The sea cucumber Apostichopus japonicus has important nutritional and medicinal value. Unfortunately, we know little of the source of active chemicals in this animal, but the plentiful pigments of these animals are thought to function in intriguing ways for translation into clinical and food chemistry usage. Here, we found key cell groups with the gene activity predicted for the color morphology of sea cucumber body using single-cell RNA-seq. We refer to these cell populations as melanocytes and quinocytes, which are responsible for the synthesis of melanin and quinone pigments, respectively. We integrated analysis of pigment biochemistry with the transcript profiles to illuminate the molecular mechanisms regulating distinct pigment formation in echinoderms. In concert with the correlated pigment analysis from each color morph, this study expands our understanding of medically important pigment production, as well as the genetic mechanisms for color morphs, and provides deep datasets for exploring advancements in the fields of bioactives and nutraceuticals.

Genetic linkage maps have become an indispensable tool for genetics and genomics research. Sea cucumber (Apostichopus japonicus), which is an economically important mariculture species in Asia, is an edible echinoderm with medicinal properties. In this study, the first SNP-based high-density genetic linkage map was constructed by sequencing 132 A. japonicus individuals (2 parents and 130 offspring) according to a genotyping-by-sequencing (GBS) method. The consensus map was 3181.54 cM long, with an average genetic distance of 0.52 cM. A total of 6144 SNPs were assigned to 22 linkage groups (LGs). A Pearson analysis and QTL mapping revealed the correlations among body weight, body length, and papillae number. An important growth-related candidate gene, protein still life, isoforms C/SIF type 2 (sif), was identified in LG18. The gene was significantly highly expressed during the larval developmental stages. Its encoded protein reportedly functions as a guanine nucleotide exchange factor. These results would facilitate the genetic analysis of growth traits and provide valuable genomic resources for the selection and breeding of new varieties of sea cucumbers with excellent production traits.

Background: Aquaculture, a vital component of global food security, faces sustainability challenges due to intensive farming practices, including water pollution, disease outbreaks, and antibiotic overuse. Probiotics, prebiotics, and synbiotics have emerged as eco-friendly alternatives to antibiotics. However, research results remain heterogeneous across aquatic species and intervention strategies. Methods: Following PRISMA 2020, we searched two databases (up to January 2026) for in vivo trials. Two reviewers screened and extracted data, and 177 eligible studies were ultimately included, covering single-/multi-strain probiotics (SSP/MSP), live/inactivated microbial preparations, and diverse synbiotic formulations. Results: Among 177 studies, Bacillus spp. were the most widely reported and effective probiotic strains. MSP and synbiotics exhibited superior efficacy in boosting aquatic animal growth performance and disease resistance over SSP in 68% of the included trials. Probiotics act through the competitive exclusion of pathogens, immune modulation, and enhanced digestive enzyme activity; prebiotics selectively stimulate beneficial gut microbiota, improving nutrient absorption and immune function through metabolites such as short-chain fatty acids; synbiotics combine the advantages of both, exerting synergistic effects. Furthermore, as water additives or fermented feed ingredients, probiotics reduce nitrogenous waste and organic pollutants, contributing to bioremediation. Conclusions: All three additives are effective. Standardized application protocols and long-term trials are needed for sustainable aquaculture. This review provides a unified evidence-based foundation for the rational use of these additives in aquaculture.

As the global demand for aquafeed ingredients continues to rise, sourcing sustainable alternatives is crucial for aquaculture industries. This study aimed to explore the potential of enzymatic hydrolysate as a substitute for traditional fishmeal and soybean meal in diets for juvenile sea cucumbers (Apostichopus japonicus). Three isonitrogenous (15% crude protein) and isolipidic (2.4% crude lipid) diets were formulated: a control diet containing 10% fishmeal and 5% soybean meal and two experimental low-fishmeal (8%) and low-soybean meal (0%) diets, supplemented with either 8% enzymatically hydrolyzed fish stickwater (EFS) or 8% enzymatically hydrolyzed chicken pulp (ECP), designated as Control, EFS, and ECP, respectively. Juvenile sea cucumbers (initial body weight, 0.25 ± 0.01 g) were fed these diets for 84 days to evaluate the effects of ECP and EFS on their growth performance, antioxidant capacity, and inflammatory responses. The results revealed significantly higher final weights and specific growth rates in both experimental groups than the control (p < 0.05). The proximate chemical compositions of sea cucumber were less affected by the diets (p > 0.05). Compared with the control group, significantly elevated levels of digestive enzymes, antioxidants, and lysozyme, together with lower malondialdehyde levels, were recorded in the experimental groups (p < 0.05). ECP appeared to exhibit greater potency than EFS in enhancing growth performance and antioxidant capacity. Similar trends were observed in the mRNA expression of SOD, CAT, and inflammation-related genes across the groups. In a nutshell, both ECP and EFS supplemented in a low-fishmeal and low-soybean meal diet could effectively promote the growth and health of A. japonicus, with ECP showing a superior effect over EFS. These findings suggest that enzymatic hydrolysate demonstrates potential as a viable alternative to traditional fishmeal and soybean meal in diets for sustainable sea cucumber aquaculture. Further investigations are warranted to reveal its underlying mechanism.

Melanin, which is a pigment produced in melanocytes, is an important contributor to sea cucumber body color. MITF is one of the most critical genes in melanocyte development and melanin synthesis pathways. However, how MITF regulates body color and differentiation in sea cucumbers is poorly understood. In this study, we analyzed the expression level and location of MITF in white, purple, and green sea cucumbers and identified the genes regulated by MITF using chromatin immunoprecipitation followed by sequencing. The mRNA and protein expression levels of MITF were all highest in purple morphs and lowest in white morphs. In situ hybridization indicated that MITF mRNA were mainly expressed in the epidermis. We also identified 984, 732, and 1191 peaks of MITF binding in green, purple, and white sea cucumbers, which were associated with 727, 557, and 887 genes, respectively. Our findings suggested that MITF contributed to the body color differentiation of green, purple, and white sea cucumbers through expression differences and regulation of downstream genes. These results provided a basis for future studies to determine the mechanisms underlying body color formation and provided insights into gene regulation in sea cucumbers.