De Novo Assembly of an Allotetraploid <i>Artemisia argyi</i> Genome
The Chinese mugwort (<i>Artemisia argyi</i> Lév. et Vaniot) is an important traditional Chinese medicine plant that is ubiquitously disturbed in Asia. However, the molecular mechanisms that reflect the natural evolution of <i>Artemisia argyi</i> remain unclear. In this study,...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-02-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/13/2/436 |
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| author | Qiming Mei Hanxiang Li Yanbin Liu Feng Wu Chuang Liu Keya Wang Hongjun Liu Cheng Peng Zhengfeng Wang Long Wang Zhanfeng Liu Junhua Yan Wei Zhang |
| author_facet | Qiming Mei Hanxiang Li Yanbin Liu Feng Wu Chuang Liu Keya Wang Hongjun Liu Cheng Peng Zhengfeng Wang Long Wang Zhanfeng Liu Junhua Yan Wei Zhang |
| author_sort | Qiming Mei |
| collection | DOAJ |
| description | The Chinese mugwort (<i>Artemisia argyi</i> Lév. et Vaniot) is an important traditional Chinese medicine plant that is ubiquitously disturbed in Asia. However, the molecular mechanisms that reflect the natural evolution of <i>Artemisia argyi</i> remain unclear. In this study, a high-quality draft assembly of the allotetraploid <i>A. argyi</i> (ArteW1-Tongbai) was conducted utilizing PacBio long-read sequencing and Hi-C technologies. The assembly is about 7.20 Gb with a contig N50 length of 0.87 Mb. The allotetraploid genome of ArteW1-Tongbai is highly heterozygous and rich in repeat sequences (the heterozygous ratio is 1.36%, and the repeat rate is 86.26%). A total of 139,245 protein-coding genes were identified. The KEGG enrichment analysis revealed that 846 species-specific genes were related to the biosynthesis of secondary metabolites. The plants with allopolyploid genomes can potentially exhibit a better adaptive capacity to environmental stresses and accumulation of secondary metabolites. Therefore, the genome assembly serves as a valuable reference for <i>Artemisia</i>, the genus characterized by species richness and diverse specialized metabolites. |
| first_indexed | 2024-03-11T09:17:30Z |
| format | Article |
| id | doaj.art-fbed19e4f8174545ac1d6331645b949f |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-11T09:17:30Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-fbed19e4f8174545ac1d6331645b949f2023-11-16T18:34:35ZengMDPI AGAgronomy2073-43952023-02-0113243610.3390/agronomy13020436De Novo Assembly of an Allotetraploid <i>Artemisia argyi</i> GenomeQiming Mei0Hanxiang Li1Yanbin Liu2Feng Wu3Chuang Liu4Keya Wang5Hongjun Liu6Cheng Peng7Zhengfeng Wang8Long Wang9Zhanfeng Liu10Junhua Yan11Wei Zhang12Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaTea Bureau of Tongbai County, Nanyang 474750, ChinaTea Bureau of Tongbai County, Nanyang 474750, ChinaTea Bureau of Tongbai County, Nanyang 474750, ChinaKey Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaPeople’s Government of Tongbai County, Nanyang 474750, ChinaKey Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaKey Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, ChinaThe Chinese mugwort (<i>Artemisia argyi</i> Lév. et Vaniot) is an important traditional Chinese medicine plant that is ubiquitously disturbed in Asia. However, the molecular mechanisms that reflect the natural evolution of <i>Artemisia argyi</i> remain unclear. In this study, a high-quality draft assembly of the allotetraploid <i>A. argyi</i> (ArteW1-Tongbai) was conducted utilizing PacBio long-read sequencing and Hi-C technologies. The assembly is about 7.20 Gb with a contig N50 length of 0.87 Mb. The allotetraploid genome of ArteW1-Tongbai is highly heterozygous and rich in repeat sequences (the heterozygous ratio is 1.36%, and the repeat rate is 86.26%). A total of 139,245 protein-coding genes were identified. The KEGG enrichment analysis revealed that 846 species-specific genes were related to the biosynthesis of secondary metabolites. The plants with allopolyploid genomes can potentially exhibit a better adaptive capacity to environmental stresses and accumulation of secondary metabolites. Therefore, the genome assembly serves as a valuable reference for <i>Artemisia</i>, the genus characterized by species richness and diverse specialized metabolites.https://www.mdpi.com/2073-4395/13/2/436<i>Artemisia argyi</i>de novo assemblyHi-C technologyallotetraploid |
| spellingShingle | Qiming Mei Hanxiang Li Yanbin Liu Feng Wu Chuang Liu Keya Wang Hongjun Liu Cheng Peng Zhengfeng Wang Long Wang Zhanfeng Liu Junhua Yan Wei Zhang De Novo Assembly of an Allotetraploid <i>Artemisia argyi</i> Genome Agronomy <i>Artemisia argyi</i> de novo assembly Hi-C technology allotetraploid |
| title | De Novo Assembly of an Allotetraploid <i>Artemisia argyi</i> Genome |
| title_full | De Novo Assembly of an Allotetraploid <i>Artemisia argyi</i> Genome |
| title_fullStr | De Novo Assembly of an Allotetraploid <i>Artemisia argyi</i> Genome |
| title_full_unstemmed | De Novo Assembly of an Allotetraploid <i>Artemisia argyi</i> Genome |
| title_short | De Novo Assembly of an Allotetraploid <i>Artemisia argyi</i> Genome |
| title_sort | de novo assembly of an allotetraploid i artemisia argyi i genome |
| topic | <i>Artemisia argyi</i> de novo assembly Hi-C technology allotetraploid |
| url | https://www.mdpi.com/2073-4395/13/2/436 |
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