Effects of microencapsulated antimicrobial peptides on the growth, immunity, infection resistance, gut microbiota, and gene transcriptome in Manila clam (Ruditapes philippinarum) larve

This dataset contains high-quality RNA-seq reads obtained from Manila clam (Ruditapes philippinarum) larvae treated with microencapsulated antimicrobial peptides (AMPs, 0.1 mg g-1). Control larvae were fed unsupplemented feed. For each replicate (800 to 1 000 larvae), total RNA was extracted with TRIzol, libraries were prepared using the NEBNext Ultra II kit, and 150 bp paired-end sequencing was performed on an Illumina NovaSeq 6000 platform.Twelve libraries were generated (6 control, 6 AMP), yielding 530,783,776 clean reads an average of 44,231,981 reads per sample. Quality metrics were excellent . Clean reads were aligned to the R. philippinarum reference genome with HISAT2, achieving mapping efficiencies of 48.80% to 60.40%. Differential expression analysis was conducted with DESeq2, and GO and KEGG enrichment analyses with clusterProfiler, revealing pathways related to larval growth, immune activation, infection resistance, and gut-microbiota regulation.