Functional annotation and Pfam scan

The mechanisms underlying high-altitude hypoxia adaptation on the Qinghai-Tibet Plateau have been extensively studied, yet the role of alternative splicing in this process remains poorly understood. Yunnan’s vertical zoning with pig breeds distributed across varying elevations provides an excellent model for investigating hypoxic adaptation. Here, we examined three indigenous Yunnan pig breeds: Diannan small-ear pigs (DSE, 500 m), Baoshan pigs (BS, 1500 m), and Diqing Tibetan pigs (DT, 3200 m). Using PacBio Iso-Seq, we obtained comprehensive full-length transcriptomes from five tissues (heart, kidney, liver, lung, and spleen), identifying 51,774 transcripts, including 34,813 novel ones, and 74,843 Alternative Splicing (AS) events across 10,686 AS genes.