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

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.

The Draft Genome Assembly of the Critically Endangered <em>Nyssa yunnanensis</em>, a Plant Species with Extremely Small Populations Endemic to Yunnan Province, China

“…Kb (Table 1). The N. yunnanensis genome size we assembled was also close to the estimated genome size of 1.23 Gb based on the raw data produced [39] for the Digitization of the Ruili Botanical Garden project [40]. The GC content of the N.…”

CNSA: a data repository for archiving omics data

“…It is worth mentioning that CNSA has created a correlation model of living samples, sample and analytical data on some projects such as the Ruili Botanical Garden project ( https://db.cngb.org/search/project/CNPhis0000538 ) [ 15 ] and Culturable Genome Reference ( https://db.cngb.org/search/project/CNP0000126/ ) [ 16 ]. Figure 1B illustrates the interrelationship of the living samples, sample and analytical data for the Ruili Botanical Garden project.…”

Genomic interventions for sustainable agriculture

“…Stimulated by the technological innovations, researchers are undertaking ambitious projects that intend to offer deeper insights into the genomic architectures and evolution (Liu et al, 2019). For example, the 3,000 Rice Genomes Project (Wang et al, 2018), 1000 plants project (1 KP, Matasci et al, 2014; https://sites.google.com/a/ualberta.ca/onekp/), 3000 chickpea genome sequencing initiative (unpublished) etc.…”