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Gigascience. 2019 Apr 1;8(4). pii: giz007. doi: 10.1093/gigascience/giz007.

Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden.

Liu H1,2,3, Wei J1,2, Yang T1,2,3, Mu W1,2,3, Song B1,2, Yang T1,2, Fu Y1,2, Wang X1,2, Hu G1,2, Li W1,2, Zhou H1,2, Chang Y1,2, Chen X1,2,3, Chen H1,2,3, Cheng L4, He X1,2, Cai H1,2, Cai X1,2, Wang M1,2,3, Li Y1,2, Sahu SK1,2,3, Yang J4, Wang Y4, Mu R5, Liu J5, Zhao J5, Huang Z1,2,3, Xu X1,2,3, Liu X1,2,3.

Author information

1
BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
2
China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China.
3
State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
4
BGI-Yunnan, No. 389 Haiyuan Road, High-tech Development Zone, Kunming, Yunnan 650106, China.
5
Forestry Bureau of Ruili, Yunnan Dehong, Ruili 678600, China.

Abstract

BACKGROUND:

Genome sequencing has been widely used in plant research to construct reference genomes and provide evolutionary insights. However, few plant species have had their whole genome sequenced, thus restraining the utility of these data. We collected 1,093 samples of vascular plant species growing in the Ruili Botanical Garden, located in southwest China. Of these, we sequenced 761 samples and collected voucher specimens stored in the Herbarium of China National GeneBank.

RESULTS:

The 761 sequenced 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 to the family level, using specimen and chloroplast sequences. In total, we generated 54 Tb of sequencing data, with an average sequencing depth of 60X per species, as estimated from genome sizes. A reference phylogeny was reconstructed with 78 chloroplast genes for molecular identification and other possible applications.

CONCLUSIONS:

The large dataset of vascular plant genomes generated in this study, which includes both high-depth whole-genome sequencing data and associated voucher specimens, is valuable for plant genome research and other applications. This project also provides insight into the feasibility and technical requirements for "planetary-scale" projects such as the 10,000 Plant Genomes Project and the Earth BioGenome Project.

KEYWORDS:

Ruili Botanical Garden; phylogeny; vascular plants; voucher specimens; whole-genome sequencing

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