Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin Biosynthesis
Bupleurum chinense DC is a plant widely used in Chinese traditional medicine. Saikosaponins are the major bioactive constituents of B. chinense DC. Saikosaponins biosynthesis in Bupleurum has been more intensively studied than any other metabolic processes or bioactive constituents. However, whole-g...
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| Format: | Article |
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Frontiers Media S.A.
2022-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.878431/full |
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| author | Quanfang Zhang Min Li Xueyan Chen Guoxia Liu Zhe Zhang Qingqing Tan Yue Hu Yangyang Fan Yanyan Liu Tongshan Zhu Xue Yang Mingming Yue Xun Bu Yongqing Zhang |
| author_facet | Quanfang Zhang Min Li Xueyan Chen Guoxia Liu Zhe Zhang Qingqing Tan Yue Hu Yangyang Fan Yanyan Liu Tongshan Zhu Xue Yang Mingming Yue Xun Bu Yongqing Zhang |
| author_sort | Quanfang Zhang |
| collection | DOAJ |
| description | Bupleurum chinense DC is a plant widely used in Chinese traditional medicine. Saikosaponins are the major bioactive constituents of B. chinense DC. Saikosaponins biosynthesis in Bupleurum has been more intensively studied than any other metabolic processes or bioactive constituents. However, whole-genome sequencing and chromosome-level assembly for Bupleurum genus have not been reported yet. Here, we report a high-quality chromosome-level genome of B. chinense DC. through the integration of PacBio long-read sequencing, Illumina short-read sequencing, and Hi-C sequencing. The genome was phased into haplotype 0 (621.27 Mb with a contig N50 of 16.86 Mb and a scaffold N50 of 92.25 Mb) and haplotype 1 (600.48 Mb with a contig N50 of 23.90 Mb and a scaffold N50 of 102.68 Mb). A total of 45,909 and 35,805 protein-coding genes were predicted in haplotypes 0 and 1, respectively. The enrichment analyses suggested that the gene families that expanded during the evolution of B. chinense DC are involved in the biosynthesis of isoquinoline alkaloid, tyrosine, and anthocyanin. Furthermore, we analyzed the genes involved in saikosaponin biosynthesis and determined the candidate P450 and UGT genes in the third stage of saikosaponins biosynthetic, which provided new insight into the saikosaponins biosynthetic. The genomic data provide a valuable resource for future investigations of the molecular mechanisms, biological functions, and evolutionary adaptations of B. chinense DC. |
| first_indexed | 2024-12-13T07:58:44Z |
| format | Article |
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| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-13T07:58:44Z |
| publishDate | 2022-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-0edfaea1a2484b93a7ab46f0abe7ebc72022-12-21T23:54:29ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-03-011310.3389/fgene.2022.878431878431Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin BiosynthesisQuanfang Zhang0Min Li1Xueyan Chen2Guoxia Liu3Zhe Zhang4Qingqing Tan5Yue Hu6Yangyang Fan7Yanyan Liu8Tongshan Zhu9Xue Yang10Mingming Yue11Xun Bu12Yongqing Zhang13Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, ChinaShandong University of Traditional Chinese Medicine, Jinan, ChinaInstitute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, ChinaInstitute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, ChinaShandong University of Traditional Chinese Medicine, Jinan, ChinaInstitute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, ChinaInstitute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, ChinaInstitute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, ChinaInstitute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, ChinaShandong University of Traditional Chinese Medicine, Jinan, ChinaInstitute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, ChinaInstitute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, ChinaInstitute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, ChinaShandong University of Traditional Chinese Medicine, Jinan, ChinaBupleurum chinense DC is a plant widely used in Chinese traditional medicine. Saikosaponins are the major bioactive constituents of B. chinense DC. Saikosaponins biosynthesis in Bupleurum has been more intensively studied than any other metabolic processes or bioactive constituents. However, whole-genome sequencing and chromosome-level assembly for Bupleurum genus have not been reported yet. Here, we report a high-quality chromosome-level genome of B. chinense DC. through the integration of PacBio long-read sequencing, Illumina short-read sequencing, and Hi-C sequencing. The genome was phased into haplotype 0 (621.27 Mb with a contig N50 of 16.86 Mb and a scaffold N50 of 92.25 Mb) and haplotype 1 (600.48 Mb with a contig N50 of 23.90 Mb and a scaffold N50 of 102.68 Mb). A total of 45,909 and 35,805 protein-coding genes were predicted in haplotypes 0 and 1, respectively. The enrichment analyses suggested that the gene families that expanded during the evolution of B. chinense DC are involved in the biosynthesis of isoquinoline alkaloid, tyrosine, and anthocyanin. Furthermore, we analyzed the genes involved in saikosaponin biosynthesis and determined the candidate P450 and UGT genes in the third stage of saikosaponins biosynthetic, which provided new insight into the saikosaponins biosynthetic. The genomic data provide a valuable resource for future investigations of the molecular mechanisms, biological functions, and evolutionary adaptations of B. chinense DC.https://www.frontiersin.org/articles/10.3389/fgene.2022.878431/fullBupleurum chinensesaikosaponin biosynthesisgenome assemblychromosome-level genomeevolutionhaplotype |
| spellingShingle | Quanfang Zhang Min Li Xueyan Chen Guoxia Liu Zhe Zhang Qingqing Tan Yue Hu Yangyang Fan Yanyan Liu Tongshan Zhu Xue Yang Mingming Yue Xun Bu Yongqing Zhang Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin Biosynthesis Frontiers in Genetics Bupleurum chinense saikosaponin biosynthesis genome assembly chromosome-level genome evolution haplotype |
| title | Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin Biosynthesis |
| title_full | Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin Biosynthesis |
| title_fullStr | Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin Biosynthesis |
| title_full_unstemmed | Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin Biosynthesis |
| title_short | Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin Biosynthesis |
| title_sort | chromosome level genome assembly of bupleurum chinense dc provides insights into the saikosaponin biosynthesis |
| topic | Bupleurum chinense saikosaponin biosynthesis genome assembly chromosome-level genome evolution haplotype |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.878431/full |
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