Pigs are valuable large animal models for biomedical and genetic research, but insights into the tissue- and cell-type-specific transcriptome and heterogeneity remain limited. By leveraging single-cell RNA sequencing, we generate a multiple-organ single-cell transcriptomic map containing over 200,000 pig cells from 20 tissues/organs. We comprehensively characterize the heterogeneity of cells in tissues and identify 234 cell clusters, representing 58 major cell types. In-depth integrative analysis of endothelial cells reveals a high degree of heterogeneity. We identify several functionally distinct endothelial cell phenotypes, including an endothelial to mesenchymal transition subtype in adipose tissues. Intercellular communication analysis predicts tissue- and cell type-specific crosstalk between endothelial cells and other cell types through the VEGF, PDGF, TGF-β, and BMP pathways. Regulon analysis of single-cell transcriptome of microglia in pig and 12 other species further identifies MEF2C as an evolutionally conserved regulon in the microglia. Our work describes the landscape of single-cell transcriptomes within diverse pig organs and identifies the heterogeneity of endothelial cells and evolutionally conserved regulon in microglia.

猪是用于生物医学和遗传研究的有价值的大型动物模型，但对组织和细胞类型特异性转录组和异质性的了解仍然有限。通过利用单细胞 RNA 测序，我们生成了一个多器官单细胞转录组图谱，其中包含来自 20 个组织/器官的超过 200,000 个猪细胞。我们全面表征了组织中细胞的异质性，并鉴定了 234 个细胞簇，代表 58 种主要细胞类型。对内皮细胞的深入综合分析揭示了高度的异质性。我们确定了几种功能不同的内皮细胞表型，包括脂肪组织中的内皮细胞到间充质细胞的转化亚型。细胞间通讯分析预测内皮细胞和其他细胞类型之间的组织和细胞类型特异性串扰VEGF、PDGF、TGF-β和BMP通路。对猪和其他 12 个物种小胶质细胞单细胞转录组的调节子分析进一步确定MEF2C是小胶质细胞中进化上保守的调节子。我们的工作描述了不同猪器官中单细胞转录组的概况，并确定了内皮细胞的异质性和小胶质细胞中进化上保守的调节子。