Transcriptome analysis of growth variation in early juvenile stage of sandfish Holothuria scabra

Abstract

The sandfish Holothuria scabra is a high-value tropical sea cucumber species representing a major mariculture prospect across the Indo-Pacific. Advancements in culture technology, rearing, and processing present options for augmenting capture production, stock restoration, and sustainable livelihood activities from hatchery-produced sandfish. Further improvements in mariculture production may be gained from the application of genomic technologies to improve performance traits such as growth. In this study, we performed de novo transcriptome assembly and characterization of fast- and slow-growing juvenile H. scabra from three Philippine populations. Analyses revealed 66 unigenes that were consistently differentially regulated in fast-growing sandfish and found to be associated with immune response and metabolism. Further, we identified microsatellite and single nucleotide polymorphism markers potentially associated with fast growth. These findings provide insight on potential genomic determinants underlying growth regulation in early juvenile sandfish which will be useful for further functional studies. HighlightsO_LIThe study explores the genomic basis of growth variation in juvenile sandfish by examining gene expression profiles of fast- and slow-growing early juvenile stages from three hatchery populations using RNA-seq. C_LIO_LISixty-six differentially regulated unigenes potentially related to growth variation are associated with several biological and molecular processes, including carbohydrate binding, extracellular matrix organization, fatty-acid metabolism, and metabolite and solute transport. C_LIO_LIA large number of potential microsatellite and growth category-associated SNP markers have been identified. C_LI