Dataset Information

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.

SUBMITTER: Liu H

PROVIDER: S-EPMC6441391 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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

Liu Huan H Wei Jinpu J Yang Ting T Mu Weixue W Song Bo B Yang Tuo T Fu Yuan Y Wang Xuebing X Hu Guohai G Li Wangsheng W Zhou Hongcheng H Chang Yue Y Chen Xiaoli X Chen Hongyun H Cheng Le L He Xuefei X Cai Hechen H Cai Xianchu X Wang Mei M Li Yang Y Sahu Sunil Kumar SK Yang Jinlong J Wang Yu Y Mu Ranchang R Liu Jie J Zhao Jianming J Huang Ziheng Z Xu Xun X Liu Xin X

GigaScience 20190401 4

<h4>Background</h4>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.<h4>Result ...[more]

PMID: 30689836

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Project description:The way functional traits affect growth of plant species may be highly context-specific. We asked which combinations of trait values are advantageous under field conditions in managed grasslands as compared to conditions without competition and land-use. In a two-year field experiment, we recorded the performance of 93 species transplanted into German grassland communities differing in land-use intensity and into a common garden, where species grew unaffected by land-use under favorable conditions regarding soil, water, and space. The plants' performance was characterized by two independent dimensions (relative growth rates (RGR) of height and leaf length vs. aboveground biomass and survival) that were differently related to the eight focal key traits in our study (leaf dry matter content (LDMC), specific leaf area (SLA), height, leaf anatomy, leaf persistence, leaf distribution, vegetative reproduction, and physical defense). We applied multivariate procrustes analyses to test for the correspondence of the optimal trait-performance relationships between field and common garden conditions. RGRs were species-specific and species ranks of RGRs in the field, and the common garden were significantly correlated. Different traits explained the performance in the field and the common garden; for example, leaf anatomy traits explained species performance only in the field, whereas plant height was found to be only important in the common garden. The ability to reproduce vegetatively, having leaves that are summer-persistent and with high leaf dry matter content (LDMC) were traits of major importance under both settings, albeit the magnitude of their influence differed slightly between the field and the common garden experiment. All optimal models included interactions between traits, pointing out the necessity to analyze traits in combination. The differences between field and common garden clearly demonstrate context dependency of trait-based growth models, which results in limited transferability of favorable trait combinations between different environmental settings.

Dataset Information

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

Publications

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

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