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SorGSD: updating and expanding the sorghum genome science database with new contents and tools
BACKGROUND: As the fifth major cereal crop originated from Africa, sorghum (Sorghum bicolor) has become a key C(4) model organism for energy plant research. With the development of high-throughput detection technologies for various omics data, much multi-dimensional and multi-omics information has b...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8336335/ https://www.ncbi.nlm.nih.gov/pubmed/34344425 http://dx.doi.org/10.1186/s13068-021-02016-7 |
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author | Liu, Yuanming Wang, Zhonghuang Wu, Xiaoyuan Zhu, Junwei Luo, Hong Tian, Dongmei Li, Cuiping Luo, Jingchu Zhao, Wenming Hao, Huaiqing Jing, Hai-Chun |
author_facet | Liu, Yuanming Wang, Zhonghuang Wu, Xiaoyuan Zhu, Junwei Luo, Hong Tian, Dongmei Li, Cuiping Luo, Jingchu Zhao, Wenming Hao, Huaiqing Jing, Hai-Chun |
author_sort | Liu, Yuanming |
collection | PubMed |
description | BACKGROUND: As the fifth major cereal crop originated from Africa, sorghum (Sorghum bicolor) has become a key C(4) model organism for energy plant research. With the development of high-throughput detection technologies for various omics data, much multi-dimensional and multi-omics information has been accumulated for sorghum. Integrating this information may accelerate genetic research and improve molecular breeding for sorghum agronomic traits. RESULTS: We updated the Sorghum Genome SNP Database (SorGSD) by adding new data, new features and renamed it to Sorghum Genome Science Database (SorGSD). In comparison with the original version SorGSD, which contains SNPs from 48 sorghum accessions mapped to the reference genome BTx623 (v2.1), the new version was expanded to 289 sorghum lines with both single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs), which were aligned to the newly assembled and annotated sorghum genome BTx623 (v3.1). Moreover, phenotypic data and panicle pictures of critical accessions were provided in the new version. We implemented new tools including ID Conversion, Homologue Search and Genome Browser for analysis and updated the general information related to sorghum research, such as online sorghum resources and literature references. In addition, we deployed a new database infrastructure and redesigned a new user interface as one of the Genome Variation Map databases. The new version SorGSD is freely accessible online at http://ngdc.cncb.ac.cn/sorgsd/. CONCLUSIONS: SorGSD is a comprehensive integration with large-scale genomic variation, phenotypic information and incorporates online data analysis tools for data mining, genome navigation and analysis. We hope that SorGSD could provide a valuable resource for sorghum researchers to find variations they are interested in and generate customized high-throughput datasets for further analysis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13068-021-02016-7. |
format | Online Article Text |
id | pubmed-8336335 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-83363352021-08-04 SorGSD: updating and expanding the sorghum genome science database with new contents and tools Liu, Yuanming Wang, Zhonghuang Wu, Xiaoyuan Zhu, Junwei Luo, Hong Tian, Dongmei Li, Cuiping Luo, Jingchu Zhao, Wenming Hao, Huaiqing Jing, Hai-Chun Biotechnol Biofuels Research BACKGROUND: As the fifth major cereal crop originated from Africa, sorghum (Sorghum bicolor) has become a key C(4) model organism for energy plant research. With the development of high-throughput detection technologies for various omics data, much multi-dimensional and multi-omics information has been accumulated for sorghum. Integrating this information may accelerate genetic research and improve molecular breeding for sorghum agronomic traits. RESULTS: We updated the Sorghum Genome SNP Database (SorGSD) by adding new data, new features and renamed it to Sorghum Genome Science Database (SorGSD). In comparison with the original version SorGSD, which contains SNPs from 48 sorghum accessions mapped to the reference genome BTx623 (v2.1), the new version was expanded to 289 sorghum lines with both single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs), which were aligned to the newly assembled and annotated sorghum genome BTx623 (v3.1). Moreover, phenotypic data and panicle pictures of critical accessions were provided in the new version. We implemented new tools including ID Conversion, Homologue Search and Genome Browser for analysis and updated the general information related to sorghum research, such as online sorghum resources and literature references. In addition, we deployed a new database infrastructure and redesigned a new user interface as one of the Genome Variation Map databases. The new version SorGSD is freely accessible online at http://ngdc.cncb.ac.cn/sorgsd/. CONCLUSIONS: SorGSD is a comprehensive integration with large-scale genomic variation, phenotypic information and incorporates online data analysis tools for data mining, genome navigation and analysis. We hope that SorGSD could provide a valuable resource for sorghum researchers to find variations they are interested in and generate customized high-throughput datasets for further analysis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13068-021-02016-7. BioMed Central 2021-08-03 /pmc/articles/PMC8336335/ /pubmed/34344425 http://dx.doi.org/10.1186/s13068-021-02016-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Liu, Yuanming Wang, Zhonghuang Wu, Xiaoyuan Zhu, Junwei Luo, Hong Tian, Dongmei Li, Cuiping Luo, Jingchu Zhao, Wenming Hao, Huaiqing Jing, Hai-Chun SorGSD: updating and expanding the sorghum genome science database with new contents and tools |
title | SorGSD: updating and expanding the sorghum genome science database with new contents and tools |
title_full | SorGSD: updating and expanding the sorghum genome science database with new contents and tools |
title_fullStr | SorGSD: updating and expanding the sorghum genome science database with new contents and tools |
title_full_unstemmed | SorGSD: updating and expanding the sorghum genome science database with new contents and tools |
title_short | SorGSD: updating and expanding the sorghum genome science database with new contents and tools |
title_sort | sorgsd: updating and expanding the sorghum genome science database with new contents and tools |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8336335/ https://www.ncbi.nlm.nih.gov/pubmed/34344425 http://dx.doi.org/10.1186/s13068-021-02016-7 |
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