Identification and characterization of a novel Foxo transcription factors in Apostichopus japonicus

Transcriptome analysis of sea cucumber (Apostichopus japonicus) polian vesicles in response to evisceration

Polian vesicles are considered as the site of coelomocyte formation, and play crucial roles in the inflammatory reaction in sea cucumber. After evisceration, coelomocytes and internal organs except polian vesicles are excreted. Our previous study found that the total number of coelomocytes was rapidly recovered at 6 h post-evisceration in sea cucumber Apostichopus japonicus, and this regeneration of coelomocytes might be closely related to polian vesicles. To further investigate the related-gene expression pattern of the polian vesicles at 6 h post-evisceration, the transcriptome analysis of polian vesicles was carried out. A total of 2752 differentially expressed genes (DEGs) were identified, including 1,453 up-regulated genes and 1299 down-regulated genes. Gene Ontology (GO) enrichment showed that most of the DEGs were classified under Regulation of transcription, Regulation of RNA metabolic process, Regulation of nucleic acid-templated transcription. Meanwhile, 11 significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified. Among them, Wnt, TGF-β and Endocytosis pathways are well-related with cell proliferation and differentiation, which may be involved in the regeneration of coelomocytes in A. japonicus after evisceration. In addition, FoxO signaling pathway plays important roles in immunoregulation, in which the expression levels of the DEGs were significantly up-regulated, inferring that polian vesicles could not only participate in the coelomocyte regeneration process, but also undertake a certain immune defense function in A. japonicus after evisceration. These findings will be beneficial for understanding the mechanisms of coelomocyte regeneration and immune defense of A. japonicus after evisceration.

Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids

Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.

Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus

Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 differentially expressed unigenes were not annotated with any database, 160 of which were apparently expressed at higher levels in papilla, 76 were expressed at higher levels in skin. We identified a total of 288 papilla-specific genes, 171 skin-specific genes and 600 co-expressed genes. Also, 40 genes in papilla-specific were not annotated with any database, 2 in skin-specific. Development-related genes were also enriched, such as fibroblast growth factor, transforming growth factor-β, collagen-α2 and Integrin-α2, which may be related to the formation of the papilla and skin in sea cucumber. Further pathway analysis identified ten KEGG pathways that were differently enriched between the papilla and skin. The findings on expression profiles between two key organs of the sea cucumber should be valuable to reveal molecular mechanisms involved in the development of organs that are related but with morphological differences in the sea cucumber.