Unveiling the Bioactive Potential of the Invasive Jellyfish Phyllorhiza punctata Through Integrative Transcriptomic and Proteomic Analyses

The white-spotted jellyfish, <i>Phyllorhiza punctata</i>, is an invasive species with significant ecological and economic relevance spreading across various regions. While its ecological impact is well-documented, its molecular and biochemical characteristics remain poorly understood. In this study, we integrate proteomic data generated by LC-MS/MS with publicly available transcriptomic information to characterize <i>P. punctata</i>, analyzing differential protein expression across three distinct tissues: oral arms, mantle, and gonads. A total of 2764 proteins and 25,045 peptides were identified, including several venom components such as jellyfish toxins (JFTs) and phospholipase A2 (PLA2), which were further investigated and compared to toxins from other species. Enrichment analyses revealed clear tissue-specific functions. Additionally, deep learning and machine learning tools identified 274 promising AMP candidates, including the α-helical, β-sheet, and αβ-motif peptides. This dataset provides new insights into the protein composition of <i>P. punctata</i> and highlights strong AMP candidates for further characterization, underscoring the biotechnological potential of underexplored cnidarian species.