MDSi: Multi-omics Database for Setaria italica
Abstract Background Foxtail millet (Setaria italica) harbors the small diploid genome (~ 450 Mb) and shows the high inbreeding rate and close relationship to several major foods, feed, fuel and bioenergy grasses. Previously, we created a mini foxtail millet, xiaomi, with an Arabidopsis-like life cyc...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-04-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-023-04238-3 |
| _version_ | 1797836577165017088 |
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| author | Xukai Li Siyu Hou Mengmeng Feng Rui Xia Jiawei Li Sha Tang Yuanhuai Han Jianhua Gao Xingchun Wang |
| author_facet | Xukai Li Siyu Hou Mengmeng Feng Rui Xia Jiawei Li Sha Tang Yuanhuai Han Jianhua Gao Xingchun Wang |
| author_sort | Xukai Li |
| collection | DOAJ |
| description | Abstract Background Foxtail millet (Setaria italica) harbors the small diploid genome (~ 450 Mb) and shows the high inbreeding rate and close relationship to several major foods, feed, fuel and bioenergy grasses. Previously, we created a mini foxtail millet, xiaomi, with an Arabidopsis-like life cycle. The de novo assembled genome data with high-quality and an efficient Agrobacterium-mediated genetic transformation system made xiaomi an ideal C4 model system. The mini foxtail millet has been widely shared in the research community and as a result there is a growing need for a user-friendly portal and intuitive interface to perform exploratory analysis of the data. Results Here, we built a Multi-omics Database for Setaria italica (MDSi, http://sky.sxau.edu.cn/MDSi.htm ), that contains xiaomi genome of 161,844 annotations, 34,436 protein-coding genes and their expression information in 29 different tissues of xiaomi (6) and JG21 (23) samples that can be showed as an Electronic Fluorescent Pictograph (xEFP) in-situ. Moreover, the whole-genome resequencing (WGS) data of 398 germplasms, including 360 foxtail millets and 38 green foxtails and the corresponding metabolic data were available in MDSi. The SNPs and Indels of these germplasms were called in advance and can be searched and compared in an interactive manner. Common tools including BLAST, GBrowse, JBrowse, map viewer, and data downloads were implemented in MDSi. Conclusion The MDSi constructed in this study integrated and visualized data from three levels of genomics, transcriptomics and metabolomics, and also provides information on the variation of hundreds of germplasm resources that can satisfies the mainstream requirements and supports the corresponding research community. |
| first_indexed | 2024-04-09T15:11:07Z |
| format | Article |
| id | doaj.art-cf1468686a374a04b329fab4038d3f41 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-09T15:11:07Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-cf1468686a374a04b329fab4038d3f412023-04-30T11:11:57ZengBMCBMC Plant Biology1471-22292023-04-012311810.1186/s12870-023-04238-3MDSi: Multi-omics Database for Setaria italicaXukai Li0Siyu Hou1Mengmeng Feng2Rui Xia3Jiawei Li4Sha Tang5Yuanhuai Han6Jianhua Gao7Xingchun Wang8Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural UniversityHou Ji Laboratory in Shanxi Province, Shanxi Agricultural UniversityCollege of Life Sciences, Shanxi Agricultural UniversitySouth China Agricultural UniversitySouth China Agricultural UniversityInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesHou Ji Laboratory in Shanxi Province, Shanxi Agricultural UniversityHou Ji Laboratory in Shanxi Province, Shanxi Agricultural UniversityHou Ji Laboratory in Shanxi Province, Shanxi Agricultural UniversityAbstract Background Foxtail millet (Setaria italica) harbors the small diploid genome (~ 450 Mb) and shows the high inbreeding rate and close relationship to several major foods, feed, fuel and bioenergy grasses. Previously, we created a mini foxtail millet, xiaomi, with an Arabidopsis-like life cycle. The de novo assembled genome data with high-quality and an efficient Agrobacterium-mediated genetic transformation system made xiaomi an ideal C4 model system. The mini foxtail millet has been widely shared in the research community and as a result there is a growing need for a user-friendly portal and intuitive interface to perform exploratory analysis of the data. Results Here, we built a Multi-omics Database for Setaria italica (MDSi, http://sky.sxau.edu.cn/MDSi.htm ), that contains xiaomi genome of 161,844 annotations, 34,436 protein-coding genes and their expression information in 29 different tissues of xiaomi (6) and JG21 (23) samples that can be showed as an Electronic Fluorescent Pictograph (xEFP) in-situ. Moreover, the whole-genome resequencing (WGS) data of 398 germplasms, including 360 foxtail millets and 38 green foxtails and the corresponding metabolic data were available in MDSi. The SNPs and Indels of these germplasms were called in advance and can be searched and compared in an interactive manner. Common tools including BLAST, GBrowse, JBrowse, map viewer, and data downloads were implemented in MDSi. Conclusion The MDSi constructed in this study integrated and visualized data from three levels of genomics, transcriptomics and metabolomics, and also provides information on the variation of hundreds of germplasm resources that can satisfies the mainstream requirements and supports the corresponding research community.https://doi.org/10.1186/s12870-023-04238-3DatabaseMulti-omicsFoxtail milletSetaria italicaTools |
| spellingShingle | Xukai Li Siyu Hou Mengmeng Feng Rui Xia Jiawei Li Sha Tang Yuanhuai Han Jianhua Gao Xingchun Wang MDSi: Multi-omics Database for Setaria italica BMC Plant Biology Database Multi-omics Foxtail millet Setaria italica Tools |
| title | MDSi: Multi-omics Database for Setaria italica |
| title_full | MDSi: Multi-omics Database for Setaria italica |
| title_fullStr | MDSi: Multi-omics Database for Setaria italica |
| title_full_unstemmed | MDSi: Multi-omics Database for Setaria italica |
| title_short | MDSi: Multi-omics Database for Setaria italica |
| title_sort | mdsi multi omics database for setaria italica |
| topic | Database Multi-omics Foxtail millet Setaria italica Tools |
| url | https://doi.org/10.1186/s12870-023-04238-3 |
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