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

Huan Liu; Jinpu Wei; Ting Yang; Weixue Mu; Bo Song; Tuo Yang; Yuan Fu; Xuebing Wang; Guohai Hu; Wangsheng Li; Hongcheng Zhou; Yue Chang; Xiaoli Chen; Hongyun Chen; Le Cheng; Xuefei He; Hechen Cai; Xianchu Cai; Mei Wang; Yang Li; Sunil Kumar Sahu; Jinlong Yang; Yu Wang; Ranchang Mu; Jie Liu; Jianming Zhao; Ziheng Huang; Xun Xu; Xin Liu

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

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

Authors

Huan Liu^{1

2

3}, Jinpu Wei^{1

2}, Ting Yang^{1

2

3}, Weixue Mu^{1

2

3}, Bo Song^{1

2}, Tuo Yang^{1

2}, Yuan Fu^{1

2}, Xuebing Wang^{1

2}, Guohai Hu^{1

2}, Wangsheng Li^{1

2}, Hongcheng Zhou^{1

2}, Yue Chang^{1

2}, Xiaoli Chen^{1

2

3}, Hongyun Chen^{1

2

3}, Le Cheng⁴, Xuefei He^{1

2}, Hechen Cai^{1

2}, Xianchu Cai^{1

2}, Mei Wang^{1

2

3}, Yang Li^{1

2}, Sunil Kumar Sahu^{1

2

3}, Jinlong Yang⁴, Yu Wang⁴, Ranchang Mu⁵, Jie Liu⁵, Jianming Zhao⁵, Ziheng Huang^{1

2

3}, Xun Xu^{1

2

3}, Xin Liu^{1

2

3}

Affiliations

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

China
Gardens / classification*
Genome Size
Genome, Plant*
Genomics* / methods
Heterozygote
Phylogeny
Plants / classification*
Plants / genetics*
Repetitive Sequences, Nucleic Acid
Whole Genome Sequencing