Unraveling the taxonomic identity and phylogenetic relationships of sea cucumber from the genus Stichopus (Holothuroidea: Stichopodidae)

The correct taxonomic classification of Stichopus species is crucial for their management and conservation, given the expanding fishery of these species. However, the taxonomic classification of the family Stichopodidae, including the genus Stichopus, has long been a challenge, leading to frequent misidentification of species. For example, Stichopus naso and Stichopus monotuberculatus, commonly harvested in the Indo-Pacific region, are often misidentified as "Stichopus horrens." In this study, we investigated the taxonomic identity of a Stichopus species harvested in Pangkor island, which had long been assumed to be Stichopus horrens. Our ossicle examination raised questions about its species identity as it lacked the characteristic tack-like table ossicles in the papillae, which are a definitive feature of S. horrens. Additionally, we observed fusiform ossicles in its tentacles, suggesting that the Stichopus species harvested in Pangkor island is actually Stichopus fusiformiossa. To further investigate the taxonomic status of this species, we extracted DNA from the collected sea cucumber for genome sequencing and mitochondrial genome assembly. The full mitochondrial genome sequence and the Cytochrome c Oxidase Subunit I (COI) sequence were submitted for NCBI BLAST search. Phylogenetic analyses were conducted via the multiple sequence alignment of partial COI sequences and complete mitochondrial genomes (13 coding sequences and 2 rRNAs equences) of different Stichopus species for phylogenetic tree construction using maximum likelihood with 1000 bootstraps. The NCBI BLAST result shows that S.monotuberculatus had the highest percentage of identity (>99%) with 100% query coverage. Both the COI-based tree and the mitogenome-based tree show that the sea cucumber collected by our group in Pangkor island is clustered with S.monotuberculatus instead of S. horrens. S. monotuberculatus is a variable assemblage that includes several sub-clades with regional differences in body wall ossicles, morphology, and colors. Previous haplotype network analyses with COI and 16S for S.monotuberculatus suggest the presence of cryptic species within S. monotuberculatus. Additionally, the sea cucumber collected in this study has unusual fusiform ossicles in its tentacles, which are not found in other Stichopus species. Therefore, further research is needed to determine if the variable ossicle shape and genetic relatedness with S. monotuberculatus are associated with different yet closely related species, such as S. fusiformiossa. In conclusion, this study provides valuable insights into the phylogenetic relationships and taxonomic classification of Stichopus species. These findings have important implications for conservation initiatives and further investigations involving these distinct marine invertebrates.