Chromosome-level genome assembly and annotation of the prickly nightshade Solanum rostratum Dunal
Abstract The prickly nightshade Solanum rostratum, an annual malignant weed, is native to North America and has globally invaded 34 countries, causing serious threats to ecosystems, agriculture, animal husbandry, and human health. In this study, we constructed a chromosome-level genome assembly and...
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Nature Portfolio
2023-06-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-023-02247-3 |
| _version_ | 1797811966045061120 |
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| author | Yue Zhang Wenchao Guo Zhili Yuan Zhen Song Zhonghui Wang Jinhui Gao Weidong Fu Guoliang Zhang |
| author_facet | Yue Zhang Wenchao Guo Zhili Yuan Zhen Song Zhonghui Wang Jinhui Gao Weidong Fu Guoliang Zhang |
| author_sort | Yue Zhang |
| collection | DOAJ |
| description | Abstract The prickly nightshade Solanum rostratum, an annual malignant weed, is native to North America and has globally invaded 34 countries, causing serious threats to ecosystems, agriculture, animal husbandry, and human health. In this study, we constructed a chromosome-level genome assembly and annotation of S. rostratum. The contig-level genome was initially assembled in 898.42 Mb with a contig N50 of 62.00 Mb from PacBio high-fidelity reads. With Hi-C sequencing data scaffolding, 96.80% of the initially assembled sequences were anchored and orientated onto 12 pseudo-chromosomes, generating a genome of 869.69 Mb with a contig N50 of 72.15 Mb. We identified 649.92 Mb (72.26%) of repetitive sequences and 3,588 non-coding RNAs in the genome. A total of 29,694 protein-coding genes were predicted, with 28,154 (94.81%) functionally annotated genes. We found 99.5% and 91.3% complete embryophyta_odb10 genes in the pseudo-chromosomes genome and predicted gene datasets by BUSCO assessment. The present genomic resource provides essential information for subsequent research on the mechanisms of environmental adaptation of S. rostratum and host shift in Colorado potato beetles. |
| first_indexed | 2024-03-13T07:31:35Z |
| format | Article |
| id | doaj.art-7665531b6a064139a4e3ea0a0fdf5058 |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-03-13T07:31:35Z |
| publishDate | 2023-06-01 |
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| spelling | doaj.art-7665531b6a064139a4e3ea0a0fdf50582023-06-04T11:06:13ZengNature PortfolioScientific Data2052-44632023-06-0110111410.1038/s41597-023-02247-3Chromosome-level genome assembly and annotation of the prickly nightshade Solanum rostratum DunalYue Zhang0Wenchao Guo1Zhili Yuan2Zhen Song3Zhonghui Wang4Jinhui Gao5Weidong Fu6Guoliang Zhang7Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural SciencesKey Laboratory of Intergraded Management of Harmful Crop Vermin of China Northwestern Oasis, Ministry of Agriculture and Rural Affairs/Institute of Plant Protection, Xinjiang Academy of Agricultural SciencesInstitute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural SciencesInstitute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural SciencesInstitute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural SciencesInstitute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural SciencesInstitute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural SciencesInstitute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural SciencesAbstract The prickly nightshade Solanum rostratum, an annual malignant weed, is native to North America and has globally invaded 34 countries, causing serious threats to ecosystems, agriculture, animal husbandry, and human health. In this study, we constructed a chromosome-level genome assembly and annotation of S. rostratum. The contig-level genome was initially assembled in 898.42 Mb with a contig N50 of 62.00 Mb from PacBio high-fidelity reads. With Hi-C sequencing data scaffolding, 96.80% of the initially assembled sequences were anchored and orientated onto 12 pseudo-chromosomes, generating a genome of 869.69 Mb with a contig N50 of 72.15 Mb. We identified 649.92 Mb (72.26%) of repetitive sequences and 3,588 non-coding RNAs in the genome. A total of 29,694 protein-coding genes were predicted, with 28,154 (94.81%) functionally annotated genes. We found 99.5% and 91.3% complete embryophyta_odb10 genes in the pseudo-chromosomes genome and predicted gene datasets by BUSCO assessment. The present genomic resource provides essential information for subsequent research on the mechanisms of environmental adaptation of S. rostratum and host shift in Colorado potato beetles.https://doi.org/10.1038/s41597-023-02247-3 |
| spellingShingle | Yue Zhang Wenchao Guo Zhili Yuan Zhen Song Zhonghui Wang Jinhui Gao Weidong Fu Guoliang Zhang Chromosome-level genome assembly and annotation of the prickly nightshade Solanum rostratum Dunal Scientific Data |
| title | Chromosome-level genome assembly and annotation of the prickly nightshade Solanum rostratum Dunal |
| title_full | Chromosome-level genome assembly and annotation of the prickly nightshade Solanum rostratum Dunal |
| title_fullStr | Chromosome-level genome assembly and annotation of the prickly nightshade Solanum rostratum Dunal |
| title_full_unstemmed | Chromosome-level genome assembly and annotation of the prickly nightshade Solanum rostratum Dunal |
| title_short | Chromosome-level genome assembly and annotation of the prickly nightshade Solanum rostratum Dunal |
| title_sort | chromosome level genome assembly and annotation of the prickly nightshade solanum rostratum dunal |
| url | https://doi.org/10.1038/s41597-023-02247-3 |
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