Genomic and Imaging Data Supporting the Digitization of Ruili Botanical Garden

Dataset type: Genomic, Imaging
Data released on January 18, 2019

Liu H; Wei j; Yang T; Mu W; Song B; Yang T; Fu Y; Wang X; Hu G; Li W; Zhou H; Chang Y; Chen X; Chen H; Cheng L; He X; Cai H; Cai X; Wang M; Li Y; Sahu SK; Yang J; Wang Y; Mu R; Liu J; Zhao J; Huang Z; Xu X; Liu X (2019): Genomic and Imaging Data Supporting the Digitization of Ruili Botanical Garden GigaScience Database. http://dx.doi.org/10.5524/100502

DOI10.5524/100502

Genome sequencing has been widely used in plant research to construct reference genomes and elucidate evolutionary insights. However, only a limited number of plant species have had their whole genome sequenced, and the limited taxon information of these species has further restrained the utility of these data.
Here, we comprehensively sampled and sequenced vascular plant species in and around Ruili Botanical Garden, located in South West China. We sequenced 761 samples out of the total 1,093 collected voucher specimens stored in the Herbarium of China National GeneBank (HCNGB). These 761 samples represented 689 vascular plant species from 137 families belonging to 49 orders. Of these, 257 samples were identified to the species level and 504 samples to the family level using specimens and chloroplast sequences. We generated 54 Tb sequencing data in total, which resulted in an average sequencing depth of 60× for these species, as estimated by the genome size. A reference phylogeny was reconstructed with 78 chloroplast genes for molecular identification and possible applications.
In this study, we established a large dataset of vascular plants’ genomes, with both the high-depth whole genome sequencing data and the voucher specimens, making it valuable dataset for plant genome researches and applications. And providing insight into the feasibility and technical requirements for “planetary scale” projects such as the 10 thousand Plant Genome Project (10KP) and Earth BioGenome Project (EBP).

Additional details

Read the peer-reviewed publication(s):

Liu, H., Wei, J., Yang, T., Mu, W., Song, B., Yang, T., … Liu, X. (2019). Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden. GigaScience, 8(4). doi:10.1093/gigascience/giz007

Accessions (data generated as part of this study):

BioProject: PRJNA438407
HTTP: gigadb.org/search/new?keyword=HCNGB%3ARUILI&type%5B%5D=dataset

Projects:







Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
RL00013487mulberry family Moraceae Description:DNA extracted from leaves of Moraceae ...
Geographic location (country and/or sea,region):Na...
Geographic location (latitude and longitude):restr...
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RL000223513rue family Rutaceae Description:DNA extracted from leaves of Rutaceae ...
Geographic location (country and/or sea,region):Na...
Geographic location (latitude and longitude):restr...
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RL00034070nightshade family Solanaceae Description:DNA extracted from leaves of Solanacea...
Geographic location (country and/or sea,region):Na...
Geographic location (latitude and longitude):restr...
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RL000423513rue family Rutaceae Description:DNA extracted from leaves of Rutaceae ...
Geographic location (country and/or sea,region):Na...
Geographic location (latitude and longitude):restr...
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RL000558023vascular plants Tracheophyta Description:Images of vouchered uncharacterized va...
Geographic location (country and/or sea,region):Na...
Geographic location (latitude and longitude):restr...
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RL000639501good luck plantti plantCordyline fruticosa Description:DNA extracted from leaves of Cordyline...
Geographic location (country and/or sea,region):Na...
Geographic location (latitude and longitude):restr...
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RL000758023vascular plants Tracheophyta Description:Images of vouchered uncharacterized va...
Geographic location (country and/or sea,region):Na...
Geographic location (latitude and longitude):restr...
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RL00083433laurel family Lauraceae Description:DNA extracted from leaves of Lauraceae...
Geographic location (country and/or sea,region):Na...
Geographic location (latitude and longitude):restr...
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RL0009179682  Excoecaria cochinchinensis Description:Images of vouchered Excoecaria cochinc...
Geographic location (country and/or sea,region):Na...
Geographic location (latitude and longitude):restr...
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RL00104050ginseng family Araliaceae Description:DNA extracted from leaves of Araliacea...
Geographic location (country and/or sea,region):Na...
Geographic location (latitude and longitude):restr...
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Displaying 1-10 of 1093 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
AlignmentsFASTA3.43 MB2018-10-12
Phylogenetic treeFASTA43.94 KB2018-10-12
AlignmentsFASTA1.3 MB2018-10-12
Phylogenetic treeFASTA48.92 KB2018-10-12
AlignmentsFASTA1.37 MB2018-10-12
Phylogenetic treeFASTA48.92 KB2018-10-12
AlignmentsFASTA385.08 KB2018-10-12
Phylogenetic treeFASTA48.67 KB2018-10-12
AlignmentsFASTA553.27 KB2018-10-12
Phylogenetic treeFASTA48.72 KB2018-10-12
Displaying 1-10 of 160 File(s).
Funding body Awardee Award ID Comments
Shenzhen Municipal Government of China Xin Liu JCYJ20150529150505656 Shenzhen Science and Technology Innovation Commission
Ministry of Science and Technology (MOST) Xun Xu 2017B030301011 Guangdong Provincial Key Laboratory of Genome Read and Write
State Commission of Science Technology of China Huan Liu 2011DQ782025 State Key Laboratory of Agricultural Genomics
Yunnan Provincial Government Le Cheng 2015DA008 For the Construction of China National GeneBank
Date Action
January 24, 2019 Dataset publish