Integrating short-read and long-read single-cell transcriptomics of pig pituitary reveals mechanisms of high-altitude hypoxia adaptation

Acting as the central endocrine hub, the pituitary gland is closely related to the mechanism of adaptation to high-altitude hypoxia. Here, by integratively combining long-read (Oxford Nanopore) and short-read (Illumina) single-cell sequencing approaches, we profiled pituitaries from Diqing Tibetan pigs, inhabiting high-altitude environments (3,200 m) and Diannan small-ear pigs from low-altitude regions (500 m), thereby generating a full-length single-cell atlas, which in turn enabled the identification of molecular mechanisms potentially underlying adaptation to high-altitude hypoxia stress. Systematically delineating pituitary structure and transcriptional dynamics, we profiled 27,339 single cells encompassing 28,932 expressed genes. Leveraging unsupervised clustering coupled with marker-based annotation, we identified ten major cell types. Expression profiling of 20 canonical marker genes revealed pronounced cell-type-specific expression patterns, ten of which were independently validated by immunofluorescence, thus substantiating the accuracy of cell-type annotation. Gene-ontology enrichment analysis further suggested that upregulated genes were predominantly involved in oxidative metabolism and energy production, whereas downregulated genes were significantly associated with protein biosynthesis and translation processes, indicating a functional reprogramming of metabolic pathways. Moreover, comparative analyses between breeds and cell-cell communication analyses highlighted pathway shifts, including broad upregulation of the collagen family and four ligand-receptor pairs that may mediate pituitary intercellular coordination. In parallel, transcription-factor activity analysis nominated several regulators, including EBF3, DBX2, and TCF21, which may collectively contribute to altitude-associated adaptation. Finally, integrating long-read sequencing data revealed widespread transcript isoform diversity, with ~28% novel annotations, indicating considerable isoform complexity in pigs. Our findings delineate cellular heterogeneity, inferred intercellular communication networks, and transcript-isoform diversity in the porcine pituitary, thereby providing a cell-resolved resource for understanding pituitary features associated with high-altitude environments.