Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth

de novo transcriptome assembly for discovering gene expressed in Holothuria leucospilota with exposed to copper

Sea cucumber is a bioremediator as it can composite organic matter and excrete inorganic matter. Sea cucumber has the potential to serve as a bioindicator in marine habitat as they provide an integrated insight into the status of their environment over long periods. Sea cucumbers are sensitive to the organic concentration in the marine environment and can effectively provide an early warning system for any organic contamination that can negatively impact the ecosystem. The availability of a reference transcriptome for sea cucumber would constitute an essential tool for identifying genes involved in crucial steps of the defence pathway. De novo assembly of RNA-seq data enables researchers to study the transcriptomes without needing a genome sequence. In this study, sea cucumbers fed with Kappaphycus alvarezii powder were treated with 0.20 mg/L copper concentration comprehensive transcriptome data containing 75,149 Unigenes, with a total length of 20,460,032 bp. A total of 8820 genes were predicted from the unigenes, annotated, and functionally categorized into 25 functional groups with approximately 20% cluster in signal transduction mechanism. The reference transcriptome presented and validated in this study is meaningful for identifying a wide range of gene(s) related to the bioindication of sea cucumber in a high copper environment.

Integrative mRNA-miRNA interaction analysis associated with the immune response of Strongylocentrotus intermedius to Vibrio harveyi infection

Strongylocentrotus intermedius is one of the most economically valuable sea urchin species in China and has experienced mass mortality owing to outbreaks of bacterial diseases such as black mouth disease. This has caused serious economic losses to the sea urchin farming industry. To investigate the immune response mechanism of S. intermedius with different tube feet colors in response to Vibrio harveyi infection, we examined the different tube feet-colored S. intermedius under V. harveyi challenge and compared their transcriptome and microRNA (miRNA) profiles using RNA-Seq. We obtained 1813 differentially expressed genes (DEGs), 28 DE miRNAs, and 303 DE miRNA-DEG pairs in different tube feet-colored S. intermedius under V. harveyi challenge. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the most significant DEGs were associated with the Notch signaling and phagosome pathways. The target genes of immune-related miRNAs (miR-71, miR-184, miR-193) and genes (CALM1, SPSB4, DMBT, CSRP1) in S. intermedius were predicted and validated. This study provides insight into the molecular mechanisms that regulate genes involved in the immune response of S. intermedius infected with V. harveyi.

Transcriptome analysis of growth variation in early juvenile stage sandfish Holothuria scabra

The sandfish Holothuria scabra is a high-value tropical sea cucumber species representing a major mariculture prospect across the Indo-Pacific. Advancements in culture technology, rearing, and processing present options for augmenting capture production, stock restoration, and sustainable livelihood activities from hatchery-produced sandfish. Further improvements in mariculture production may be gained from the application of genomic technologies to improve performance traits such as growth. In this study, we performed de novo transcriptome assembly and characterization of fast- and slow-growing juvenile H. scabra from three Philippine populations. Analyses revealed 66 unigenes that were consistently differentially regulated in fast-growing sandfish and found to be associated with immune response and metabolism. Further, we identified microsatellite and single nucleotide polymorphism markers potentially associated with fast growth. These findings provide insight on potential genomic determinants underlying growth regulation in early juvenile sandfish which will be useful for further functional studies.

Gibberellic acid-induced fatty acid metabolism and ABC transporters promote astaxanthin production in Phaffia rhodozyma

AIMS

Astaxanthin is an important natural antioxidant with various biological functions; however, the production of astaxanthin does not meet the requirements for industrialization. The aim of the present study was to identify an inducer that increases astaxanthin yield and to evaluate the regulatory mechanism of the induction of astaxanthin synthesis in Phaffia rhodozyma.

METHODS AND RESULTS

The effects of indole-3-acetic acid (IAA), jasmonic acid (JA) and gibberellic acid (GA) on astaxanthin synthesis were studied by fermentation kinetics analysis. Then, combined transcriptomics and metabolomics approaches were used to analyse differential metabolites and expressed genes involved in astaxanthin synthesis induced by GA. The results indicated that GA significantly increased astaxanthin production; however, IAA and JA had no significant effect on astaxanthin synthesis. The induction by GA significantly enhanced fatty acid metabolism and ABC transporters, increased the expression of fatty acid desaturase and ABC transporter genes, and elevated the contents of unsaturated fatty acids.

CONCLUSIONS

These results suggested that fatty acid saturation plays an important role in astaxanthin accumulation and that ABC transporters may be the efflux pumps for astaxanthin.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study reveals metabolic mechanism of GA-induced astaxanthin synthesis and proposes a new strategy of transporter engineering to improve astaxanthin production.

Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus

Overfishing of sea cucumber Isostichopus badionotus from Yucatan has led to a major population decline. They are being captured as an alternative to traditional species despite a paucity of information about their health-promoting properties. The transcriptome of the body wall of wild and farmed I. badionotus has now been studied for the first time by an RNA-Seq approach. The functional profile of wild I. badionotus was comparable with data in the literature for other regularly captured species. In contrast, the metabolism of first generation farmed I. badionotus was impaired. This had multiple possible causes including a sub-optimal growth environment and impaired nutrient utilization. Several key metabolic pathways that are important in effective handling and accretion of nutrients and energy, or clearance of harmful cellular metabolites, were disrupted or dysregulated. For instance, collagen mRNAs were greatly reduced and deposition of collagen proteins impaired. Wild I. badionotus is, therefore, a suitable alternative to other widely used species but, at present, the potential of farmed I. badionotus is unclear. The environmental or nutritional factors responsible for their impaired function in culture remain unknown, but the present data gives useful pointers to the underlying problems associated with their aquaculture.

Bacillus baekryungensis MS1 regulates the growth, non-specific immune parameters and gut microbiota of the sea cucumber Apostichopus japonicus

Winter is a high incidence period of skin ulceration syndrome in the sea cucumber Apostichopus japonicus. Disease control during the overwintering of sea cucumber can help increase yield and reduce losses. The purpose of this study was to study the effect of the low temperature-resistant probiotic Bacillus baekryungensis MS1 on the growth and immune parameters of sea cucumbers and preliminarily investigate the molecular mechanism of the effects. A low temperature-resistant bacterium, B. baekryungensis MS1, was isolated from a sea cucumber pond in winter and used for culture experiments. After 10 days of prefeeding, the experiment was divided into the control group (fed with commercial diet) and the MS1 group (fed with diet containing B. baekryungensis MS1 at 10⁷ cfu g^-1) for a total of 60 days. The specific growth rate was measured at the end of the culture period to evaluate the growth performance of the sea cucumber. Samples were taken on days 30 and 60 to determine the immune parameters (including superoxide dismutase activity, catalase activity, alkaline phosphatase activity, acid phosphatase activity, nitric oxide synthetase activity, phagocytosis and respiratory burst), aquaculture water microbiota and gut microbiota of the sea cucumber. Finally, transcriptome sequencing and qRT-PCR verification of the two groups of sea cucumbers were performed to study the mechanism of B. baekryungensis MS1 to improve the immunity of the sea cucumber. The results showed that after 60 days of feeding, B. baekryungensis MS1 significantly improved the growth performance and immune enzyme activity and formed a healthier structure of the gut microbiota in the sea cucumber. The challenge test showed that B. baekryungensis MS1 significantly reduced the mortality of sea cucumbers infected with Vibrio splendidus. Transcriptome and gene expression analysis indicated that B. baekryungensis MS1 activated the ubiquitin-mediated proteolysis pathway and inhibited the mTOR signaling pathway to regulate the immunity of the sea cucumber. In summary, the low temperature-resistant bacterium B. baekryungensis MS1 could be applied for the aquiculture of sea cucumber in winter to improve health status and resist pathogenic bacteria such as V. splendidus.

Transcriptome analysis of body wall reveals growth difference between the largest and smallest individuals in the pure and hybrid populations of Apostichopus japonicus

Long-term inbreeding of sea cucumber has resulted in a decrease in its growth rate, which has severely affected yield and economic efficiency. In this study, three Apostichopus japonicus families were constructed and screened into the weight of smallest and largest, which included Russian, Chinese, and their hybrids (RC). We examined the transcriptional profiles of hybrid (RC) and purebred (CC and RR). A total of 49.69 Gb clean reads were obtained, and the Q30 base percentage was above 90.47%. A total of 5191 novel genes were discovered, of which 2592 genes were annotated. Differentially expressed genes (DEGs) were identified, and functional annotation and enrichment analysis were performed. Approximately 1874 DEGs were screened in the Chinese sea cucumber (CC) difference group; 2591 DEGs were obtained in the hybrid sea cucumber difference group (RC), and 3006 DEGs were obtained in the Russian sea cucumber difference group (RR). In Gene Ontology (GO) analysis, highest DEG enrichment was observed for the functional categories of cellular process and metabolic process. In terms of cellular components, DEG enrichment was observed in cell part, cell; for molecular function, DEG enrichment was detected in catalytic activity, binding, hydrolase activity, transferase activity. According to the differential expression analysis, we found that 15 heat shock protein (HSP) genes that have the same expression trends, which were upregulated in the smallest weight of three sea cucumber lines. In addition, COG analysis of defense genes was conducted. All defense genes (ATP-binding cassette transporters (ABCs), multidrug resistance protein (MRPs), and beta-lactamase) showed the same expression trend, which was significantly upregulated in smallest individuals compared to that of largest individuals in RC lines, which implied the smallest individuals are exposed to more pressure during growth. These results may lead to the smallest individuals showing slow growth. Additionally, we selected 12 DEGs to validate the result by qPCR. Those DEGs were included in growth-related and resistance genes. Sequencing of the A. japonicus transcriptome improves our understanding of the transcriptional regulatory apparatus that controls individual development and growth.

Transcriptome profiling reveals key roles of phagosome and NOD-like receptor pathway in spotting diseased Strongylocentrotus intermedius

Spotting disease is a common disease in the process of aquaculture and restocking of the sea urchin Strongylocentrotus intermedius and leads to mass mortality. To characterize the molecular processes and candidate genes related to spotting disease in S. intermedius, we conducted next-generation sequencing to assess the key genes/pathways in spotting diseased sea urchin (DUG) compared to healthy ones (HUG). A total of 321.1 million clean reads were obtained and assembled into 93,877 Unigenes with an N50 of 1185 bp, in which 86.48% of them matched to the genome sequence of the sea urchin S. purpuratus and 27,456 Unigenes mapped to Nr database. Salmon expression analysis revealed 1557 significantly differently expressed genes (DEGs) between DUG and HUG. These DEGs were enriched into 151 KEGG pathways including a core set of immune correlated pathways notably in phagosome and NOD-like receptor signaling. DUG displayed an obvious downregulation in these immune pathways. The expression patterns of six DEGs were confirmed by RT-qPCR, and the expressions were consistent with the results of RNA-seq. Furthermore, 15,990 SSRs were identified and a total of 235,249 and 295,567 candidate SNPs were identified from DUG and HUG, respectively. All these results provided basic information for our understanding of spotting disease outbreak in sea urchin.

Genome-wide identification of HSP70/110 genes in sea cucumber Apostichopus japonicus and comparative analysis of their involvement in aestivation

HSP70/110s are a subgroup of heat shock proteins and play crucial roles in protein homeostasis. HSP70/110s can enhance cell survival in response to a multitude of stressful stimuli, of which the most studied one is heat stress. To perform a systematic study of HSP70/110s in sea cucumber Apostichopus japonicus, 15 HSP70/110 genes, including 13 HSP70s and two HSP110s, were identified and characterized from the transcriptome and genome of sea cucumber. Moderate expansion and conserved structure were found by the phylogenetic and syntenic analysis. Differential expression patterns of HSP70/110s were observed in adult individuals during aestivation, with the comparison of juvenile individuals without aestivation in chronic heat stress. Tissue-specific expression profiles were found both in adult and juvenile individuals, which might indicate that the functional tissues (intestine and respiratory tree) could be restored to normal physiological activity prior to protecting and sporting tissues (body wall and muscle). Differential expression profiles were also observed between the adult and juvenile individuals, which was mainly due to the hypometabolism in aestivation. Taken together, tissue-specific pattern and individual-specific pattern were observed in the HSP70/110 expression profiles in sea cucumber during aestivation. These findings could provide early insight into the involvement of HSP70/110s in the aestivation of marine invertebrate.