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SorGSD: updating and expanding the sorghum genome science database with new contents and tools

文献类型：期刊论文

作者Liu, Yuanming; Wang, Zhonghuang1,5,7; Wu, Xiaoyuan; Zhu, Junwei1,5,7; Luo, Hong; Tian, Dongmei1,5,7; Li, Cuiping1,5,7; Luo, Jingchu2,3; Zhao, Wenming1,5,7; Hao, Huaiqing
刊名BIOTECHNOLOGY FOR BIOFUELS
出版日期2021
卷号14期号:1
关键词Sorghum Bio-energy plant Variation SNPs Small INDELs Phenotype Database
DOI10.1186/s13068-021-02016-7
文献子类Article
英文摘要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 . 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.
学科主题Biotechnology & Applied Microbiology ; Energy & Fuels
出版地LONDON
电子版国际标准刊号1754-6834
WOS关键词IDEOTYPES GENETIC-IMPROVEMENT ; WIDE ASSOCIATION ; FORMAT
WOS研究方向Science Citation Index Expanded (SCI-EXPANDED)
语种英语
WOS记录号WOS:000680904900001
出版者BMC
资助机构National Key R&D Program of China [2018YFD1000701] ; CAS-Commonwealth Scientific and Industrial Research Organization Bilateral Collaboration Project [151111KYSB20180049] ; Strategic Priority Research Program of Chinese Academy of Sciences [XDA26050101] ; National Natural Science Foundation of China [32072026]
源URL[http://ir.ibcas.ac.cn/handle/2S10CLM1/26689]  
专题中科院北方资源植物重点实验室
作者单位1.Chinese Acad Sci, Natl Genom Data Ctr, Beijing Inst Genom, Beijing 100101, Peoples R China
2.Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100101, Peoples R China
3.Peking Univ, Coll Life Sci, Beijing 100871, Peoples R China
4.Peking Univ, Ctr Bioinformat, Beijing 100871, Peoples R China
5.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
6.Chinese Acad Sci, Inst Bot, Engn Lab Grass Based Livestock Husb, Beijing 100093, Peoples R China
7.China Natl Ctr Bioinformat, Beijing 100101, Peoples R China
8.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China
推荐引用方式
GB/T 7714		 Liu, Yuanming,Wang, Zhonghuang,Wu, Xiaoyuan,et al. SorGSD: updating and expanding the sorghum genome science database with new contents and tools[J]. BIOTECHNOLOGY FOR BIOFUELS,2021,14(1).
APA Liu, Yuanming.,Wang, Zhonghuang.,Wu, Xiaoyuan.,Zhu, Junwei.,Luo, Hong.,...&Jing, Hai-Chun.(2021).SorGSD: updating and expanding the sorghum genome science database with new contents and tools.BIOTECHNOLOGY FOR BIOFUELS,14(1).
MLA Liu, Yuanming,et al."SorGSD: updating and expanding the sorghum genome science database with new contents and tools".BIOTECHNOLOGY FOR BIOFUELS 14.1(2021).

入库方式： OAI收割

来源：植物研究所

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