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. 2022 Jun 27:2022:baac046.
doi: 10.1093/database/baac046.

GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba

Kai-Jie Gu  1 , Chen-Feng Lin  1 , Jun-Jie Wu  1 , Yun-Peng Zhao  1
Affiliations

GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba

Kai-Jie Gu et al. Database (Oxford). .

Abstract

Although an increasing number of species-specific databases have been constructed to facilitate the global research community, comprehensive databases remain rare with multidimensional research resources rather than genomic data solely, in particular for non-model species. Here we introduced GinkgoDB, the ecological genome database for the world-renowned living fossil, Ginkgo biloba L., a tree species with extreme longevity, exceptional resistance, global landscape application and dioecy. The present version of GinkgoDB consists of four modules of genome, occurrence, quadrat and gallery. The genome module includes two versions of chromosome-level assembled genomes with high-quality annotation, expression profiles of each sex for different tissues and variants from 545 ginkgo genomes. A suite of tools were also deployed online for search, blast and further analyses. The occurrence module contains distribution information of over one million records across the world with an emphasis on 8926 individual-level tagged trees with phenotypic trait data in eastern Asia. The quadrat module provides monitoring data of both species and habitats from 27 plots of natural ginkgo forests and periodic data of functional traits measured for the entire plant communities. The gallery module collects field morphological photos and scanned phenotypic images of various ginkgo materials. GinkgoDB showcases a comprehensive and persistently growing database for a single non-model species. Database URL: https://ginkgo.zju.edu.cn/.

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Figures

Figure 1.
Figure 1.
Database architecture of GinkgoDB.
Figure 2.
Figure 2.
Search and result pages of GinkgoDB. Users can take a query for the specific genome segment or gene, which would return the summary (A), all the gene (B) and SNPs (C) of the queried region, a link to the JBrowse page (D).
Figure 3.
Figure 3.
Gene page of GinkgoDB. The gene page displays specific gene summary (A), sequence, translated protein sequence, expression (transcripts per million, TPM) (B) and annotation information (C), in each collected sample.
Figure 4.
Figure 4.
Expression analysis tool and phylogeny of GinkgoDB. Users can select specific sample combinations for the traits under study to analyze the expression differences of target genes among different experiments (A), which will be visualized by an expression heatmap, which could be downloaded as PDF(B). (C) The neighbor-joining phylogeny tree of wild individuals. Each sample ID could be clicked and links to the sample information page.
Figure 5.
Figure 5.
Individual page with detail information of GinkgoDB. (A) Summary. (B) Content list with location tagged on the map. (C) Sample traits if available. (D) Biological materials collection of the individual. (E) Integrated visualization of phylogeny, PCA and population structure.
Figure 6.
Figure 6.
Comprehensive data for ginkgo conservation. Distribution map (A) of documented mature trees and heatmap (B) of reported trees. (C) Species list in each quadrat. (D) The gallery model collects various material type of trees.
See this image and copyright information in PMC

References

    1. Crane P.R. (2018) An evolutionary and cultural biography of ginkgo. Plants, People, Planet, 1, 32–37.
    1. Gong W., Chen C., Dobes C.. et al. (2008) Phylogeography of a living fossil: pleistocene glaciations forced Ginkgo biloba L. (Ginkgoaceae) into two refuge areas in China with limited subsequent postglacial expansion. Mol. Phylogenet. Evol., 48, 1094–1105. - PubMed
    1. Zhao Y.P., Paule J., Fu C.X.. et al. (2010) Out of China: distribution history of Ginkgo biloba L. Taxon, 59, 495–504.
    1. Crane P. (2013) Ginkgo: The Tree That Time Forgot. Yale University Press, New Haven, USA.
    1. Shi C., Liu J., Wu F.M.. et al. (2010) Ginkgo biloba extract in Alzheimer’s Disease: from action mechanisms to medical practice. Int. J. Mol. Sci., 11, 107–123. - PMC - PubMed

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