Chromosome-level genome assembly and annotation of Gypsophila vaccaria
Abstract Gypsophila vaccaria Sm., a member of the Caryophyllaceae family, is known for its dry mature seeds, which are widely used in traditional Chinese medicine as “Wang Bu Liu Xing”. This study presents a high-quality, chromosome-scale genome assembly of G. vaccaria, integrating Hi-C technology w...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-05-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-05121-6 |
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| author | Chaoqiang Zhang Jiayin Zhang Bin Yang Yunchen Zhao Liang Yin Enjun Wang Yaqiu Zhao Jinglong Li |
| author_facet | Chaoqiang Zhang Jiayin Zhang Bin Yang Yunchen Zhao Liang Yin Enjun Wang Yaqiu Zhao Jinglong Li |
| author_sort | Chaoqiang Zhang |
| collection | DOAJ |
| description | Abstract Gypsophila vaccaria Sm., a member of the Caryophyllaceae family, is known for its dry mature seeds, which are widely used in traditional Chinese medicine as “Wang Bu Liu Xing”. This study presents a high-quality, chromosome-scale genome assembly of G. vaccaria, integrating Hi-C technology with PacBio and Illumina sequencing data. The final assembled genome measures 1.09 Gb in total length, with a contig N50 of 9.73 Mb and a scaffold N50 of 73.3 Mb, and complete benchmarking universal single-copy orthologs (BUSCO) for the genome and protein modes were 95.9% and 94.9%. Notably, 99.93% of the sequences are anchored to 15 pseudo-chromosomes. A total of 21,795 protein-coding genes were predicted, and repetitive elements were found to constitute 80.43% of the assembled genome. This chromosome-level genome assembly serves as an invaluable resource for future research, including functional genomics and molecular breeding of G. vaccaria. |
| format | Article |
| id | doaj-art-8010643dc51442d9b67ebb2667df6d12 |
| institution | DOAJ |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-8010643dc51442d9b67ebb2667df6d122025-08-20T03:08:22ZengNature PortfolioScientific Data2052-44632025-05-011211910.1038/s41597-025-05121-6Chromosome-level genome assembly and annotation of Gypsophila vaccariaChaoqiang Zhang0Jiayin Zhang1Bin Yang2Yunchen Zhao3Liang Yin4Enjun Wang5Yaqiu Zhao6Jinglong Li7College of Life Sciences and Engineering, Key Laboratory of Hexi Corridor Resources Utilization of Gansu, Hexi UniversityMinistry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan UniversityCollege of Life Sciences and Engineering, Key Laboratory of Hexi Corridor Resources Utilization of Gansu, Hexi UniversityCollege of Agriculture and Ecological Engineering, Hexi UniversityCollege of Agriculture and Ecological Engineering, Hexi UniversityCollege of Agriculture and Ecological Engineering, Hexi UniversityState Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesState Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityAbstract Gypsophila vaccaria Sm., a member of the Caryophyllaceae family, is known for its dry mature seeds, which are widely used in traditional Chinese medicine as “Wang Bu Liu Xing”. This study presents a high-quality, chromosome-scale genome assembly of G. vaccaria, integrating Hi-C technology with PacBio and Illumina sequencing data. The final assembled genome measures 1.09 Gb in total length, with a contig N50 of 9.73 Mb and a scaffold N50 of 73.3 Mb, and complete benchmarking universal single-copy orthologs (BUSCO) for the genome and protein modes were 95.9% and 94.9%. Notably, 99.93% of the sequences are anchored to 15 pseudo-chromosomes. A total of 21,795 protein-coding genes were predicted, and repetitive elements were found to constitute 80.43% of the assembled genome. This chromosome-level genome assembly serves as an invaluable resource for future research, including functional genomics and molecular breeding of G. vaccaria.https://doi.org/10.1038/s41597-025-05121-6 |
| spellingShingle | Chaoqiang Zhang Jiayin Zhang Bin Yang Yunchen Zhao Liang Yin Enjun Wang Yaqiu Zhao Jinglong Li Chromosome-level genome assembly and annotation of Gypsophila vaccaria Scientific Data |
| title | Chromosome-level genome assembly and annotation of Gypsophila vaccaria |
| title_full | Chromosome-level genome assembly and annotation of Gypsophila vaccaria |
| title_fullStr | Chromosome-level genome assembly and annotation of Gypsophila vaccaria |
| title_full_unstemmed | Chromosome-level genome assembly and annotation of Gypsophila vaccaria |
| title_short | Chromosome-level genome assembly and annotation of Gypsophila vaccaria |
| title_sort | chromosome level genome assembly and annotation of gypsophila vaccaria |
| url | https://doi.org/10.1038/s41597-025-05121-6 |
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