ABSTRACT

Drosophila pseudoobscura is a classic model system for the study of evolutionary genetics and genomics. Given this long-standing interest, many genome sequences have accumulated for D. pseudoobscura and closely related species D. persimilis, D. miranda, and D. lowei. To facilitate the exploration of genetic variation within species and comparative genomics across species, we present PseudoBase, a database that couples extensive publicly available genomic data with simple visualization and query tools via an intuitive graphical interface, amenable for use in both research and educational settings. All genetic variation (SNPs and indels) within the database is derived from the same workflow, so variants are easily comparable across data sets. Features include an embedded JBrowse interface, ability to pull out alignments of individual genes/regions, and batch access for gene lists. Here, we introduce PseudoBase, and we demonstrate how this resource facilitates use of extensive genomic data from flies of the Drosophila pseudoobscura subgroup.

摘要

Drosophila pseudoobscura是研究进化遗传学和基因组学的经典模型系统。鉴于这种长期的兴趣，已经为D. pseudoobscura和密切相关的物种D. persimilis、 D. miranda和D. lowei积累了许多基因组序列. 为了促进探索物种内的遗传变异和跨物种的比较基因组学，我们提出了 PseudoBase，这是一个数据库，它通过直观的图形界面将广泛的公开可用的基因组数据与简单的可视化和查询工具相结合，适用于研究和教育环境。数据库中的所有遗传变异（SNP 和插入缺失）均来自相同的工作流程，因此变异很容易在数据集之间进行比较。功能包括嵌入式 JBrowse 界面、提取单个基因/区域比对的能力以及基因列表的批量访问。在这里，我们介绍了 PseudoBase，并展示了该资源如何促进使用来自Drosophila pseudoobscura亚群的果蝇的广泛基因组数据。