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

Autor: Liu Y; Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; University of Chinese Academy of Sciences, Beijing, 100049, China., Wang Z; University of Chinese Academy of Sciences, Beijing, 100049, China.; China National Center for Bioinformation, Beijing, 100101, China.; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China., Wu X; Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China., Zhu J; China National Center for Bioinformation, Beijing, 100101, China.; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China., Luo H; Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China., Tian D; China National Center for Bioinformation, Beijing, 100101, China.; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China., Li C; China National Center for Bioinformation, Beijing, 100101, China.; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China., Luo J; College of Life Sciences and Center for Bioinformatics, Peking University, Beijing, 100871, China., Zhao W; University of Chinese Academy of Sciences, Beijing, 100049, China. zhaowm@big.ac.cn.; China National Center for Bioinformation, Beijing, 100101, China. zhaowm@big.ac.cn.; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. zhaowm@big.ac.cn.; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. zhaowm@big.ac.cn., Hao H; Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. hqhao@ibcas.ac.cn., Jing HC; Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; Engineering Laboratory for Grass-Based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.
Jazyk: angličtina
Zdroj: Biotechnology for biofuels [Biotechnol Biofuels] 2021 Aug 03; Vol. 14 (1), pp. 165. Date of Electronic Publication: 2021 Aug 03.
DOI: 10.1186/s13068-021-02016-7
Abstrakt: 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.
(© 2021. The Author(s).)
Databáze: MEDLINE
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