Updated occurrence, habitat associations, and genomic resources of syngnathids in the Sembilan Archipelago, Malaysia

Syngnathid fishes, including seahorses and pipefishes, are ecologically and economically important but remain vulnerable to overfishing, habitat degradation, and trade-driven exploitation. This study documents syngnathid occurrence, habitat associations, body-size observations, and genomic resources in the Sembilan Archipelago, Malaysia, using SCUBA-based visual surveys and high-resolution photographic analysis. Across 32 dives at seven reef sites, we recorded 54 occurrence records belonging to four species: Hippocampus kuda , H. comes , Doryrhamphus janssi , and Trachyrhamphus bicoarctatus . Species differed in their observed habitat associations, while size–depth relationships varied among species. A brooding male and two juvenile seahorses provided evidence of local reproductive activity during the survey period. To establish baseline genomic resources for Malaysian syngnathids, we generated high-quality PacBio HiFi genome assemblies for six individuals from three species, with genome sizes ranging from 0.45–0.61 Gbp and BUSCO completeness scores of 92.3–98.8%. The assemblies were characterized through repeat annotation, protein-coding gene prediction, orthology analysis, and phylogenomics. Complete mitochondrial genomes were generated for all six individuals. These genomic resources provide a foundation for future comparative and population genomic studies of genetic diversity, connectivity, and evolutionary relationships. Together, the ecological observations and genomic resources provide a baseline for future standardized monitoring and conservation research on Malaysian syngnathids.