SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomics
Soybean (Glycine max (L.) Merr.) is a globally significant crop, widely cultivated for oilseed production and animal feeds. In recent years, the rapid growth of multi-omics data from thousands of soybean accessions has provided unprecedented opportunities for researchers to explore genomes, genetic...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023002246 |
| _version_ | 1797384045654441984 |
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| author | Haoran Li Tiantian Chen Lihua Jia Zhizhan Wang Jiaming Li Yazhou Wang Mengjia Fu Mingming Chen Yuping Wang Fangfang Huang Yingru Jiang Tao Li Zhengfu Zhou Yang Li Wen Yao Yihan Wang |
| author_facet | Haoran Li Tiantian Chen Lihua Jia Zhizhan Wang Jiaming Li Yazhou Wang Mengjia Fu Mingming Chen Yuping Wang Fangfang Huang Yingru Jiang Tao Li Zhengfu Zhou Yang Li Wen Yao Yihan Wang |
| author_sort | Haoran Li |
| collection | DOAJ |
| description | Soybean (Glycine max (L.) Merr.) is a globally significant crop, widely cultivated for oilseed production and animal feeds. In recent years, the rapid growth of multi-omics data from thousands of soybean accessions has provided unprecedented opportunities for researchers to explore genomes, genetic variations, and gene functions. To facilitate the utilization of these abundant data for soybean breeding and genetic improvement, the SoybeanGDB database (https://venyao.xyz/SoybeanGDB/) was developed as a comprehensive platform. SoybeanGDB integrates high-quality de novo assemblies of 39 soybean genomes and genomic variations among thousands of soybean accessions. Genomic information and variations in user-specified genomic regions can be searched and downloaded from SoybeanGDB, in a user-friendly manner. To facilitate research on genetic resources and elucidate the biological significance of genes, SoybeanGDB also incorporates a variety of bioinformatics analysis modules with graphical interfaces, such as linkage disequilibrium analysis, nucleotide diversity analysis, allele frequency analysis, gene expression analysis, primer design, gene set enrichment analysis, etc. In summary, SoybeanGDB is an essential and valuable resource that provides an open and free platform to accelerate global soybean research. |
| first_indexed | 2024-03-08T21:29:48Z |
| format | Article |
| id | doaj.art-073121a3e12a44a7b2b4dfa04f0fc3b4 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:29:48Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-073121a3e12a44a7b2b4dfa04f0fc3b42023-12-21T07:31:41ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-012133273338SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomicsHaoran Li0Tiantian Chen1Lihua Jia2Zhizhan Wang3Jiaming Li4Yazhou Wang5Mengjia Fu6Mingming Chen7Yuping Wang8Fangfang Huang9Yingru Jiang10Tao Li11Zhengfu Zhou12Yang Li13Wen Yao14Yihan Wang15National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, ChinaHenan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; Corresponding authors.National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; Corresponding authors.National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; Corresponding authors.Soybean (Glycine max (L.) Merr.) is a globally significant crop, widely cultivated for oilseed production and animal feeds. In recent years, the rapid growth of multi-omics data from thousands of soybean accessions has provided unprecedented opportunities for researchers to explore genomes, genetic variations, and gene functions. To facilitate the utilization of these abundant data for soybean breeding and genetic improvement, the SoybeanGDB database (https://venyao.xyz/SoybeanGDB/) was developed as a comprehensive platform. SoybeanGDB integrates high-quality de novo assemblies of 39 soybean genomes and genomic variations among thousands of soybean accessions. Genomic information and variations in user-specified genomic regions can be searched and downloaded from SoybeanGDB, in a user-friendly manner. To facilitate research on genetic resources and elucidate the biological significance of genes, SoybeanGDB also incorporates a variety of bioinformatics analysis modules with graphical interfaces, such as linkage disequilibrium analysis, nucleotide diversity analysis, allele frequency analysis, gene expression analysis, primer design, gene set enrichment analysis, etc. In summary, SoybeanGDB is an essential and valuable resource that provides an open and free platform to accelerate global soybean research.http://www.sciencedirect.com/science/article/pii/S2001037023002246SoybeanBioinformatic platformGenome databaseGenomic variationZhonghuang 13 |
| spellingShingle | Haoran Li Tiantian Chen Lihua Jia Zhizhan Wang Jiaming Li Yazhou Wang Mengjia Fu Mingming Chen Yuping Wang Fangfang Huang Yingru Jiang Tao Li Zhengfu Zhou Yang Li Wen Yao Yihan Wang SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomics Computational and Structural Biotechnology Journal Soybean Bioinformatic platform Genome database Genomic variation Zhonghuang 13 |
| title | SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomics |
| title_full | SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomics |
| title_fullStr | SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomics |
| title_full_unstemmed | SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomics |
| title_short | SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomics |
| title_sort | soybeangdb a comprehensive genomic and bioinformatic platform for soybean genetics and genomics |
| topic | Soybean Bioinformatic platform Genome database Genomic variation Zhonghuang 13 |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023002246 |
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