CRISPR/Cas9 is a powerful tool for editing genomes, but design decisions are generally made with respect to a single reference genome. With population genomic data becoming available for an increasing number of model organisms, researchers are interested in manipulating multiple strains and lines. CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing for diverse yeast and bacterial strains. The current implementation designs and predicts the activity of guide RNAs against more than 1000 Saccharomyces cerevisiae genomes, including 167 strains frequently used in bioenergy research. Zymomonas mobilis, an increasingly popular bacterial bioenergy research model, is also supported. CRISpy-pop is available as a web application (https://CRISpy-pop.glbrc.org/) with an intuitive graphical user interface. CRISpy-pop also cross-references the human genome to allow users to avoid the selection of guide RNAs with potential biosafety concerns. Additionally, CRISpy-pop predicts the strain coverage of each guide RNA within the supported strain sets, which aids in functional population genetic studies. Finally, we validate how CRISpy-pop can accurately predict the activity of guide RNAs across strains using population genomic data.

CRISPR/Cas9 是编辑基因组的强大工具，但设计决策通常是针对单个参考基因组做出的。随着越来越多的模型生物体获得群体基因组数据，研究人员对操纵多个菌株和品系感兴趣。 CRISpy-pop 是一款 Web 应用程序，可生成和过滤引导 RNA 序列，用于多种酵母和细菌菌株的 CRISPR/Cas9 基因组编辑。当前的实施针对 1000 多种酿酒酵母基因组（包括生物能源研究中常用的 167 种菌株）设计并预测了指导 RNA 的活性。运动发酵单胞菌（Zymomonas mobilis ）是一种日益流行的细菌生物能研究模型，也得到了支持。 CRISpy-pop 可作为 Web 应用程序 (https://CRISpy-pop.glbrc.org/) 提供，具有直观的图形用户界面。 CRISpy-pop 还交叉引用人类基因组，让用户避免选择存在潜在生物安全问题的指导 RNA。此外，CRISpy-pop 还可以预测支持的菌株集中每个指导 RNA 的菌株覆盖率，这有助于功能群体遗传学研究。最后，我们验证了 CRISpy-pop 如何使用群体基因组数据准确预测跨菌株的指导 RNA 的活性。