Genomic DNA Methylation Levels and Transcriptome Differences of Apostichopus japonicus in Response to Vibrio splendidus Infection and Their Association Analysis

Abstract:

DNA methylation is an important epigenetic modification that plays a key role in gene expression regulation. In this study, two groups of sea cucumbers (Apostichopus japonicus) were prepared. One group had skin ulceration syndrome body wall (PT16S) under stress from Vibrio splendidus infection at a concentration of 1×106 CFU/mL (LD50); the other group had a healthy body wall (PT10H). Genomic DNA methylation levels and gene expression differences between the two groups were detected using whole-genome bisulfite sequencing (WGBS) and transcriptome sequencing. The key gene ontology (GO) terms and KEGG terms engaged in the immune response were selected using association analysis. The results showed that the total methylation levels of the A. japonicus genome of PT10H and PT16S were (3.59±0.04)% and (3.87±0.27)%, respectively. The methylation levels of the A. japonicus genome under pathogen challenge significantly increased; mCpG accounted for 83.06% and 81.91% of all the methylated sites in PT16S and PT10H, respectively, indicating that mCpG was the most important methylation form in the sea cucumber. A total of 626 677 differentially methylated regions (DMRs) were screened and annotated into 23 706 functional genes. A total of 496 differentially expressed genes were screened, including 214 up-regulated and 282 down-regulated genes. A total of 180 negatively correlated genes were isolated using association analysis between genomic methylation and transcriptome, of which 60 genes had DMRs located in promoter regions. Based on GO and KEGG enrichment of the 180 negatively correlated genes, key genes such as LRR, Hsp20, and CARD were selected to play a critical role in the immune response. The results would provide primary data for the epigenetic regulatory mechanisms of A. japonicus and provide a theoretical reference for A. japonicus breeding.