Decoding the Impacts of Mating Behavior on Ovarian Development in Mud Crab (Scylla paramamosain): Insights from SMRT RNA-Seq

The mud crab Scylla paramamosain is a commercially valuable aquaculture species whose reproductive success depends heavily on ovarian maturation. However, the molecular effects of mating behavior on ovarian development remain poorly understood. In this study, we used Single Molecule Real-Time (SMRT) RNA-seq to construct a high-quality full-length transcriptome of female crabs at four stages: before molting (BM), unmated (UM), 1-day post-mating (M1), and 3-days post-mating (M3). A total of 59.6 million subreads (34.0 GB) yielded 880,044 circular consensus sequences (CCSs), from which 59,156 high-quality isoforms (average length: 2,074.8 bp) were obtained. After collapsing, 51,637 isoforms remained. Alternative splicing analysis identified alternative first exon (AF) as the most frequent event, followed by A5, A3, AL, RI, SE, and MX. Gene Ontology enrichment indicated protein-related processes as dominant. Comparative analysis revealed 21 differential alternative splicing (DAS) events and 1,157 differentially expressed transcripts (DETs) between UM and M1, mainly enriched in amino acid metabolism pathways. Between UM and M3, 34 DAS events and 1,963 DETs were associated with energy metabolism and detoxification. These findings highlight mating behavior-induced shifts in gene expression and splicing, particularly in metabolic and detoxification pathways, offering new insights into reproductive regulation and broodstock management in crustacean aquaculture.