Biosynthesis of saponin defensive compounds in sea cucumbers.

Soft-bodied slow-moving sea creatures such as sea stars and sea cucumbers lack an adaptive immune system and have instead evolved the ability to make specialized protective chemicals (glycosylated steroids and triterpenes) as part of their innate immune system. This raises the intriguing question of how these biosynthetic pathways have evolved. Sea star saponins are steroidal, while those of the sea cucumber are triterpenoid. Sterol biosynthesis in animals involves cyclization of 2,3-oxidosqualene to lanosterol by the oxidosqualene cyclase (OSC) enzyme lanosterol synthase (LSS). Here we show that sea cucumbers lack LSS and instead have two divergent OSCs that produce triterpene saponins and that are likely to have evolved from an ancestral LSS by gene duplication and neofunctionalization. We further show that sea cucumbers make alternate sterols that confer protection against self-poisoning by their own saponins. Collectively, these events have enabled sea cucumbers to evolve the ability to produce saponins and saponin-resistant sterols concomitantly.

Chromosome-level genome assembly of sea scallop Placopecten magellanicus provides insights into the genetic characteristics and adaptive evolution of large scallops.

Placopecten magellanicus (Gmelin, 1791), a deep-sea Atlantic scallop, holds significant commercial value as a benthic marine bivalve along the northwest Atlantic coast. Recognizing its economic importance, the need to reconstruct its genome assembly becomes apparent, fostering insights into natural resources and generic breeding potential. This study reports a high-quality chromosome-level genome of P. magellanicus, achieved through the integration of Illumina short read sequencing, PacBio HiFi sequencing, and Hi-C sequencing techniques. The resulting assembly spans 1778 Mb with a scaffold N50 of 86.71 Mb. An intriguing observation arises - the genome size of P. magellanicus surpasses that of its Pectinidae family peers by 1.80 to 2.46 times. Within this genome, 28,111 protein-coding genes were identified. Comparative genomic analysis involving five scallop species unveils the critical determinant of this expanded genome: the proliferation of repetitive sequences recently inserted, contributing to its enlarged size. The landscape of whole genome collinearity sheds light on the relationships among scallop species, enhancing our broader understanding of their genomic framework. This genome provides genomic resources for future molecular biology research on scallops and serves as a guide for the exploration of longevity-related genes in scallops.

Whole-genome resequencing reveals genetic differences and the genetic basis of parapodium number in Russian and Chinese Apostichopus japonicus.

BACKGROUND: Apostichopus japonicus is an economically important species in the global aquaculture industry. Russian A. japonicus, mainly harvested in the Vladivostok region, exhibits significant phenotypic differentiation, including in many economically important traits, compared with Chinese A. japonicus owing to differences in their habitat. However, both the genetic basis for the phenotypic divergence and the population genetic structure of Russian and Chinese A. japonicus are unknown. RESULT: In this study, 210 individuals from seven Russian and Chinese A. japonicus populations were sampled for whole-genome resequencing. The genetic structure analysis differentiated the Russian and Chinese A. japonicus into two groups. Population genetic analyses indicated that the Russian population showed a high degree of allelic linkage and had undergone stronger positive selection compared with the Chinese populations. Gene ontology terms enriched among candidate genes with group selection analysis were mainly involved in immunity, such as inflammatory response, antimicrobial peptides, humoral immunity, and apoptosis. Genome-wide association analysis yielded eight single-nucleotide polymorphism loci significantly associated with parapodium number, and these loci are located in regions with a high degree of genomic differentiation between the Chinese and Russia populations. These SNPs were associated with five genes. Gene expression validation revealed that three of these genes were significantly differentially expressed in individuals differing in parapodium number. AJAP08772 and AJAP08773 may directly affect parapodium production by promoting endothelial cell proliferation and metabolism, whereas AJAP07248 indirectly affects parapodium production by participating in immune responses. CONCLUSIONS: This study, we performed population genetic structure and GWAS analysis on Chinese and Russian A. japonicus, and found three candidate genes related to the number of parapodium. The results provide an in-depth understanding of the differences in the genetic structure of A. japonicus populations in China and Russia, and provide important information for subsequent genetic analysis and breeding of this species.

Transcriptome analysis reveals core lncRNA-mRNA networks regulating melanization and biomineralization in Patinopecten yessoensis shell-infested by Polydora.

BACKGROUND: Patinopecten yessoensis, a large and old molluscan group, has been one of the most important aquaculture shellfish in Asian countries because of its high economic value. However, the aquaculture of the species has recently been seriously affected by the frequent outbreaks of Polydora disease, causing great economic losses. Long non-coding RNAs (lncRNAs) exhibit exhibit crucial effects on diverse biological processes, but still remain poorly studied in scallops, limiting our understanding of the molecular regulatory mechanism of P. yessoensis in response to Polydora infestation. RESULTS: In this study, a high-throughput transcriptome analysis was conducted in the mantles of healthy and Polydora-infected P. yessoensis by RNA sequencing. A total of 19,133 lncRNAs with 2,203 known and 16,930 novel were identified. The genomic characterizations of lncRNAs showed shorter sequence and open reading frame (ORF) length, fewer number of exons and lower expression levels in comparison with mRNAs. There were separately 2280 and 1636 differentially expressed mRNAs and lncRNAs (DEGs and DELs) detected in diseased individuals. The target genes of DELs were determined by both co-location and co-expression analyses. Functional enrichment analysis revealed that DEGs involved in melanization and biomineralization were significantly upregulated; further, obviously increased melanin granules were observed in epithelial cells of the edge mantle in diseased scallops by histological and TEM study, indicating the crucial role of melanizaiton and biomineralization in P. yessoensis to resist against Polydora infestation. Moreover, many key genes, such as Tyrs, Frizzled, Wnts, calmodulins, Pifs, perlucin, laccase, shell matrix protein, mucins and chitins, were targeted by DELs. Finally, a core lncRNA-mRNA interactive network involved in melanization and biomineralization was constructed and validated by qRT-PCR. CONCLUSIONS: This work provides valuable resources for studies of lncRNAs in scallops, and adds a new insight into the molecular regulatory mechanisms of P. yessoensis defending against Polydora infestation, which will contribute to Polydora disease control and breeding of disease-resistant varieties in molluscs.

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.

Development of a high-throughput SNP array for sea cucumber (Apostichopus japonicus) and its application in genomic selection with MCP regularized deep neural networks.

High-throughput single nucleotide polymorphism (SNP) genotyping assays are powerful tools for genetic studies and genomic breeding applications for many species. Though large numbers of SNPs have been identified in sea cucumber (Apostichopus japonicus), but, as yet, no high-throughput genotyping platform is available for this species. In this study, we designed and developed a high-throughput 24 K SNP genotyping array named HaishenSNP24K for A. japonicus, based on the multi-objective-local optimization (MOLO) algorithm and HD-Marker genotyping method. The SNP array exhibited a relatively high genotyping call rate (> 96%), genotyping accuracy (>95%) and exhibited highly polymorphic in sea cucumber populations. In addition, we also assessed its application in genomic selection (GS). Deep neural networks (DNN) that can capture the complicated interactions of genes have been proposed as a promising tool in GS for SNP-based genomic prediction of complex traits in animal breeding. To overcome the problem of over-fitting when using the HaishenSNP24K array as high-dimensional DNN input, we developed minmax concave penalty (MCP) regularization for sparse deep neural networks (DNN-MCP) that finds an optimal sparse structure of a DNN by minimizing the square error subject to the non-convex penalty MCP on the parameters (weights and biases). Compared to two linear models, namely RR-GBLUP and Bayes B, and the nonlinear model DNN, DNN-MCP has greatly improved the genomic prediction ability for three quantitative traits (e.g., wet weight, dry weight and survival time) in the sea cucumber population. To the best of our knowledge, this is the first work to develop a high-throughput SNP array for A. japonicus and a new model DNN-MCP for genomic prediction of complex traits in GS. The present results provide evidence that supports the HaishenSNP24K array with DNN-MCP will be valuable for genetic studies and molecular breeding in A. japonicus.

Chemical Comparison and Identification of Xanthine Oxidase Inhibitors of Dioscoreae Hypoglaucae Rhizoma and Dioscoreae Spongiosae Rhizoma by Chemometric Analysis and Spectrum-Effect Relationship.

Dioscoreae hypoglaucae Rhizoma (DH) and Dioscoreae spongiosae Rhizoma (DS) are two similar Chinese herbal medicines derived from the Dioscorea family. DH and DS have been used as medicines in China and other Asian countries for a long time, but study on their phytochemicals and bioactive composition is limited. This present study aimed to compare the chemical compositions of DH and DS, and explore the anti-xanthine oxidase components based on chemometric analysis and spectrum-effect relationship. Firstly, an HPLC method was used to establish the chemical fingerprints of DH and DS samples, and nine common peaks were selected. Then, hierarchical clustering analysis, principal component analysis and orthogonal partial least squares discriminant analysis were employed to compare and discriminate DH and DS samples based on the fingerprints data, and four steroidal saponins compounds (protodioscin, protogracillin, dioscin, gracillin) could be chemical markers responsible for the differences between DH and DS. Meanwhile, the anti-xanthine oxidase activities of these two herbal medicines were evaluated by xanthine oxidase inhibitory assay in vitro. Pearson correlation analysis and partial least squares regression analysis were subsequently used to investigate the spectrum-effect relationship between chemical fingerprints and xanthine oxidase inhibitory activities. The results showed that four steroidal saponins, including protodioscin, protogracillin, methyl protodioscin and pseudoprogracillin could be potential anti-xanthine oxidase compounds in DH and DS. Furthermore, the xanthine oxidase inhibitory activities of the four selected inhibitors were validated by anti-xanthine oxidase inhibitory assessment and molecular docking experiments. The present work provided evidence for understanding of the chemical differences and the discovery of the anti-xanthine oxidase constituent of DH and DS, which could be useful for quality evaluation and bioactive components screening of these two herbal medicines.

Effects of Supplementary Kelp Feeding on the Growth, Gonad Yield, and Nutritional and Organoleptic Quality of Subadult Sea Urchin (Strongylocentrotus intermedius) with Soya Lecithin Intake History.

A 23-week feeding experiment was conducted to investigate the effects of supplementary kelp feeding on the growth, gonad development, and nutritional and sensory properties of sea urchin (Strongylocentrotus intermedius) with soya lecithin (SL) intake history. The feeding experiment was divided into experimental phase I and phase II. During phase I, 48 subadult sea urchins (initial weight: 6.28 ± 0.07 g) were fed one of the feeds with different levels of SL (0%, 1.6%, 3.2%) or kelp (Saccharina japonica) for 12 weeks. Then, all sea urchins were fed kelp for the next 11 weeks during the phase II. Each diet was randomly allocated to six cages of sea urchins. The results of phase I showed that weight gain rate (WGR), gonadosomatic index (GSI), gonad sensory properties (color and texture), and essential amino acid (EAA) contents were not significantly affected by SL level in the feed groups. High level (3.2%) of SL suppressed gonad development of S. intermedius with retarded gametogenesis in the 3.2% SL group (stage Ⅱ) compared to those fed 0% and 1.6% SL groups (stage Ⅲ). Sea urchins fed dry feeds exhibited significantly lower WGR and values of color (redness and yellowness) and texture (hardness and gumminess) but higher contents of EAA in the gonads than those fed kelp. The n-3/n-6 polyunsaturated fatty acid (PUFA) and eicosapentaenoic acid (EPA) of gonads in the groups fed with dry feeds showed no significant differences, but were significantly lower than that of kelp group. At the end of phase II, the gonad yellowness and EPA content of gonads in all dry feed groups were significantly increased by supplementary kelp feeding, with a higher increase observed in S. intermedius with SL intake history, while arachidonic acid (ARA) content was significantly improved by supplementary kelp feeding in S. intermedius with SL intake history. Gonad texture was improved to some extent by supplementary kelp feeding. These results indicated that S. intermedius fed dry feeds showed significantly higher GSI and EAA but poorer organoleptic quality and lower n-3/n-6 PUFA and EPA than those fed kelp. Kelp supplementary feeding improved the fatty acid value and organoleptic quality of gonads, especially for the sea urchins with SL intake history.

Isolation and characterization of four pathogenic strains of Vibrio spp. from farmed sea urchins, Strongylocentrotus intermedius, in China.

The sea urchin Strongylocentrotus intermedius, famous for its gonadal quality, is one of the most important farmed species in the sea area of northern China. Since 2020, outbreaks of black peristomial membrane disease (commonly called black mouth disease) have frequently occurred in spring and winter in cultured S. intermedius. In this study, we isolated the predominant bacteria from different tissues of diseased sea urchins from a North China farm in the spring of 2021. Four pathogenic strains (named SIBMPM01, SIBMPM02, SIBMPM03 and SIBMCF01) were obtained and characterized by Gram staining, morphological observation, artificial infection tests, and metabolic characteristics. Our results showed that: 1) all obtained strains belonged to the genus Vibrio and had morphological differences. Phylogenetic analysis indicated that the four obtained strains might be novel Vibrio species. 2) Laboratory-based artificial infection tests showed that sea urchins infected with either SIBMPM01, SIBMPM02, SIBMPM03 or SIBMCF01 exhibited pathological symptoms of a black peristomial membrane in a dosage-dependent and temperature-dependent manner. The virulence of SIBMCF01 was greater than those of the others. 3) Metabolic characterization data showed that SIBMPM01, SIBMPM02, SIBMPM03 and SIBMCF01 shared similar metabolic characteristics. 4) Antimicrobial susceptibility tests demonstrated that the four obtained strains were all sensitive to ampicillin, doxycycline, norfloxacin, ofloxacin, furazolidone and chloramphenicol. SIBMPM01 was specifically sensitive to neomycin, and SIBMCF01 was specifically sensitive to carboxybenzyl penicillin.

Integrated miRNA-mRNA analysis provides potential biomarkers for selective breeding in bay scallop (Argopecten irradians).

Growth traits were compared between selected Argopecten irradians (BA) and non-selected A. irradians (NA; as a control). The results indicated that 1) the BA line exhibited greater average body weight and adductor muscle wet weight increase compared with the NA line at the same age of 10 months. 2) Comparative and integrated microRNA (miRNA) and mRNA transcriptome analyses identified 3373 differentially expressed genes (DEGs), 33 differentially expressed miRNAs (DEMs), and 39 "DEM-DEG" pairs in the BA line compared with the control. DEGs, DEMs, and "DEM-DEG" pairs involved in insulin signaling, immune related pathways, and actin cytoskeleton regulation were identified as candidates correlated with growth improvement in the BA line. A total of 259 positively selected genes were also identified. Collectively, our observations in this study will enrich the molecular information for A. irradians and provide potential biomarkers for future selective breeding and new seed creation in scallops.

Chemical comparison and discrimination of two plant sources of Angelicae dahuricae Radix, Angelica dahurica and Angelica dahurica var. formosana, by HPLC-Q/TOF-MS and quantitative analysis of multiple components by a single marker.

INTRODUCTION: Angelica dahurica(BZ) and Angelica dahurica var. formosana(HBZ) are two plant sources of Angelicae dahuricae Radix. Although BZ and HBZ are commonly used herbal medicines with great medicinal and dietary values, study on their phytochemicals and bioactive compositions is limited. OBJECTIVE: To compare the chemical compositions of BZ and HBZ and find the chemical makers for discrimination and quality evaluation of the two botanical origins of Angelicae dahuricae Radix. METHODOLOGY: A high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry method was established for chemical profiling of BZ and HBZ. Then, a quantitative analysis of multiple components by a single marker method was developed for simultaneous determination of nine bioactive coumarins (xanthotoxol, oxypeucedanin hydrate, byakangelicin, xanthotoxin, bergapten, oxypeucedanin, phellopterin, imperatorin and isoimperatorin). Moreover, chemometrics were performed to compare and discriminate BZ and HBZ samples. RESULTS: A total of 30 coumarins compounds were identified, and the chemical compositions in BZ and HBZ were quite similar. The quantitative analysis showed that there were significant differences in the contents of bioactive coumarins, and the chemometric analysis indicated five coumarins (xanthotoxol, xanthotoxin, bergapten, phellopterin and isoimperatorin) were responsible for the significant differences between BZ and HBZ, which could be used as chemical markers to distinguish the two original plant sources of Angelicae dahuricae Radix. CONCLUSION: The present work provided useful information for understanding the chemical differences between BZ and HBZ and also provided feasible methods for quality evaluation and discrimination of herbal medicines originating from multiple botanical sources.

[Dynamic changes of volatile components in Forsythia suspensa at different harvest periods based on GC-MS and chemometrics analysis].

Forsythiae Fructus is the dried fruit of Forsythia suspensa and the volatile compounds are its main bioactive components. According to the different harvest periods, F. suspensa can be divided into Qingqiao(mature F. suspensa) and Laoqiao(ripe F. suspensa). To investigate dynamic changes of volatile components in Qingqiao and Laoqiao samples collected at different periods, the present study extracted and analyzed the total volatile oils in Qingqiao and Laoqiao samples(four harvest periods for Qingqiao and two for Laoqiao) by steam distillation method. The results indicated that the content of volatile oils in F. suspensa samples at different harvest periods was significantly different. The content of volatile oils in Qingqiao samples(except those harvested in the first period) was higher than that of Laoqiao, and the content of volatile oils in both Qingqiao and Laoqiao increased with the harvest period. Furthermore, volatile compounds in F. suspensa were qualitatively analyzed by the gas chromatography-mass spectrometry(GC-MS), and 28 volatile compounds were identified. Chemometrics analyses including principal component analysis(PCA) and partial least squares discriminant analysis(PLS-DA) were further applied to explore differential markers and dynamic changes of volatile components in Qingqiao and Laoqiao samples at different harvest periods. Finally, four volatile compounds, including α-pinene, sabinene, ß-pinene, and 4-terpenol were selected as potential differential markers. The relative content of α-pinene and 4-terpenol was consistent with that of total volatile oils in the changing trend.

Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing.

BACKGROUND: Mollusca, a phylum of highly rich species, possess vivid shell colours, but the underlying molecular mechanism remains to be elucidated. DNA methylation, one of the most common epigenetic modifications in eukaryotes, is believed to play a vital role in various biological processes. However, analysis of the effects of DNA methylation on shell colouration has rarely been performed in molluscs, limiting the current knowledge of the molecular mechanism of shell colour formation. RESULTS: In the present study, to reveal the role of epigenetic regulation in shell colouration, WGBS, the "gold standard" of DNA methylation analysis, was first performed on the mantle tissues of Yesso scallops (Patinopecten yessoensis) with different shell colours (brown and white), and DNA methylomes at single-base resolution were generated. About 3% of cytosines were methylated in the genome of the Yesso scallop. A slight increase in mCG percentage and methylation level was found in brown scallops. Sequence preference of nearby methylated cytosines differed between high and low methylation level sites and between the brown- and white-shelled scallops. DNA methylation levels varied among the different genomic regions; all the detected regions in the brown group exhibited higher methylation levels than the white group. A total of 41,175 DMRs (differentially methylated regions) were detected between brown and white scallops. GO functions and pathways associated with the biosynthesis of melanin and porphyrins were significantly enriched for DMRs, among which several key shell colour-related genes were identified. Further, different correlations between mRNA expression levels and DNA methylation status were found in these genes, suggesting that DNA methylation regulates shell colouration in the Yesso scallop. CONCLUSIONS: This study provides genome-wide DNA methylation landscapes of Yesso scallops with different shell colours, offering new insights into the epigenetic regulatory mechanism underlying shell colour.

Natural Deep Eutectic Solvents for the Extraction of Bioactive Steroidal Saponins from Dioscoreae Nipponicae Rhizoma.

In the present study, a simple and environmentally friendly extraction method based on natural deep eutectic solvents (NADESs) was established to extract four bioactive steroidal saponins from Dioscoreae Nipponicae Rhizoma (DNR). A total of twenty-one types of choline chloride, betaine, and L-proline based NADESs were tailored, and the NADES composed of 1:1 molar ratio of choline chloride and malonic acid showed the best extraction efficiency for the four steroidal saponins compared with other NADESs. Then, the extraction parameters for extraction of steroidal saponins by selected tailor-made NADES were optimized using response surface methodology and the optimal extraction conditions are extraction time, 23.5 min; liquid-solid ratio, 57.5 mL/g; and water content, 54%. The microstructure of the DNR powder before and after ultrasonic extraction by conventional solvents (water and methanol) and the selected NADES were observed using field emission scanning electron microscope. In addition, the four steroidal saponins were recovered from NADESs by D101 macroporous resin with a satisfactory recovery yield between 67.27% and 79.90%. The present research demonstrates that NADESs are a suitable green media for the extraction of the bioactive steroidal saponins from DNR, and have a great potential as possible alternatives to organic solvents for efficiently extracting bioactive compounds from natural products.

Distant hybrids of Heliocidaris crassispina (♀) and Strongylocentrotus intermedius (♂): identification and mtDNA heteroplasmy analysis.

BACKGROUND: Distant hybridization between the sea urchin Heliocidaris crassispina (♀) and the sea urchin Strongylocentrotus intermedius (♂) was successfully performed under laboratory conditions. A new variety of hybrid sea urchin (HS hybrid) was obtained. However, the early-development success rates for the HS hybrids were significantly lower than those of purebred H. crassispina or S. intermedius offspring. In addition, it was difficult to distinguish the HS-hybrid adults from the pure H. crassispina adults, which might lead to confusion in subsequent breeding attempts. In this study, we attempted to develop a method to quickly and effectively identify HS hybrids, and to preliminarily investigate the molecular mechanisms underlying the poor early-development success rates in the HS hybrids. RESULTS: The hybrid sea urchins (HS hybrids) were identified both morphologically and molecularly. There were no significant differences in the test height to test diameter ratios between the HS hybrids and the parents. The number and arrangement of ambulacral pore pairs in the HS hybrids differed from those of the parental lines, which might serve as a useful morphological character for the identification of the HS hybrids. A primer pair that identified the HS hybrids was screened by comparing the mitochondrial genomes of the parental lines. Moreover, paternal leakage induced mitochondrial DNA heteroplasmy in the HS hybrids, which might explain the low rates of early development success in these hybrids. CONCLUSIONS: The distant-hybrid sea urchins were accurately identified using comparative morphological and molecular genetic methods. The first evidence of mtDNA heteroplasmy after the distant hybridization of an echinoderm was also provided.

[Dynamic changes of volatile components of Qiai from different harvest time based on GC-MS and chemometrics analysis].

Artemisiae Argyi Folium, the dried leaves of Artemisia argyi, has been widely used in traditional Chinese and folk medicines for a long time. Qiai is one of the top-geoherb of Artemisiae Argyi Folium. Qiai contains various bioactive constituents, such as volatile oils, phenolic acids, flavonoids and terpenoids. Phytochemical studies demonstrated that volatile compounds are the main bioactive constituents in Qiai. Try to investigate dynamic changes of volatile components of Qiai from different harvest time and explore the optimum harvest time of Qiai, in this study, the contents of total volatile oils in Qiai collected from five different harvest time were analyzed by steam distillation method. The results showed that the contents of volatile oils of Qiai were higher in the third harvest time(around the Dragon Boat Festival), which is basically consistent with the traditional harvest time. Furthermore, a sensitive method based on gas chromatography-mass spectrometry(GC-MS) was established for qualitative analysis of volatile compounds in Qiai, and a total of thirty volatile compounds were identified. Chemometrics methods including principal component analysis(PCA) and orthogonal partial least-squares discriminate analysis(OPLS-DA) were applied to explore chemical markers and dynamic changes of volatile components in Qiai from different harvest time, and the results indicated that there were obvious differences in the relative contents of volatile compounds of Qiai samples from different harvest time. Eight volatile compounds, including α-terpinene, γ-terpinene, D-camphor, trans-carveol, α-copaene, isobornylisobutyrate, humulene, and caryophyllene oxide were selected as potential chemical markers. Among the eight chemical markers, the relative contents of α-terpinene, γ-terpinene, α-copaene and caryophyllene oxide were higher in the third harvest period(around the Dragon Boat Festival), which is consistent with the contents of total volatile oils. The present study could provide the basis for investigating the optimum harvest time of Qiai, and might be useful for the quality control of this herbal medicine.

MicroRNAs involved in innate immunity regulation in the sea cucumber: A review.

The sea cucumber is one of the most economically significant echinoderms. The immunity against exogenous stimulation of sea cucumber is of great academic and economic importance. MicroRNAs (miRNAs) are a class of short endogenous non-coding RNAs (ncRNAs) that are considered as vital regulators of both innate and adaptive immune responses in most eukaryotes. In sea cucumbers, some miRNAs (such as miR-133, miR-137, and miR-2008, among others) that participate in the regulation of innate immunity have been recently identified and characterized. This review focuses on those known miRNAs and their corresponding target genes that participate in the regulation of the complement system, Toll-like receptor (TLR) pathway, reactive oxygen species (ROS) production and apoptosis pathways in sea cucumbers. Moreover, we cover immune-related miRNA investigations in sea cucumbers that provide insights into developing more miRNA-based biomarkers and therapeutic strategies for sea cucumber diseases.

Transcriptome sequencing reveals phagocytosis as the main immune response in the pathogen-challenged sea urchin Strongylocentrotus intermedius.

The clarification of host immune responses to causative bacteria of spotting disease in the sea urchin Strongylocentrotus intermedius is vital to preventing and controlling this disease, especially to selective breeding for disease resistance. For this purpose, sea urchins were challenged with the causative bacterium Vibrio sp. to obtain spotting diseased and undiseased samples. We conducted next-generation sequencing to assess the key genes/pathways in control (CG), diseased (DG), and undiseased (UG) groups. A total of 454.1 million clean reads were obtained and assembled into 23,899 UniGenes with an N50 of 1359 bp, with 86.11% of them matching the genome sequence of the sea urchin S. purpuratus. A total of 8415 UniGenes were mapped to the non-redundant database. Salmon expression analysis revealed 725 significantly differentially expressed genes (DEGs) among CG, DG, and UG. These DEGs were enriched into 72 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including a core set of immune correlated pathways notably in the phagosome, vitamin digestion and absorption, Wnt signaling, and Notch signaling pathways. DG was evidently upregulated in these immune pathways and could enhance phagocytosis directly or indirectly. Thus, phagocytosis was the main coelomic cellular immune response in S. intermedius challenged by spotting disease causative bacterium. The expression patterns of 10 DEGs were confirmed via RT-qPCR, and the expression levels were consistent with the results of RNA-seq. Furthermore, 9899 SSRs were identified, and 123,692, 151,827, and 114,368 candidate SNPs were identified from CG, DG, and UG, respectively. These results provide basic information for our understanding of sea urchin antibacterial immunity.

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.

Transcriptomes reveal genes involved in covering and sheltering behaviors of the sea urchin Strongylocentrotus intermedius exposed to UV-B radiation.

Although the potential link exists between behavioral responses to UV-B radiation and the maximization of fitness, molecular mechanisms of these UV-B induced behaviors remain poorly understood. For the first time, we investigated the transcriptomes of covered (CB), sheltered (SB) and non-protected (NA) sea urchins Strongylocentrotus intermedius exposed to UV-B radiation. A total of 330 differentially expressed genes were revealed by transcriptome comparisons. By comparing with the group NA, we found 79 up-regulated and 118 down-regulated genes in SB group, as well as 26 up-regulated and 67 down-regulated genes in group CB. There were 34 up-regulated genes and 52 down-regulated genes in group SB, compared with group CB. These differentially expressed genes failed to enrich either Gene Ontology (GO) or Kyoto Encyclopedia of Genes and Genomes (KEGG), only except an enrichment in KEGG. We highlighted TRPA1 and Opsin as key neurobiological genes involved in the molecular mechanisms of covering and sheltering behaviors of sea urchins exposed to UV-B radiation. What's more, other identified genes provide valuable resources for future investigations on the molecular basis of covering and sheltering behaviors of sea urchins.