Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)

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.

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

“…S6 ). This outcome is consistent with that of Han (Han et al 2021 ). The measurement results revealed that the proportions of triploid A. japonicus in the 12–18- and 6–12-cm groups were higher than those in the diploid control group (Fig.…”

“…During the breeding process, the water was changed every 2 days, and feeding was done once a day (feed formula: sea mud, compound feed, spirulina powder, purslane powder). We used flow cytometry (Sysmex, Japan) to determine the ploidy of A. japonicus , and the procedure was the same as Han’s (Han et al 2021 ).…”

“…To determine the ploidy of A. japonicus , a tiny amount of tube feet was cut and dissolved in 1.2-ml cell lysate (cystatin UV precise P/05–5002, Japan) in a 1.5-ml centrifuge tube. Flow cytometry was used to detect A. japonicus after the cell components had been destroyed (Han et al 2021 ). Flow cytometry detected 2682 A. japonicus , including 510 triploid A. japonicus and 2172 diploid A. japonicus .…”

“…RNA detected with a purity between 2.0 and 2.1 was stored at − 80 ℃. Gene expression was measured by the FPKM value (Li et al 2021 ; Han et al 2021 ).…”

“…Ding then proposed the method of inducing triploid A. japonicus by hydrostatic pressure (Ding et al 2007 ). Han et al ( 2021 ) used transcriptome and methylation to study the role of methylation changes of different genes in triploid A. japonicus . However, the molecular mechanism of controlling the dominant traits such as fast growth and short aestivation time of triploid A. japonicus is not clear.…”