Integrated Full-Length Transcriptomics, RNA-Seq and Peptidomics Define an Isoform-Resolved Skin Defense Repertoire in the Chinese Spiny Frog (Quasipaa spinosa)

This is the authors' abstract. We don't add key points for this paper.

Amphibian skin relies on secreted effectors and inducible immune pathways, but short-read RNA sequencing cannot reliably resolve the transcript isoforms and precursor structures underlying this defense system. We generated the first full-length skin transcriptome for the Chinese spiny frog (Quasipaa spinosa) by integrating pooled PacBio Iso-Seq data with six Illumina RNA-seq libraries and six skin peptidomic libraries from control and Proteus mirabilis-challenged frogs. Because Iso-Seq RNA was pooled across conditions, the long-read data were used to define transcript structure rather than condition-specific isoform changes. The reference contained 58,388 transcripts from 34,247 genes, including 32,215 non-reference models, and 5907 of 19,143 reconstructed loci had multiple isoforms. Among 108,147 predicted ORFs, 17,169 carried an N-terminal secretion signal, and 72 secretory and immune-effector ORFs from 46 genes were prioritized. Gene-level RNA-seq identified 72 differentially expressed genes at Benjamini–Hochberg-adjusted p < 0.05 and |log2FC| ≥ 1; 27 had higher expression in challenged skin and 45 in control skin. No GO term remained significant after correction, whereas three KEGG pathways did. Among these 72 genes, 60 (83.3%) had at least two full-length models, 53 (73.6%) contained at least one complete ORF, and 4 (5.6%) had peptide-sequence support. Reported peptide sequences matched 1029 entries across the full-length catalog, but shared peptide matches were not treated as ORF-specific evidence. Together, these data establish an isoform-resolved skin-defense resource for Q. spinosa and a framework for prioritizing secretory and immune candidates for isoform-specific and functional validation.