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The lysin motif (LysM)-containing protein is one of widespread pattern-recognition receptors in prokaryotes and eukaryotes. Numerous LysM-containing gene sequences are present in gene databases; however, few have been well characterized, especially in echinoderms. In this study, the full-length cDNA of a novel LysM-containing gene was obtained from the sea cucumber Apostichopus japonicus, named AjLysM-1, using polymerase chain reaction (PCR) combined with rapid amplification of cDNA ends. We prepared and expressed recombinant AjLysM-1 protein (rAjLysM-1) and determined its pathogen-recognition ability by enzyme-linked immunosorbent and immunofluorescence assays. We also analyzed the tissue expression pattern and response to immune challenges of AjLysM-1 using quantitative real-time reverse transcription-PCR and in situ hybridization. The AjLysM-1 protein was predicted to be an intracellular non-secreted LysM-containing protein, highly homologous to the same protein in other marine echinoderms. AjLysM-1 transcripts were highest expressed in coelomocytes and were strikingly induced by challenge with representative bacterial and fungal polysaccharides. rAjLysM-1 showed weak binding to mannan, Pseudoalteromonas nigrifaciens, and Shewanella baltica, implying that AjLysM-1 might provide inadequate defense against Gram-negative bacteria and fungi. Notably, rAjLysM-1 also interacted with tyrosine protein kinase and filamin-B, indicating that it could be involved in focal adhesion in A. japonicus. These findings improve our understanding of the functions of LysM-containing proteins in marine echinoderms.

The sea cucumber Apostichopus japonicus is one of the most dominant and economically important aquaculture species in China. Saponin, which possesses notable biological and pharmacological properties, is a key determinant of the nutritional and health value of A. japonicus. In the present study, we amplified the full-length cDNA of a phosphomevalonate kinase (PMK) gene (named AjPMK) using rapid amplification of cDNA ends (RACE). Subsequently, we engineered a recombinant AjPMK (rAjPMK) protein and assessed its enzymatic activity by enzyme-linked immunosorbent assay (ELISA). Proteins that interact with rAjPMK were screened and identified via pull-down assay combined with liquid chromatography with tandem mass spectrometry (LC-MS/MS). We found that the full-length cDNA of AjPMK contained 1354 bp and an open reading frame (ORF) of 612 bp. The AjPMK protein was predicted not to contain a signal peptide but to contain a phosphonolate kinase domain seen in higher eukaryotes and a P-loop with a relatively conserved nucleoside triphosphate hydrolase domain. The molecular weight of the AjPMK protein was estimated to be 23.81 kDa, and its isoelectric point was predicted to be 8.72. Phylogenetic analysis showed that AjPMK had a closer evolutionary relationship with genes from starfish than with those of other selected species. Besides, we found that rAjPMK synthesized mevalonate-5-diphosphate, interacted either directly or indirectly with crucial pattern recognition receptors (PRRs) and was regulated by immune-related processes, including antioxidative reactions, stress resistance responses and enzyme hydrolysis. Moreover, AjPMK also interacted with farnesyl pyrophosphate synthase, an enzyme reported to be involved in saponin biosynthesis. Together, our findings implied that AjPMK may be directly involved in saponin biosynthesis and the regulation of various innate immune processes.

Nowadays, the true economic and nutritional value of food is underpinned by both origin and quality traits, more often expressed as increased quality benefits derived from the origin source. Gut microbiota contribute to food metabolism and host health, therefore, it may be suitable as a qualifying indicator of origin and quality of economic species. Here, we investigated relationships between the gut microbiota of the sea cucumber (Apostichopus japonicus), a valuable aquaculture species in Asia, with their origins and quality metrics. Based on data from 287 intestinal samples, we generated the first biogeographical patterns for A. japonicus gut microbiota from origins across China. Importantly, A. japonicus origins were predicted using the random forest model that was constructed using 20 key gut bacterial genera, with 97.6% accuracy. Furthermore, quality traits such as saponin, fat and taurine were also successfully predicted by random forest models based on gut microbiota, with approximately 80% consistency between predicted and true values. We showed that substantial variations existed in the gut microbiota and quality variables in A. japonicus across different origins, and we also demonstrated the great potential of gut microbiota to track A. japonicus origins and predict their quality traits.

The gender differences of immunity have been elucidated in many vertebrates and invertebrates. However, the information of this difference was still not clear in the sea cucumber Apostichopus japonicus, which is one of the most valuable aquaculture species and susceptible to diseases caused by pathogen infection. In the present study, the transcriptome of coelomocytes from female and male A. japonicus before and after spawning was obtained by RNA-sequencing technology. A total of 4,538 and 8,248 differentially expressed genes were identified between female and male A. japonicus before and after spawning, respectively, indicating that the gender differences of gene expression profiles in A. japonicus were more remarkable after spawning. Further KEGG enrichment analyses were conducted for both male and female up-regulated genes before and after spawning. The results revealed that the capacity to kill pathogens in female A. japonicus might be more powerful than that in males no matter before and after spawning; the antioxidant ability in male A. japonicus was probably stronger than that in females after spawning; the complement system in male A. japonicus might be more effective than that in females after spawning; and the apoptosis was likely to be more serious in male A. japonicus before spawning. Moreover, we speculated that the fatty acid composition might be one of the inducements for gender specific immune differences of A. japonicus. Overall, the results of our study illustrated the global gender specific immune differences of A. japonicus and contributed to understanding of the molecular mechanisms underlying sea cucumber immune regulation.

The sea cucumber Apostichopus japonicus is an important aquaculture species in China because of its high nutritional and medicinal values. Gender, as a factor affecting the physiology of organisms, is always considered when improving the breeding efficiency of economically important animals. In the present study, protein expression profiles of the gonads and tube feet of male and female A. japonicus were investigated using a comparative proteomics approach. A set of 7499 proteins were identified, which covered a broad range of functions based on function annotations. A significant difference in protein expression profiles was observed between the gonads and tube feet of A. japonicus; gonads showed more apparent gender differences than tube feet. Moreover, the findings revealed that male A. japonicus had more specific functions and most of these functions were associated with energy consumption. Further analyses suggested that the regulation of ERK activity and the capacity of tyrosine production and virus immunity might be more powerful in male and female A. japonicus, respectively. Some candidate proteins were also recognized as potential targets for gender identification of A. japonicus. Overall, our study provides new insights into the understanding of molecular mechanisms underlying gender-based physiological differences in A. japonicus. Significance The current study aimed to reveal gender differences in the physiological characteristics of gonads and tube feet of the sea cucumber A. japonicus. To the best of our knowledge, this is the first proteomics study to analyze the differences in the protein expression profiles of external organs between male and female A. japonicus. The analysis revealed gender differences in the protein expression profiles of both gonads and tube feet of A. japonicus, and the gender differences in gonads were quite apparent. Moreover, according to the recognition of differentially expressed proteins and the enrichment analyses based on Kyoto Encyclopedia of Genes and Genomes, a draft view of how the physiological functions of A. japonicus were affected by gender was obtained. Male A. japonicus could have more specific functions related to energy consumption than females. The regulation of ERK activity and virus immunity might be more robust in male and female A. japonicus, respectively. Some candidate proteins were also recognized as potential targets for gender identification of A. japonicus. The findings presented here will improve the understanding of researchers about the molecular mechanisms underlying gender-based differences in A. japonicus and contribute to the meticulous breeding of A. japonicus.

Background Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date. Findings In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina, and Hi-C sequencing technologies. The final genome assembly was ∼275.42 Mb, with a contig N50 length of 1.13 Mb. Using Hi-C technology to identify the contacts among contigs, 260.17 Mb (94.46%) of the assembled genome were anchored onto 21 pseudochromosomes with a scaffold N50 of 12.97 Mb. We identified 17,219 protein-coding genes, with an average CDS length of 1,575 bp. The genome-wide phylogenetic analysis indicated that R. esculentum might have evolved more slowly than the other scyphozoan species used in this study. In addition, 127 toxin-like genes were identified, and 1 toxin-related “hub” was found by a genomic survey. Conclusions We have generated a chromosome-level genome assembly of R. esculentum that could provide a valuable genomic background for studying the biology and pharmacology of jellyfish, as well as the evolutionary history of Cnidaria.

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.

The sea cucumber Apostichopus japonicus is an economically important marine organism, and its aquaculture has rapidly developed in China. The very large market demand puts forward higher requirements for the economically efficient breeding of sea cucumbers. Sex and the associated reproductive processes have been reported to affect the physiological characteristics of sea cucumbers. However, little is known about the metabolism differences that related to sex and the associated reproductive processes and their potential effects on the efficiency of A. japonicus aquaculture. In this study, ultra-performance liquid chromatography was applied to investigate the variations in metabolic profiles in cell-free coelomic fluids (CCFs) of sea cucumbers of different sexes and reproductive states. A total of 4435 metabolites were detected, and the metabolic profiles of A. japonicus were significantly affected by both sexes and reproductive process. The differentially abundant metabolites in CCFs of A. japonicus of different sexes and reproductive states were also screened and analyzed. The findings revealed that unsaturated fatty acid synthesis and phenylalanine metabolism were the most significantly changed pathways. Moreover, the weakest ability to synthesize capsaicin using phenylalanine was found in A. japonicus after spawning. Our study provides new insights into the metabolic response of A. japonicus during the reproductive process, and also provides valuable references for the economically efficient breeding of A. japonicus.

To investigate the effects of Lactobacillus acidophilus and tussah immunoreactive substances (TIS) supplementation alone or together on the growth performance, digestive and immune-related enzyme activities, and intestinal microbiota of the sea cucumber Apostichopus japonicus, a feeding experiment was conducted. The supplementation of L. acidophilus and TIS together produced the maximum digestive and immune activities, while the minimum values occurred in the control group. No remarkable differences in enzyme activities were observed when supplemented individually. Dietary L. acidophilus and TIS in combination might be more capable of improving digestive capacity, food utilization rate, phosphatase-responsiveness and antioxidants. Furthermore, the supplementation of L. acidophilus and TIS in combination demonstrated a greater ability to optimize the intestinal microbiota of A. japonicus by increasing the potentially beneficial bacteria involved in energy production and biosynthesis, and suppressing the opportunistic pathogens. These results collectively indicated that the combined supplementation of L. acidophilus and TIS has a synergistic effect on enhancing immunity and digestibility, and could improve the intestinal microbiota structure of A. japonicus, suggesting potential for industrial feeding applications.

Due to the importance of characteristics associated with the immunity and physiology of organisms, gender is always taken into account when improving the breeding efficiency of economically important animals. Protein variations in the cell-free ceolomic fluid (CCF) of male and female Apostichopus japonicus before and after spawning were investigated using a comparative proteomic approach, for the purpose of understanding the influence of gender and gender associated reproductive processes on humoral immunity and physiological characteristics of the sea cucumber, A. japonicus. A total of 6839 peptides were obtained and a set of 1466 proteins were identified in the CCF of male and female A. japonicus before and after spawning. Partial least squares discrimination analysis indicated that protein expression profiles in the CCF of A. japonicus were significantly affected by both gender and reproductive processes. In addition, the differentially expressed proteins (DEPs) in the CCF of different genders and reproductive stages of A. japonicus were determined and immune-related proteins in these DEPs were screened. Findings revealed that the alternative pathway of complement activation in both male and female A. japonicus before spawning might take precedence over that after spawning. Further KEGG enrichment analyses of DEPs suggested that the capacity of muscle contraction in A. japonicus females, and food digestion, nutrition absorption, epithelial differentiation as well as growth in A. japonicus males might be enhanced after spawning. Further, compared with A. japonicus females, males may have an advantage in growth in the stages following spawning. Besides, according to KEGG annotation related to metabolism, arginine biosynthesis and purine metabolism were dominant in the CCF of male and female A. japonicus, respectively, suggesting notable metabolic differences in female and male A. japonicus. Overall, our study provides new insight into the understanding of molecular mechanisms underlying gender-determined immune and physiological differences in A. japonicus. SIGNIFICANCE: The current study aimed to reveal the gender differences in humoral immunity and physiological characteristics associated with reproduction in the sea cucumber Apostichopus japonicus. To the best of our knowledge, this is the first proteomic study analyzing the differences in protein profile between male and female A. japonicus. By analyzing the expression differences of the proteome via label-free proteomic technology, we revealed that both gender and reproduction could alter the protein composition and abundance in the cell-free colemic fluid (CCF) of A. japonicus. Based on the recognition of differentially expressed proteins (DEPs) related to immune function among the CCFs, shifts in humoral immunity of male and female A. japonicus that underwent reproduction were obtained. Moreover, according to the enrichment analyses of DEPs based on Kyoto Encyclopedia of Genes and Genomes, a draft view of how the male and female A. japonicus affected by reproduction physiologically was drawn. The results suggested that the alternative pathway of complement activation in both male and female A. japonicus were weakened after spawning. In addition, after reproduction, the capacity of muscle contraction might be enhanced in female A. japonicus, and the nutrients consumption, epithelial differentiation and growth might be strengthened in males. Further, ipath analysis indicated that A. japonicus with different genders also had notable differences in metabolism that related to arginine biosynthesis and purine metabolism. The findings presented here will improve the cognition of researchers in the molecular mechanism underlying the gender-determined immune and phyisological differences of A. japonicus and contribute for the meticulous breeding of A. japonicus.

Diseases during aquaculture can limit the growth and survival of sea cucumber (Apostichopus japonicus), one of the most valuable aquaculture species in China. Recently, a novel disease, named body vesicular syndrome (BVS), has been frequently observed, resulting in the blister, lysis, and rupture of A. japonicus after boiling. Information regarding BVS in A. japonicus, however, has not been addressed. In the present study, the intestinal fungal communities from healthy and BVS A. japonicus were measured by the high-throughput sequencing technology. Significant higher richness and diversity were observed from the intestinal fungal communities of BVS A. japonicus compared to the healthy controls. Moreover, the results of principal coordinate analysis and PERMANOVA revealed that the composition structures of intestinal fungal communities were significantly changed in the A. japonicus with BVS. Further abundance difference analyses were conducted for both the composition and predicted functions of the intestinal fungal communities between the healthy and BVS A. japonicus. The results showed that the classes of Tremelloycetes and Eurotiomycetes were enriched in the intestines of A. japonicus with BVS. Meanwhile, the abundances of animal pathogen and fungal parasite were also significantly enhanced in the intestines of BVS A. japonicus. Overall, the results of our study illustrated the associations of BVS and intestinal fungal communities in A. japonicus and expanded our understanding of this disease.

Bacteria communities in the aquaculture environment have been shown to greatly influence the growth of culture species. The sea cucumber (Apostichopus japonicus) is one of the most important aquaculture species in China, with numerous economic benefits. The growth and physiological characteristics of A. japonicus exhibit remarkable seasonal variation. However, current knowledge regarding the bacterial communities in A. japonicus culture ponds and their potential roles in the regulation of A. japonicus growth and physiology remain unclear. In the present study, Illumina sequencing based on the bacterial 16S rRNA gene was used to investigate the variations in bacterial communities in the surface water and sediment of A. japonicus culture ponds for a period of 1 year. The sediments exhibited a higher diversity of bacterial communities, and a higher abundance of microorganisms involved in sulfur metabolism; however, the surface water had a higher abundance of bacterial species associated with the degradation of organic matter. Furthermore, the bacterial communities in the water column showed a “3 + 1” monthly pattern and those in the sediments exhibited a seasonal succession. The higher abundances of bacteria associated with organic pollution degradation and functions associated with bio-active compound secretion were detected in water samples collected in April, August, and December. In contrast, bacteria that are considered to be food sources for A. japonicus were more abundant in pond sediments in autumn and spring. Finally, correlation analysis demonstrated that water temperature negatively regulated the sulfur cycling efficiency of bacterial communities in sediments of A. japonicus culture ponds. This study provides an important theoretical basis for the micro-ecological regulation of pond-cultured A. japonicus.

Bacteria are the most abundant organisms in natural environment and dominant drivers of multiple geochemical functions. Drawing a global picture of microbial community structure and understanding their ecological status remain a grand challenge. As a typical artificial process, aquaculture provides a large amount of foods and creates great economic benefits for human beings. However, few studies are aimed at the microbial community in the aquaculture environment of aquatic plants. We analyzed microbial communities from 21 water samples in a coastal aquaculture area during the whole cultural process of Undaria pinnatifida by using high-throughout sequencing of 16S rRNA gene. The progression of U. pinnatifida aquaculture can be divided into three stages, named Seeding, Growth, and Maturity, respectively. Microbial community structures in water of the aquaculture area were significantly changed during the progression of U. pinnatifida aquaculture. The relative abundance of Flavobacteriia and Thaumarchaeota classes increased in Growth stage, and β-proteobacteria and Acidimirobiia classes decreased with the growth of U. pinnatifida. Meanwhile, environmental factors shaping the microbial community structures were uncovered during the U. pinnatifida aquaculture by using canonical correspondence analysis and Mantel test, in which temperature, dissolved oxygen, pH and nitrogen could be the major influencing factors. In addition, the microbial functions based on KEGG pathways were predicted from the microbial community compositions by PICRUSt. The comparison of predicted functions suggested that Environmental Information Processing and Genetic Information Processing were the functional categories with the most obvious shift in abundance among different stages of U. pinnatifida aquaculture. The findings of this study allowed us to better understand the microbial community in coastal aquaculture systems and the impact of seaweed cultivation on coastal ecosystems.

Background Sea cucumber Apostichopus japonicus is an important economic species in China, which is affected by various diseases; skin ulceration syndrome (SUS) is the most serious. In this study, we characterized the transcriptomes in A. japonicus challenged with Vibrio splendidus to elucidate the changes in gene expression throughout the three stages of SUS progression. Results RNA sequencing of 21 cDNA libraries from various tissues and developmental stages of SUS-affected A. japonicus yielded 553 million raw reads, of which 542 million high-quality reads were generated by deep-sequencing using the Illumina HiSeq™ 2000 platform. The reference transcriptome comprised a combination of the Illumina reads, 454 sequencing data and Sanger sequences obtained from the public database to generate 93,163 unigenes (average length, 1,052 bp; N50 = 1,575 bp); 33,860 were annotated. Transcriptome comparisons between healthy and SUS-affected A. japonicus revealed greater differences in gene expression profiles in the body walls (BW) than in the intestines (Int), respiratory trees (RT) and coelomocytes (C). Clustering of expression models revealed stable up-regulation as the main pattern occurring in the BW throughout the three stages of SUS progression. Significantly affected pathways were associated with signal transduction, immune system, cellular processes, development and metabolism. Ninety-two differentially expressed genes (DEGs) were divided into four functional categories: attachment/pathogen recognition (17), inflammatory reactions (38), oxidative stress response (7) and apoptosis (30). Using quantitative real-time PCR, twenty representative DEGs were selected to validate the sequencing results. The Pearson’s correlation coefficient (R) of the 20 DEGs ranged from 0.811 to 0.999, which confirmed the consistency and accuracy between these two approaches. Conclusions Dynamic changes in global gene expression occur during SUS progression in A. japonicus. Elucidation of these changes is important in clarifying the molecular mechanisms associated with the development of SUS in sea cucumber. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2810-3) contains supplementary material, which is available to authorized users.