| URL: | https://www.evomicslab.org/db/ScRAPdb/ |
| Full name: | an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel |
| Description: | As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tractability, serving as a long-standing classic model for both basic and applied studies. Recently, S. cerevisiae further emerged as a leading system for studying natural diversity of genome evolution and its associated functional implication at population scales. Having high-quality comparative and functional genomics data is critical for such efforts. Here we exhaustively expanded the Telomere-to-Telomere (T2T) S. cerevisiae reference assembly panel (ScRAP) that we previously constructed for 142 strains to cover high-quality genome assemblies and annotations for 264 S. cerevisiae strains from diverse geographical and ecological niches and also 33 outgroup strains from the other Saccharomyces species described in the genus. We created a dedicated online database, ScRAPdb (https://www.evomicslab.org/db/ScRAPdb/), to host this expanded pangenome collection. On top of the pangenome, ScRAPdb also integrates a population-scale pan-omics atlas (pantranscriptome, panproteome, and panphenome) and rich data exploration toolkits for intuitive genomics analyses. All curated data and downstream analysis results could be easily downloaded from the database. We expect ScRAPdb to become a highly valuable platform for the yeast community and beyond, leading to a pan-omics understanding of the global genetic and phenotypic diversity. |
| Year founded: | 2024 |
| Last update: | 2024-09-30 |
| Version: | v20240930 |
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| Country/Region: | China |
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| University/Institution: | Sun Yat-sen University Cancer Center |
| Address: | Jia-Xing Yue's Group (Evomics Lab), 9th floor, Building F, Ascendas OneHub Business Park, Sino-Singaporc Guangzhou Knowledge City Huangpu District, 510555 Guangzhou Guangdong Province China |
| City: | Guangzhou |
| Province/State: | Guangdong |
| Country/Region: | China |
| Contact name (PI/Team): | Jia-Xing Yue |
| Contact email (PI/Helpdesk): | yuejiaxing@gmail.com |
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ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel. [PMID: 39470715]
As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tractability, serving as a long-standing classic model for both basic and applied studies. Recently, S. cerevisiae further emerged as a leading system for studying natural diversity of genome evolution and its associated functional implication at population scales. Having high-quality comparative and functional genomics data are critical for such efforts. Here, we exhaustively expanded the telomere-to-telomere (T2T) S. cerevisiae reference assembly panel (ScRAP) that we previously constructed for 142 strains to cover high-quality genome assemblies and annotations of 264 S. cerevisiae strains from diverse geographical and ecological niches and also 33 outgroup strains from all the other Saccharomyces species complex. We created a dedicated online database, ScRAPdb (https://www.evomicslab.org/db/ScRAPdb/), to host this expanded pangenome collection. Furthermore, ScRAPdb also integrates an array of population-scale pan-omics atlases (pantranscriptome, panproteome and panphenome) and extensive data exploration toolkits for intuitive genomics analyses. All curated data and downstream analysis results can be easily downloaded from ScRAPdb. We expect ScRAPdb to become a highly valuable platform for the yeast community and beyond, leading to a pan-omics understanding of the global genetic and phenotypic diversity. |