Long-read sequencing reveals novel transcript diversity in Polypterus senegalus

Polypterus senegalus is a fish species characterized by primitive traits and unique physiological-anatomical features, representing a transitional stage toward terrestrial vertebrates. Diverging from other ray-finned fishes approximately 420 million years ago, it serves as a key model for vertebrate evolutionary studies. In this study, we identified 19,295 unique P. senegalus transcripts using Pacific Biosciences Iso-Seq, with most classified as novel exon combinations, intron retentions, or novel start and stop codons. This high-quality, full-length transcriptome revealed previously unreported isoforms and investigated their functional roles to enhance our understanding of the genomic complexity and evolutionary traits of the species. Notably, these isoforms were identified in genes associated with Polypterus's distinctive features, including limb flexibility (ACTN3B, MYBPC1), lung function (FAM13A, ERBB2, TCF7), and circulation (FBN1, MYH11B, MEF2CB). These findings offer molecular insights into early vertebrate terrestrial adaptation and the functional integration of key tissues in extant species.