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Mar Biotechnol (NY)
2022 Mar 01;241:151-162. doi: 10.1007/s10126-022-10093-4.
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Transcriptomic and Metabolomic Analyses Provide Insights into the Growth and Development Advantages of Triploid Apostichopus japonicus.
Xie J, Sun Y, Cao Y, Han L, Li Y, Ding B, Gao C, Hao P, Jin X, Chang Y, Song J, Yin D, Ding J.
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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.
No.31772849 National Natural Science Foundation of China, DL201901 Liaoning Provincial Department of Education in 2019, LT2019003 Program for Liaoning Innovative Research Team in University, 2020RD03 High-level talent support grant for innovation in Dalian
Fig. 1. Box diagram of body length (A) and body weight (B) of triploid and diploid Apostichopus japonicus
Fig. 2. Volcano plot of differentially abundant genes. Note that the red dots represent up-regulation and the blue dots represent down-regulation. A Triploid Apostichopus japonicus and B diploid Apostichopus japonicus
Fig. 3. Quantitative RT-PCR validation of differentially expressed genes. *Significant differences at p < 0.05 vs. diploid (triploid). **Highly significant differences at p < 0.01 vs. diploid (triploid). The results are expressed as mean ± SEM and one-way ANOVA
Fig. 4. Comparison group PLS-DA analysis. Note that each point in the figure represents a sample, and the similarities and differences among all samples are reflected in the tendency of separation and aggregation of samples in the figure. The aggregation of points indicates that the observed variables have a high degree of similarity, while the dispersion of points indicates that the observed variables have obvious differences. A Triploid Apostichopus japonicus and B diploid Apostichopus japonicus
Fig. 5. Triploid and diploid Apostichopus japonicus replacement test. Note that Q2 represents the prediction rate of the model and R2 represents the interpretation rate of the model. Q2 = −0.56510 < 0, R2 = 0.8762
Fig. 6. Volcano plot of differentially abundant metabolites. Note that the red dots represent up-regulation and the green dots represent down-regulation. A Triploid Apostichopus japonicus and B diploid Apostichopus japonicus
Fig. 7. Results of combined transcriptomic and metabolomic analyses
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