Developing genomic resources for the sea cucumber, Holothuria scabra, in support of broodstock selection and genetic stock management


June Feliciano Ordoñez

PhD Student
Advisors: Tim Wollesen

Unit for Integrative Zoology, Department of Evolutionary Biology
University of Vienna

Contributing authors: Galindez GG1, Gulay KT1, Fitak RR2, Ravago-Gotanco R1
1The Marine Science Institute, University of the Philippines Diliman, Diliman, Quezon City, Philippines
2Department of Biology, University of Central Florida, Florida, USA


The sandfish (Holothuria scabra) is a commercially valuable fishery and aquaculture species contributing to the multimillion dollar-valued sea cucumber industry. However, the increase in global demand for sea cucumbers has led to unregulated harvesting and overall decline of the wild stocks and production over the past decade across many fishery areas, including the Philippines. While a culture system for sandfish is currently in place, a commercial-level production to meet the growing demand has yet to be achieved. Advancements in genomic technologies, such as high-throughput sequencing, have opened plenty of opportunities for the development of tools to improve culture production and natural resource management of many economically important species in the aquaculture and fishery sectors. Initiatives for genetic-based applications on economically important seafood, such as H. scabra, however, have been limited by the lack of comprehensive genomic resources. In this talk, I will discuss how RNA sequencing (RNA-Seq) was used to investigate the molecular underpinnings of growth variation (fast-growth vs slow-growth) in the early-stage juvenile sandfish and develop Single Nucleotide Polymorphisms (SNPs) for population-of-origin assignment in three sandfish populations. Briefly, RNA-Seq was applied to sequence the transcriptome of juvenile sandfish and generate a de novo transcriptome assembly, which was consequently used for differential gene expression analysis and SNP marker discovery. Differential gene expression analysis between the two sandfish growth categories revealed 66 differentially expressed unigenes that are related to potentially key molecular pathways and biological processes controlling growth variation, which include carbohydrate binding, extra-cellular matrix organization, fatty-acid metabolism, and metabolite and solute transport. Further, transcriptome-derived SNPs allowed the assignment of sandfish individuals to their population of origin, with an overall assignment accuracy of >80%. Overall, the results of this research represent an invaluable genomic resource to facilitate future genomics-based research and applications in sandfish and other sea cucumbers, including selecting for genes associated with faster-growing phenotypes for marker-assisted selection and broodstock enhancement and facilitating the development of genetic traceability tools applicable in the context of sandfish fisheries management and conservation.