Abstract
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.
Highlights
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
Through the KEGG enrichment analysis of methylated differentially expressed genes, the results showed that differentially methylated genes at CCGG sites were significantly enriched in the pentose phosphate pathway, cell cycle, and disease; differentially methylated genes at CCWGG sites were significantly enriched in virus infection and glycerophosphate metabolism, and the PI3K Akt signaling pathway was the most abundant pathway
Through the KEGG enrichment analysis of these 19 genes, we found that they were mainly enriched in the basic metabolic pathways such as glucose metabolism, lipid metabolism, histidine metabolism, carbon metabolism, purine metabolism, protein digestion and absorption, as well as cell division and cell cycle, MAPK signaling pathway, HIF-1 signaling pathway, insulin signaling pathway, p53 signaling pathway, FoxO signaling pathway, and PI3K Akt signaling pathway, which are related to growth and development
Summary
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. Jiang et al carried out DNA methylation analysis of a triploid oyster (C. gigas) using F-MSAP technology, and showed that some methylation sites of diploid and triploid oysters were ploidy specific, and the mutation rates of methylated sites and unmethylated sites in triploid oysters were higher than those in diploid o ysters[21] They found that the CGer gene was highly expressed in triploid oysters, and its methylation rate was high, which suggested that CGer might play a role in the sterility of triploid o ysters[22]. With the rapid development of RNA-seq technology, it has been widely used to study gene expression regulation and gene screening of echinoderms, especially the sea cucumbers. Zeng et al sequenced the DNA from muscle tissues of diploid and triploid oysters, and found that there were 2045 differential genes, and 28 differential genes expressed only in triploid oysters[26]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
