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Sea cucumber Apostichopus japonicus is an important economic species in echinoderms; however, its culture frequently suffered from diseases. Environmental stress was found to be a dominant inducer of A. japonicus diseases, and thus, discovering the characteristics of immune system under environmental stress is of great significance for disease control in A. japonicus culture. Phenoloxidase (PO) is recognized as a crucial immune‐related enzyme in invertebrates. In order to preliminarily illustrate the different roles that A. japonicus PO isoforms play under environmental stresses, the transcriptional expression of three identified A. japonicus PO isoforms (named as AjPOI, AjPOII and AjPOIII respectively) after different in vivo environmental stress simulations was determined with quantitative real‐time PCR method. Meanwhile, the transcriptional expression analysis of other representational immune‐related factors under environmental stresses was also performed for the evaluation of relationships between AjPOs and other immune‐related factors. The correlations between AjPOs and other immune‐related factors were analysed using Pearson correlation coefficient, and the effects of AjPOs on other immune‐related factors were then tested by dsRNA interference method. The results of transcriptional expression analysis indicated that AjPOI was involved in the resistance to low salinity, low temperature and hypoxia; AjPOII and AjPOIII were both required for the resistance to low salinity, high temperature, low temperature and hypoxia; and all three AjPOs were excluded from the response against high salinity. In addition, three AjPOs were found to take part in different periods of resistance to environmental stresses, and this property made A. japonicus PO system capable of outputting resistance activities continuously. The correlation analysis combined with dsRNA interference test revealed that AjPOI was capable of regulating AjCTSD, AjI‐LYZ and AjMTF expression; AjPOII and AjPOIII both played important roles in the regulation of AjC‐LYZ expression; and AjPOIII was also able to regulate AjToll expression. These findings suggested that A. japonicus PO isoforms function in innate immunity not only via catalysing the oxidative reactions, but also by broadly regulating the expression of other immune‐related factors. On the whole, three AjPOs showed obvious differences among each other in the resistance to environmental stresses and the regulation of other immune‐related factors, but comparatively, AjPOII and AjPOIII shared more similarity. [ABSTRACT FROM AUTHOR]

DNA methylation is an important epigenetic modification that regulates gene expression in many biological processes, including immune response. In this study, whole-genome bisulfite sequencing (WGBS) was carried out on healthy body wall (HB) and skin ulceration syndrome (SUS) infected body wall (SFB) to gain insights into the epigenetic regulatory mechanism in sea cucumber Apostichopus japonicus. After comparison, a total of 116,522 differentially methylated regions (DMRs) were obtained including 67,269 hyper-methylated and 49,253 hypo-methylated DMRs (p < 0.05, FDR < 0.001). GO enrichment analysis indicated that regulation of DNA-templated transcription (GO: 0006355), where DNA methylation occurred, was the most significant term in the biology process. The integration of methylome and transcriptome analysis revealed that 10,499 DMRs were negatively correlated with 496 differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these DEGs were enriched in the phosphoinositide 3-kinase-protein kinase B (PI3K/Akt)/mammalian target of rapamycin (mTOR) signaling pathway. Interestingly, two serine/threonine-protein kinases, nemo-like kinase (NLK) and mTOR, were highlighted after functional analysis. The variations of methylation in these two genes were associated with SUS infection and immune regulation. They regulated gene expression at different levels and showed interaction during response process. The validation of methylation sites showed high consistency between pyrosequencing and WGBS. WGBS analysis not only revealed the changes of DNA methylation, but also presented important information about the regulation of key genes after SUS infection in A. japonicus. • WGBS were conducted on the healthy and SUS-infected body wall of Apostichopus japonicus. • A total of 116,522 DMRs were obtained including 67,269 hyper-methylated and 49,253 hypo-methylated DMRs. • The integration of methylome and transcriptome revealed that 10,499 DMRs had a negative correlation with 496 DEGs. • The variations of methylation in mTOR and NLK were associated with SUS infection and immune regulation. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are small non-coding RNAs that mediate mRNA degradation or translation repression. Previous study showed that the expression of miRNAs was significantly changed in the body wall of sea cucumber Apostichopus japonicus after skin ulceration syndrome (SUS) infection, which is a dynamic process. However, the critical miRNAs from body wall that involved in different infection stages of SUS remain unknown. In this study, four cDNA libraries were constructed with the body wall from healthy and three SUS-infected stages of A. japonicus . A total of 248 conserved miRNAs and five novel miRNAs were identified through Illumina HiSeq 2000 platform. Compared to the control, 238 miRNAs showed significant differential expression at three stages of SUS progression. Totally, 3149 miRNA-mRNA pairs were identified by target prediction and 314 miRNA-mRNA pairs showed negative correlation. It is noteworthy that 15 miRNAs and four mRNAs were located at the crucial positions of the network built with the anti-correlated miRNA-mRNA pairs. GO and KEGG enrichment analysis indicated that the predicted targets were involved in many immune-related processes. Deep analysis of miR-31c-5p, miR-29b-3p, NF-kB, mucin 2 and titin showed that they may play important roles in the pathogens attachment and recognition, signaling transduction and lesions repair of A. japonicus after SUS infection. These results would be useful for further investigating the potential roles of critical miRNAs and mRNAs in A. japonicus immune regulation. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are small non-coding RNAs that are involved in many biological processes. To investigate the miRNAs related to skin ulceration syndrome (SUS) of Apostichopus japonicus , small RNA libraries of body wall, intestine, respiratory tree and coelomocytes from healthy and diseased A. japonicus were sequenced on Illumina Hiseq 2000 platform. A total of 247 conserved and 10 novel miRNAs were identified across all libraries. After pair-wise comparisons, 215 miRNAs in body wall, 36 in intestine, 2 in respiratory tree and 38 in coelomocytes showed significant expression differences. Further analyses were conducted on some tissue-specific differentially expressed miRNAs: miR-8 and miR-486-5p in body wall, miR-200-3p, let-7-5p and miR-125 in intestine, miR-278a-3p and bantam in respiratory, miR-10a and miR-184 in coelomocytes. Notably, these miRNAs in some species were reported to function in various physiological or pathological processes associated with immune regulations. Using stem-loop quantitative real time PCR, six representative miRNAs in four tissues were selected to validate the sequencing results. The Pearson's correlation coefficient ( R ) of the six miRNAs ranged from 0.777 to 0.948, which confirmed the consistency and accuracy between these two approaches. This study provides comprehensive expression and regulation patterns of functional miRNAs in different tissues and gives insights into the tissue-specific immune response mechanisms in SUS-infected A. japonicus . [ABSTRACT FROM AUTHOR]