Alternative splicing and polyadenylation facilitate transcriptome diversity underlying high-altitude adaptation in pigs.

Alternative splicing (AS) and alternative polyadenylation (APA) are critical post-transcriptional mechanisms that regulate gene expression and increase transcriptome and proteome diversity. The landscape and functional impact of AS and APA in pigs under high-altitude conditions remains poorly explored. Employing polyA-selected Iso-Seq, we obtained a high-quality transcriptome from the heart, liver, spleen, lung, and kidney of low-altitude Diannan small-ear pigs (DSE, 500 m) and high-altitude Diqing Tibetan pigs (DT, 3200 m). Numerous unannotated transcripts were identified, including novel isoforms of both known and novel genes. AS- and APA-driven transcriptome diversity revealed distinct splicing and polyadenylation patterns, with marked differences in alternative major transcript (AMT) and alternative major polyadenylation (AMP) usage between low- and high-altitude pigs. Differentially regulated genes across five tissues were clearly enriched in high-altitude adaptation-related pathways, including heme binding, HIF-1, iron ion binding, oxidoreductase activity, and mitochondrial membrane components. Hub genes potentially associated with high-altitude adaptation were identified. RT-PCR and qPCR validation confirmed AS-driven transcriptomic diversity, highlighted the utility of Iso-Seq for AS profiling, and revealed transcripts and key genes expression differences underlying high-altitude adaptation in pigs. Collectively, our findings demonstrate that AS and APA play vital roles in shaping transcriptome diversity and may regulate genes involved in high-altitude adaptation in pigs.