Ligand-receptor pairs play important roles in cell–cell communication for multicellular organisms in response to environmental cues. Recently, the emergence of single-cell RNA-sequencing (scRNA-seq) provides unprecedented opportunities to investigate cellular communication based on ligand-receptor expression. However, so far, no reliable ligand-receptor interaction database is available for plant species. In this study, we developed PlantPhoneDB (https://jasonxu.shinyapps.io/PlantPhoneDB/), a pan-plant database comprising a large number of high-confidence ligand-receptor pairs manually curated from seven resources. Also, we developed a PlantPhoneDB R package, which not only provided optional four scoring approaches that calculate interaction scores of ligand-receptor pairs between cell types but also provided visualization functions to present analysis results. At the PlantPhoneDB web interface, the processed datasets and results can be searched, browsed, and downloaded. To uncover novel cell–cell communication events in plants, we applied the PlantPhoneDB R package on GSE121619 dataset to infer significant cell–cell interactions of heat-shocked root cells in Arabidopsis thaliana. As a result, the PlantPhoneDB predicted the actively communicating AT1G28290-AT2G14890 ligand-receptor pair in atrichoblast–cortex cell pair in Arabidopsis thaliana. Importantly, the downstream target genes of this ligand-receptor pair were significantly enriched in the ribosome pathway, which facilitated plants adapting to environmental changes. In conclusion, PlantPhoneDB provided researchers with integrated resources to infer cell–cell communication from scRNA-seq datasets.

中文翻译：

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PlantPhoneDB：手动管理的配体-受体对的泛植物数据库推断细胞间通信


配体-受体对在多细胞生物响应环境信号的细胞间通讯中发挥着重要作用。最近，单细胞 RNA 测序 (scRNA-seq) 的出现为研究基于配体-受体表达的细胞通讯提供了前所未有的机会。然而，到目前为止，还没有可靠的植物物种配体-受体相互作用数据库。在这项研究中，我们开发了 PlantPhoneDB (https://jasonxu.shinyapps.io/PlantPhoneDB/)，这是一个泛植物数据库，包含从七个资源中手动整理的大量高置信度配体-受体对。此外，我们还开发了 PlantPhoneDB R 软件包，它不仅提供了可选的四种评分方法来计算细胞类型之间配体-受体对的相互作用评分，而且还提供了可视化功能来呈现分析结果。在PlantPhoneDB Web界面上，可以搜索、浏览和下载处理后的数据集和结果。为了揭示植物中新的细胞间通讯事件，我们在 GSE121619 数据集上应用 PlantPhoneDB R 包来推断拟南芥热休克根细胞的显着细胞间相互作用。因此，PlantPhoneDB 预测了拟南芥原毛细胞-皮层细胞对中活跃通讯的 AT1G28290-AT2G14890 配体-受体对。重要的是，该配体-受体对的下游靶基因在核糖体途径中显着富集，这有助于植物适应环境变化。总之，PlantPhoneDB 为研究人员提供了从 scRNA-seq 数据集推断细胞间通信的综合资源。