SorGSD: updating and expanding the sorghum genome science database with new contents and tools.
Yuanming Liu,Zhonghuang Wang,Xiaoyuan Wu,Junwei Zhu,Hong Luo,Dongmei Tian,Cuiping Li,Jingchu Luo,Wenming Zhao,Huaiqing Hao,Hai-Chun Jing +10 more
TLDR
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 and could provide a valuable resource for sorghum researchers to find variations they are interested in and generate customized high-throughput datasets for further analysis.Abstract:
As the fifth major cereal crop originated from Africa, sorghum (Sorghum bicolor) has become a key C4 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 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 (v21), 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 (v31) 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://ngdccncbaccn/sorgsd/
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 analysisread more
Citations
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Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022.
TL;DR: The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry.
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Genomic footprints of sorghum domestication and breeding selection for multiple end uses.
Xiaoyuan Wu,Yuanming Liu,Hong-bing Luo,Li Shang,Chuan-Yuan Leng,Zhiquan Liu,Zhigang Li,Xiaochun Lu,Hongwei Cai,Huaiqing Hao,Hai-Chun Jing +10 more
TL;DR: In this article , population genomics analyses were performed on a worldwide collection of 445 sorghum accessions, covering wild and four end-use subpopulations with diverse agronomic traits.
Journal ArticleDOI
TeaPVs: a comprehensive genomic variation database for tea plant (Camellia sinensis)
TL;DR: Wang et al. as discussed by the authors constructed the first tea tree variation web service database TeaPVs (http://47.106.91:8025/ and http://liushang.top.
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