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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...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016290/ https://www.ncbi.nlm.nih.gov/pubmed/32082980 http://dx.doi.org/10.1016/j.apsb.2019.08.004 |
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author | Liu, Yisong Tang, Qi Cheng, Pi Zhu, Mingfei Zhang, Hui Liu, Jiazhe Zuo, Mengting Huang, Chongyin Wu, Changqiao Sun, Zhiliang Liu, Zhaoying |
author_facet | Liu, Yisong Tang, Qi Cheng, Pi Zhu, Mingfei Zhang, Hui Liu, Jiazhe Zuo, Mengting Huang, Chongyin Wu, Changqiao Sun, Zhiliang Liu, Zhaoying |
author_sort | Liu, Yisong |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7016290 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-70162902020-02-20 Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans Liu, Yisong Tang, Qi Cheng, Pi Zhu, Mingfei Zhang, Hui Liu, Jiazhe Zuo, Mengting Huang, Chongyin Wu, Changqiao Sun, Zhiliang Liu, Zhaoying Acta Pharm Sin B Short Communication 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. Elsevier 2020-02 2019-08-16 /pmc/articles/PMC7016290/ /pubmed/32082980 http://dx.doi.org/10.1016/j.apsb.2019.08.004 Text en © 2020 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V. http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Short Communication Liu, Yisong Tang, Qi Cheng, Pi Zhu, Mingfei Zhang, Hui Liu, Jiazhe Zuo, Mengting Huang, Chongyin Wu, Changqiao Sun, Zhiliang Liu, Zhaoying Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans |
title | Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans |
title_full | Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans |
title_fullStr | Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans |
title_full_unstemmed | Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans |
title_short | Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans |
title_sort | whole-genome sequencing and analysis of the chinese herbal plant gelsemium elegans |
topic | Short Communication |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016290/ https://www.ncbi.nlm.nih.gov/pubmed/32082980 http://dx.doi.org/10.1016/j.apsb.2019.08.004 |
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