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, 10 (2), 374-382

Whole-genome Sequencing and Analysis of the Chinese Herbal Plant Gelsemium elegans

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Whole-genome Sequencing and Analysis of the Chinese Herbal Plant Gelsemium elegans

Yisong Liu et al. Acta Pharm Sin B.

Abstract

Background: Gelsemium elegans (G. elegans) (2n = 2x = 16) is genus of flowering plants belonging to the Gelsemicaeae family.

Method: Here, a high-quality genome assembly using the Oxford Nanopore Technologies (ONT) platform and high-throughput chromosome conformation capture techniques (Hi-C) were used.

Results: A total of 56.11 Gb of raw GridION X5 platform ONT reads (6.23 Gb per cell) were generated. After filtering, 53.45 Gb of clean reads were obtained, giving 160 × coverage depth. The de novo genome assemblies 335.13 Mb, close to the 338 Mb estimated by k-mer analysis, was generated with contig N50 of 10.23 Mb. The vast majority (99.2%) of the G. elegans assembled sequence was anchored onto 8 pseudo-chromosomes. The genome completeness was then evaluated and 1338 of the 1440 conserved genes (92.9%) could be found in the assembly. Genome annotation revealed that 43.16% of the G. elegans genome is composed of repetitive elements and 23.9% is composed of long terminal repeat elements. We predicted 26,768 protein-coding genes, of which 84.56% were functionally annotated.

Conclusion: The genomic sequences of G. elegans could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.

Keywords: Gelsemium elegans; Genome annotation; Genome assembly; Hi-C; Monoterpene indole alkaloid; Nanopore sequencing.

Figures

Image 1
Figure 1
Figure 1
Example of the Gelsemium elegans (Gou Wen or Duan Chang Cao). (A) Natural habitat of Gelsemium elegans (image from Qi Tang). (B) Gelsemium elegans (image from Yisong Liu). (C) The flower of Gelsemium elegans (image from Qi Tang).
Figure 2
Figure 2
Genome-wide Hi-C map of Gelsemium elegans. Interaction frequency distribution of Hi-C links among chromosomes shows in color key of heatmap ranging from light yellow to dark red indicated the frequency of Hi-C interaction links from low to high (0–10).
Figure 3
Figure 3
Venn diagram of shared gene families between Gelsemium elegans and 8 other plants. Each number represents a gene family number.
Figure 4
Figure 4
Inferred phylogenetic tree across 9 plant species. The estimated divergence time (Mya) is shown at each node.
Figure 5
Figure 5
Whole-genome duplication (WGD) events of 5 plants (Gelsemium elegans, Arabidopsis thaliana, Glycine max, Olea europaea and Vitis vinifera) inferred by 4-fold synonymous third-codon transversion (4DTv) estimations. (A) 4DTv; (B) Ks.
Scheme 1
Scheme 1
Key steps in monoterpene indole alkaloid (MIA) biosynthesis, catalyzed by the enzymes tryptophan decarboxylase (TDC), strictosidine synthase (STR), strictosidine glucosidase (SDG), geissoschizine dehydrogenase (GSD) and sarpagan bridge enzyme (SBE). The pathway diverges after strictosidine aglycone and leads to very different alkaloids in the plants Gelsemium elegans. Several representative alkaloids for Gelsemium elegans are shown.

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