Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans
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 u...
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Elsevier,
2020-02-01T00:00:00Z.
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| 001 | doaj_02d36096d15a4598a3a265cd53bcd0e3 | ||
| 042 | |a dc | ||
| 100 | 1 | 0 | |a Yisong Liu |e author |
| 700 | 1 | 0 | |a Qi Tang |e author |
| 700 | 1 | 0 | |a Pi Cheng |e author |
| 700 | 1 | 0 | |a Mingfei Zhu |e author |
| 700 | 1 | 0 | |a Hui Zhang |e author |
| 700 | 1 | 0 | |a Jiazhe Liu |e author |
| 700 | 1 | 0 | |a Mengting Zuo |e author |
| 700 | 1 | 0 | |a Chongyin Huang |e author |
| 700 | 1 | 0 | |a Changqiao Wu |e author |
| 700 | 1 | 0 | |a Zhiliang Sun |e author |
| 700 | 1 | 0 | |a Zhaoying Liu |e author |
| 245 | 0 | 0 | |a Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans |
| 260 | |b Elsevier, |c 2020-02-01T00:00:00Z. | ||
| 500 | |a 2211-3835 | ||
| 500 | |a 10.1016/j.apsb.2019.08.004 | ||
| 520 | |a 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. KEY WORDS: Gelsemium elegans, Nanopore sequencing, Genome assembly, Hi-C, Genome annotation, Monoterpene indole alkaloid | ||
| 546 | |a EN | ||
| 690 | |a Therapeutics. Pharmacology | ||
| 690 | |a RM1-950 | ||
| 655 | 7 | |a article |2 local | |
| 786 | 0 | |n Acta Pharmaceutica Sinica B, Vol 10, Iss 2, Pp 374-382 (2020) | |
| 787 | 0 | |n http://www.sciencedirect.com/science/article/pii/S2211383519305143 | |
| 787 | 0 | |n https://doaj.org/toc/2211-3835 | |
| 856 | 4 | 1 | |u https://doaj.org/article/02d36096d15a4598a3a265cd53bcd0e3 |z Connect to this object online. |