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Breeding of polyploid aquatic animals is still an important approach and research hotspot for realizing the economic benefits afforded by the improvement of aquatic animal germplasm. To better understand the molecular mechanisms of the growth of triploid sea cucumbers, we performed gene expression and genome-wide comparisons of DNA methylation using the body wall tissue of triploid sea cucumbers using RNA-seq and MethylRAD-seq technologies. We clarified the expression pattern of triploid sea cucumbers and found no dosage effect. DEGs were significantly enriched in the pathways of nucleic acid and protein synthesis, cell growth, cell division, and other pathways. Moreover, we characterized the methylation pattern changes and found 615 differentially methylated genes at CCGG sites and 447 differentially methylated genes at CCWGG sites. Integrative analysis identified 23 genes (such as Guf1, SGT, Col5a1, HAL, HPS1, etc.) that exhibited correlations between promoter methylation and expression. Altered DNA methylation and expression of various genes suggested their roles and potential functional interactions in the growth of triploid sea cucumbers. Our data provide new insights into the epigenetic and transcriptomic alterations of the body wall tissue of triploid sea cucumbers and preliminarily elucidate the molecular mechanism of their growth, which is of great significance for the breeding of fine varieties of sea cucumbers.

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Polyploid breeding is widely used in aquaculture as an important area of new research. We have previously grown Apostichopus japonicus triploids with a growth advantage. The body length, body weight, and aestivation time of triploid and diploid A. japonicus were measured in this study, and the transcriptome and metabolome were used to examine the growth advantage of triploids A. japonicus. The results showed that the proportion of triploid A. japonicus with a body length of 6–12 cm and 12–18 cm was significantly higher than that of diploid A. japonicus, and triploid A. japonicus had a shorter aestivation time (39 days) than diploid (63 days). We discovered 3296 differentially expressed genes (DEGs); 13 DEGs (for example, cyclin-dependent kinase 2) related to growth advantage, immune regulation, and energy storage were screened as potential candidates. According to Gene Ontology (GO) enrichment analysis, DEGs were significantly enriched in the cytoplasm (cellular component), ATP binding process (molecular function), oxidation–reduction process (biological process), and other pathways. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment data, DEGs were significantly enriched in ribosome production and other areas. We discovered 414 significant differential metabolites (SDMs), with 11 important SDMs (for example, nocodazole) linked to a growth advantage. SDMs are significantly enriched in metabolic pathways, as well as other pathways, according to the KEGG enrichment results. According to a combined transcriptome and metabolome analysis, 6 DEGs have regulatory relationships with 11 SDMs, which act on 11 metabolic pathways together. Our results further enrich the biological data of triploid A. japonicus and provide useful resources for genetic improvement of this species.

Strongylocentrotus intermedius has high nutritional value because it is rich in proteins, amino acids and long‐chain polyunsaturated fatty acids (LC‐PUFA). LC‐PUFA are essential nutrients that not only determine the nutritional value of sea urchins but also guarantee normal growth and reproduction performance. To better understand the molecular basis of LC‐PUFA biosynthesis in S. intermedius, the Δ6Fad‐like, Elovl4‐like and Elovl5‐like genes were cloned and fatty acid compositions during the early developmental stages of sea urchins were detected. The full‐length of Δ6Fad‐like was 2,199 bp, with a putative open reading frame of 1,248 bp encoding a polypeptide of 415 amino acid (AA). The Elovl4‐like and Elovl5‐like genes encoded 310 and 234 AA, respectively, which exhibited all of the characteristics of the Elovl family, such as a histidine box motif and putative transmembrane‐spanning domains. Tissue distribution analysis revealed that Δ6Fad‐like, Elovl4‐like and Elovl5‐like genes were expressed at the highest levels in the gonads and intestine, and the expression levels gradually increased in embryos during development. These results can help to understand the role of the Δ6Fad‐like, Elovl4‐like and Elovl5‐like genes in the different developmental stages of the sea urchin and to clarify the biosynthetic pathways of LC‐PUFA during the development of the sea urchin and provide a theoretical basis for improving the quality and breeding of excellent traits in sea urchins.

Sea cucumber (Apostichopus japonicus), an important cultured species in northern China, is widely reared in ponds or shallow marine sea areas, (Daniel Azari et al., 2021). Liaoning and Shandong Provinces are the main production areas with cultivation sites distributed around the Bohai Sea and the Yellow Sea (Han et al., 2016).In these regions, there are diverse aquaculture models, including cage culturing, pond culturing and bottom sowing (Hamel et al., 2001). Apostichopus japonicus is of extremely high nutritional value and rich in amino acids, fatty acid and trace elements (Haide et al., 2015), which enhance immunity, reduce inflammation, decrease

Strongylocentrotus intermedius is an economically valuable sea urchin species in China. However, its growth and survival are severely constrained by ocean warming and the hypoxia that often accompanies high water temperatures. MicroRNAs (miRNAs) are important regulators of gene expression in response to environmental change. In this study, high-throughput RNA sequencing was used to investigate changes in miRNA expression in S. intermedius under heat (25°C), hypoxia (2 mg/L O2), and combined heat and hypoxia stresses. Twelve small RNAs libraries were constructed and 17, 14, and 23 differentially expressed miRNAs (DEMs) were identified in the heat, hypoxia, and combined stress groups (P<0.05), respectively. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway functional analyses of putative target genes of the DEMs suggested that these miRNAs were important in basal metabolism, apoptosis, oxidative stress, and immune-related pathways. By co-analysis with published transcriptome data, key DEMs (miR-193, miR-184, miR-133, miR-125, miR-2008) and their key target genes (EGF3, ABCB4, CYCL, PAN2, CALN) were identified. Quantitative real-time PCR analysis of the expression of 10 DEMs and their key target genes confirmed the RNA sequencing results. These results provide information on gene expression regulation of the molecular mechanisms underlying the response of S. intermedius to multi-cause environmental stresses.