based on JavaScript for visual analysis of the genome annotation. Blast server (E) to perform homology searches with different data sets. (F) Compounds page. Search for the distribution, known metabolic pathways, or other characteristics of a particular compound.
Figure 3
Figure 3
Page on population and download. Population page contains three subpages: Statistics (A), Analysis (B), and Variations (C). Download page (D), summary and presentation of Panax omics information including transcriptome sequencing, genome, metagenome, and chloroplast genome.
See this image and copyright information in PMC

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