Revealing the Diversity of Sequences, Structures, and Targets of Peptides from South China Sea Macrodactyla doreensis Based on Transcriptomics

The South China Sea is rich in sea anemone resources, and the protein and peptide components from sea anemone toxins comprise an important treasure trove for researchers to search for leading compounds. This study conducted a comprehensive transcriptomic analysis of the tentacles and column of <i>Macrodactyla doreensis</i> and explored the distribution and diversity of proteins and peptides in depth using bioinformatics, initially constructing a putative protein and peptide database. In this database, typical peptide families are identified through amino acid sequence analysis, and their 3D structures and potential biological activities are revealed through AlphaFold2 modeling and molecular docking. A total of 4239 transcripts were identified, of which the putative protein accounted for 81.53%. The highest content comprised immunoglobulin and a variety of proteases, mainly distributed in the column and related to biological functions. Importantly, the putative peptide accounted for 18.47%, containing ShK domain and Kunitz-type peptides, mainly distributed in the tentacles and related to offensive predatory behavior. Interestingly, 40 putative peptides belonging to eight typical peptide families were identified, and their structures and targets were predicted. This study reveals the diversity and complexity of <i>Macrodactyla doreensis</i> toxins and predicts their structure and targets based on amino acid sequences, providing a feasible approach for research regarding the discovery of peptides with potentially high activity.