Transcriptomic and Metabolomic Analyses Provide Insights into the Growth and Development Advantages of Triploid Apostichopus japonicus

Abstract

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.

Sea cucumbers: an emerging system in evo-devo

“…Because sea cucumbers show the remarkable ability of quickly replacing injured organs, transcriptomes have been generated on H. glaberrima, E. fraudatrix , and A. japonic us during gut evisceration and regeneration [ 44 , 115 , 123 , 124 , 136 , 144 , 145 ], radial organ complex regeneration [ 109 ], and muscle regeneration [ 111 ]. Other studies explored gene expression during aestivation, a process that so far has been exclusively observed in sea sponges and sea cucumbers [ 159 , 174 – 176 ]. Moreover, transcriptomes exploring the response of the immune system have been generated in different conditions, such as air exposure stress [ 150 ], continuous heat stress [ 162 ], skin ulceration [ 167 ], microplastic [ 105 ] and nanoplastic toxicity [ 177 ], miRNA regulation in coelomocytes during host–pathogen interaction [ 179 ] and lipopolysaccharide treatment [ 109 ], knock-down of ajpacifastin-like gene [ 93 ], and exposure to Vibrio splendidus [ 130 ].…”

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

“…Interestingly, in eastern oysters, Zeng and Guo (2022) identified a set of genes that are both important for biomineralization and growth. With triploid sea cucumber Apostichopus japonicus , the term ribosome production was enriched in fast growing sea cucumbers, and a set of 11 significant differential metabolites were found to be associated with growth advantage ( Xie et al, 2022 ).…”

Transcriptome analysis and gene expression analysis related to salinity-alkalinity and low temperature adaptation of Triplophysa yarkandensis

“…Liver transcriptome analysis not only identified that genes were involved in the responses of turbot to different salinity conditions, but also demonstrated that low salinity exposure disorders turbot lipid metabolism ( Liu et al, 2020 ). Transcriptomic and metabolomic analyses indicated that when compared with diploid Apostichopus japonicus , triploid A. japonicus had more advantages in immunity, growth and development, stress resistance and adaptability to a harsh living environment ( Xie et al, 2022 ). Based on RNA-seq, comparative transcriptome analysis of different tissues in Lota dalliance provided a reference for enriching gene resource ( Yang et al, 2020 ).…”