ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel
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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.
酿酒酵母（Saccharomyces cerevisiae）作为一类单细胞真核出芽酵母，在生物复杂性与实验可操作性之间达成了独特平衡，长期以来一直是基础与应用研究领域的经典模型系统。近年来，酿酒酵母进一步成为研究种群尺度下基因组进化自然多样性及其相关功能影响的前沿模型系统。高质量的比较基因组学与功能基因组学数据，是这类研究开展的关键前提。本研究对我们此前针对142株酿酒酵母构建的端粒到端粒（Telomere-to-Telomere, T2T）酿酒酵母参考组装面板（ScRAP）进行了全面扩展，新增覆盖了来自不同地理来源与生态位的264株酿酒酵母的高质量基因组组装与注释结果，同时纳入了该属其他酿酒酵母物种的33株外类群菌株。我们搭建了专属在线数据库ScRAPdb（https://www.evomicslab.org/db/ScRAPdb/），用于托管这套扩展后的泛基因组（pangenome）数据集。除泛基因组（pangenome）外，ScRAPdb还整合了种群尺度的泛组学（pan-omics）图谱，包含泛转录组（pantranscriptome）、泛蛋白质组（panproteome）与泛表型组（panphenome），同时配备了丰富的数据探索工具集，可支持直观的基因组学分析操作。所有经过整理的数据集与下游分析结果，均可从该数据库便捷下载获取。我们期望ScRAPdb能够成为酵母研究领域乃至更广泛科研共同体的高价值平台，助力实现对全球遗传与表型多样性的泛组学认知。
