Ginkgo DB is a multiscale comprehensive germplasm database for Ginkgo biloba having been developed since 2020. The multi-omic genetic database and occurrence database are two core components of GinkgoDB. Around them, a series of databases like growth monitoring, phenological observation, environment data, as well as photos and articals about ginkgo have been being organized and posted on our site.
GinkgoDB aims at sharing with the world the results of research on the evolutionary ecology of ginkgo and empowering the conservation of wild population of this fascinating species.
This work was supported by National Key Research and Development Program of China (No. 2017YFA0605104) and the National Natural Science Foundation of China (No. 31870190, 32071484).
Ginkgo, or the maidenhair tree (Ginkgo biloba L.) is one of the best-known and most distinctive deciduous trees, native to China, with medicinal and horticultural importance. Known as a living fossil, ginkgo has remained essentially unchanged in morphology for more than 200 million years. Ginkgo represents one of the four gymnosperm lineages (Ginkgoidae, Cycadidae, Pinidae and Gnetidae) with no living relatives.
Ginkgo is one of the oldest living plants and a fascinating example of how people have saved a species from extinction and assisted its resurgence. As Charles Darwin anticipated, living fossils like Ginkgo provide excellent opportunities to study evolutionary questions related to extinction, competition, and adaptation.
Ginkgo has a very large genome size of ~10.6Gb, and a haploid chromosome number of 12. The draft of ginkgo genome was published in article Draft Genome of the Living Fossil Ginkgo Biloba in GigaScience. In 2019, Guan et. al. updated ginkgo genome assembly to chromosome level with Hi-C technology and obtained high-quality ginkgo genome . In 2021, Liu et. al. presented another ginkgo genome assembly based on long reads (PacBio RSII platform) .
Each assembly were collected and resigned according to the published year, for example, “Ver. 2019”.
For the assembly published at 2019 (Ver. 2019), the gene models were predicted using protein sequences from five land plants (Selaginella moellendorffii, Picea abies, Pinus taeda, Arabidopsis thaliana and Oryza sativa) coupled with transcriptomes assembled from RNA-seq data and EST data downloaded from NCBI. Function annotation via mapping to functional databases identified 68.12% protein sequences with known homologous genes.
For the assembly published at 2021 (Ver. 2021), de novo prediction of coding genes was performed using repeat-masked genome sequences. The gene model parameters of AUGUSTUS were trained using gene sets processed by PASA. For homology-based prediction, the protein sequences of five angiosperm and gymnosperm species (A. thaliana, O. sativa, Amborella trichopoda, P. taeda and P. abies) were aligned to the G. biloba genome using tblastn (E-value < 1×10–5). GenBlastA was then applied to cluster adjacent high-scoring pairs from the same protein alignments, and accurate gene structures were identified by GeneWise (v.2.4.1). Quality-controlled reads from all RNA libraries were mapped to the G. biloba genome using TopHat2. Subsequently, Cufflinks (v.2.2.1) was employed to predict gene models. Finally, all genes predicted with the three approaches were integrated with EVidenceModeler to generate high-confidence gene sets.
By re-sequencing the whole genome of 545 ginkgo trees around the world, a massive amount of data of 44Tb was generated. Using the chromosome-level ginkgo reference genome, we obtained 214.33 million raw SNPs and 161.04 million high quality SNPs. These dataset constructed the largest variation database of non-model species to date. The research paper Resequencing 545 Ginkgo across the world reveals the Evolutionary History of the Living Fossil was published in Nature Communications.
Researchers who wish to use GinkgoDB are encouraged to refer to our publication or specific data sources :
Kai-Jie Gu, Chen-Feng Lin, Jun-Jie Wu, Yun-Peng Zhao* (2022) GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba. Database 2022, baac046
Pan-Pan Bai, Han-Yang Lin, Yue Sun, Jun-Jie Wu, Kai-Jie Gu & Yun-Peng Zhao*(2022) Temporal dynamic transcriptome landscape reveals regulatory network during the early differentiation of female strobilus buds in Ginkgo biloba. Frontiers in Plant Science 13, 863330
He Zhang, Rui Zhang, Xianwei Yang, Kai-Jie Gu, Wenbin Chen, Yue Chang, Qiwu Xu, Qun Liu, Yating Qin, Xiaoning Hong, Yin, Inge Seim, Han-Yang Lin, Wen-Hao Li, Jinfu Tian, Shanshan Li, Liu, Junnian Liu, Shanshan Liu, Xiaoshan Su, Congyan Wang, Fu-Ming Zhang, Song Ge, Cheng-Xin Fu, Simon Ming-Yuen Lee, Yiji Xia, Jian Wang, Huanming Yang, Guangyi Fan*, Xun Xu*, Yun-Peng Zhao* & Xin Liu*(2019) Recent origin of an XX/XY sex-determination system in the ancient plant lineage Ginkgo biloba. bioRxiv
Rui Guan, Yunpeng Zhao, He Zhang, Guangyi Fan, Xin Liu, Wenbin Zhou, Chengcheng Shi, Jiahao Wang, Weiqing Liu, Xinming Liang, Yuanyuan Fu, Kailong Ma, Lijun Zhao, Fumin Zhang, Zuhong Lu, Simon Ming-Yuen Lee, Xun Xu, Jian Wang, Huanming Yang, Chengxin Fu*, Song Ge* & Wenbin Chen* (2016) Draft genome of the living fossil Ginkgo biloba. GigaScience 5, 49
Rui Guan, Yunpeng Zhao, He Zhang, Guangyi Fan, Xin Liu, Wenbin Zhou, Chengcheng Shi, Jiahao Wang, Weiqing Liu, Xinming Liang, Yuanyuan Fu, Kailong Ma, Lijun Zhao, Fumin Zhang, Zuhong Lu, Simon Ming-Yuen Lee, Xun Xu, Jian Wang, Huanming Yang, Chengxin Fu*, Song Ge* & Wenbin Chen* (2019) Updated genome assembly of Ginkgo biloba. GigaScience Database
Yun-Peng Zhao, Guangyi Fan, Ping-Ping Yin, Shuai Sun, Ning Li, Xiaoning Hong, Gang Hu, He Zhang, Fu-Min Zhang, Jing-Dan Han, Ya-Jun Hao, Qiwu Xu, Xianwei Yang, Wenjie Xia, Wenbin Chen, Han-Yang Lin, Rui Zhang, Jiang Chen, Xiao-Ming Zheng, Simon Ming-Yuen Lee, Joongku Lee, Koichi Uehara, Jian Wang, Huanming Yang, Cheng-Xin Fu*, Xin Liu*, Xun Xu* & Song Ge* (2019) Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil. Nature Communications 10, 4201
Hailin Liu, Xiaobo Wang, Guibin Wang, Peng Cui, Shigang Wu, Cheng Ai, Nan Hu, Alun Li, Bing He, Xiujuan Shao, Zhichao Wu, Hu Feng, Yuxiao Chang, Desheng Mu, Jing Hou, Xiaogang Dai, Tongming Yin*, Jue Ruan* & Fuliang Cao* (2021) The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution. Nature Plants 7, 748-756
Steve Rozen, Helen Skaletsky (1999) Primer3 on the WWW for general users and for biologist programmers. In Stephen Misener, Stephen A Krawetz (Eds.) Bioinformatics Methods and Protocols. Totowa, NJ: Humana Press, pp. 365-386
Andreas Untergasser, Ioana Cutcutache, Triinu Koressaar, Jian Ye, Brant C. Faircloth, Maido Remm, Steven G. Rozen* (2012) Primer3-new capabilities and interfaces. Nucleic Acids Research 40, e115
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We study evolutionary ecology of relict tree species using the living fossil Ginkgo biloba (maidenhair tree) as major study systems by integrating field observatory and monitoring data, multi-omic data and experimental data. The key question We have been focused on is the evolutionary causes and genetic bases underlying regulation mechanisms of population size and distribution with an emphasis on three key ecological processes, i.e., reproduction, morality and dispersal. The specific questions include response strategies to global climate change and adaptive evolution, sex chromosome evolution and sexual dimorphism, evolution of secondary metabolites, plant-microbial coupling and coevolution.
Group leader: Prof. Dr. Yun-Peng Zhao, E-mail: email@example.com, homepage: person.zju.edu.cn/en/ypzhao
Web Designer and Developer: Chen-feng Lin, E-mail: firstname.lastname@example.org
Data support: Kai-jie Gu, E-mail: email@example.com; Jun-Jie Wu, E-mail: firstname.lastname@example.org
Address: 浙江省 杭州市 余杭塘路866号 浙江大学紫金港校区生命科学学院 植物系统进化与生物多样性研究室，310058
Lab of Systematic & Evolutionary Botany and Biodiversity, College of Life Science, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, P.R. China