Search Results (25)

The identification of mRNA isoforms in biological samples is crucial for studying tissue- and cell-specific isoform expression, activity of tissue-specific promoters, alternative splicing events, and alternative polyadenylation signals in genes. For single or several genes, expressed mRNA isoforms can be found using RT-PCR and RT-qPCR. Available transcriptome short-read archives deposited in GenBank or as laboratory data can be used to identify mRNA isoforms instead of or prior to wet analysis by other methods in eukaryotic organisms with annotated genomes. However, isoform expression analysis requires advanced bioinformatics skills and may be time-consuming. In addition, this analysis generates a large amount of unnecessary data. To detect mRNA isoforms encoded by one gene of interest, screening of expressed mRNAs in NGS data can be simplified by mapping NGS short reads to a single-gene or transcript sequence. Using single-gene/transcript mapping, we analyzed the expression of the Otx gene at the mRNA isoform level in some embryonic and adult tissue mRNA libraries of the sea urchin Strongylocentrotus purpuratus available in GenBank. The presence of expressed Otx mRNA isoforms was confirmed by RT-qPCR in the same tissues and at the same developmental stages of the closely related species Strongylocentrotus intermedius. We showed that single-gene/transcript mapping is a suitable approach for qualitative evaluation of the expression of mRNA isoforms and recognition of at least two expressed isoforms in the same biological sample. Full article

The genus Bizionia, a member of the Bacteroidota phylum, is considered a polyphyletic taxonomic group requiring a phylogenetic revision of its members. A novel strain 041-53-Ur-6^T was isolated from the cavity fluid of the sea urchin Strongylocentrotus intermedius from the Sea of Okhotsk. Analysis of the 16S rRNA gene sequence showed that 041-53-Ur-6^T belongs to the family Flavobacteriaceae, and its closest neighbor is [Bizionia] algoritergicola with 97.5% sequence similarity. Phylogenomic analysis confirmed the phylogenetic heterogeneity of the genus Bizionia and the clear separation of the genera “Algorimicrobium” and Hanstruepera. The inter-genus AAI values between them were 74.0–76.4%, which is slightly lower than the inter-species AAI values observed for each genus. The strain 041-53-Ur-6^T (= KMM 8389^T) formed a separated branch within the [B.] algoritergicola clade, demonstrating the highest ANI/AAI values of 80.1/81.0% with the strain [B.] algoritergicola APA-1^T. The dDDH values between strain KMM 8389^T and representatives of the genus “Algorimicrobium” ranged from 22.6% to 26.7%. Major fatty acids were iso-C_15:1 ω10c, iso-C_15:0 and iso-C_15:0 Δ2-OH. The polar lipids included a phosphatidylethanolamine, a phosphatidylglycerol, five unidentified lipids, two unidentified aminolipids, a phosphatidylcholine, and an unidentified aminophospholipid. The genome KMM 8389^T is a circular chromosome of 3,031,910 bp in size with a DNA G + C content of 33.5%. It comprises 2702 protein-coding genes and four rrn operons. Functional genomic analysis indicated the potential of KMM 8389^T for degrading starch, glycogen, and alginate due to the presence of genes encoding GH13, GH31, and GH65. Furthermore, KMM 8389^T possessed PLs 6, 7, 12, and 17, specialized for alginate, confirming the potential adaptation of this strain to algal substrates and surfaces. On the basis of the results of genotypic, chemotaxonomic, and phenotypic analyses, it is clear that the strain KMM 8389^T represents a novel species with [B.] algoritergicola, [B.] argentinensis, [B.] echini, [B.] hallyeonensis, [B.] myxarmorum, [B.] psychrotolerans, and [B.] sediminis as the nearest neighbors. These taxa are classified in a single novel genus, as Algorimicrobium algoritergicola gen. nov., comb. nov., A. argentinensis comb. nov., A. echini comb. nov., A. hallyeonensis comb. nov., A. myxarmorum comb. nov., A. psychrotolerans comb. nov., A. sediminis comb. nov., and Algorimicrobium bowmanii sp. nov. 041-53-Ur-6^T (=KMM 8389^T, =KCTC 72011^T). Full article

Driven by the concept of sustainable aquaculture, natural feed additives with growth-promoting, antioxidant, and immune-enhancing properties have become a key research focus. This study assessed the effects of dietary red pepper powder (Capsicum annuum) supplementation at 0%, 0.5%, 1.0%, and 2.0% over 50 days on the growth, digestive function, immune and antioxidant capacities, intestinal microbiota, and gene expression in Strongylocentrotus intermedius (S. intermedius). The results indicated that red pepper powder significantly promoted growth and decreased the feed conversion ratio (FCR) (p < 0.05), with the 1.0% group showing the highest growth rate. Additionally, supplementation improved gonadal coloration and increased crude protein and lipid contents in the gonads, particularly in the 1.0% and 2.0% groups (p < 0.05). Supplementation with 1.0% and 2.0% red pepper powder enhanced digestive, immune, and antioxidant enzyme activities, while reducing malondialdehyde (MDA) levels, indicating lower lipid peroxidation. α-diversity analysis revealed the highest ACE, Chao, and Shannon indices and the lowest Simpson index in the 1.0% group, indicating greater microbial diversity. Community analysis revealed that in the red pepper powder treatment groups, beneficial bacteria, such as Firmicutes and Unclassified_f__Rhodobacteraceae, increased in relative abundance, while potential pathogens like Arcobacter, and Epsilonbacteraeota were less abundant. Red pepper powder supplementation upregulated key immune- and antioxidant-related genes while downregulating pro-inflammatory and stress-associated genes. Overall, optimal dietary supplementation of red pepper powder, particularly at 1.0%, enhanced antioxidant and immune functions, optimized intestinal microbiota, mitigated oxidative stress, and consequently promoted growth, improved gonadal quality, and strengthened overall health in S. intermedius. Full article

Sea urchin aquaculture has experienced remarkable growth in recent years. However, this growth has been accompanied by increased disease prevalence. Notably, spotting disease has particularly severe impacts. In this study, we isolated the pathogen HZ-3-2 from 10 sea urchins with spotting disease, and it was identified as Vibrio splendidus through morphological observations, 16S rDNA sequencing, and whole-genome sequencing. Subsequently, experimental infection confirmed that V. splendidus (HZ-3-2) is the causative agent of spotting disease in this outbreak. The drug sensitivity confirmed the presence of drug resistance genes, such as CPR, QNRS5, and rsmA, which were identified in the genome. The tests indicated that V. splendidus was sensitive to various antibiotics, including fluoroquinolones and florfenicol. Finally, we used the transcriptome to explore the molecular response of the diseased sea urchin. Compared to the control group, a group of sea urchins immersed in a pathogen suspension with a concentration of 10⁷ CFU/mL (group M) resulted in 439 annotated differentially expressed genes. KEGG pathway analysis indicated significant activation of cholesterol metabolism and starch and sucrose metabolism in the S. intermedius. This study highlights the genes NPC1, AMY2A, and MGAM as critical regulators of energy metabolism, and cholesterol synthesis in infected sea urchins. These findings confirm V. splendidus as the bacterium responsible for spotting disease and provide valuable insights into the intestinal molecular response of S. intermedius to infection. Full article

This study examined the effects of calcium, magnesium, and potassium ion concentrations on Strongylocentrotus intermedius through seven experimental rearing groups: two calcium ion levels (550 mg/L and 733 mg/L), two magnesium ion levels (1727 mg/L and 2302 mg/L), two potassium ion levels (533 mg/L and 710 mg/L), and a control. After 45 days of cultivation, 733 mg/L of calcium ions significantly reduced the S. intermedius survival rate, while 550 mg/L of calcium ions had no significant adverse effects on survival, growth (SGR), the feed conversion ratio (FCR), gonad colour, or immune enzyme activity, and it significantly increased the gonad index (GI). Meanwhile, 2302 mg/L of magnesium ions caused 100% mortality within 2 days, and 1727 mg/L of magnesium ions significantly reduced the survival rate and SGR while increasing the FCR. Additionally, 710 mg/L of potassium ions had no significant impact on the survival rate but significantly reduced SGR, the GI, and gonad colour while increasing the FCR, whereas 533 mg/L of potassium ions showed no significant adverse effects on survival, SGR, the FCR, gonad colour, digestive enzyme activity, or immune enzyme activity. The study results indicate that when formulating artificial seawater using source water with elevated calcium, magnesium, and potassium ion concentrations for S. intermedius aquaculture, calcium ions under 550 mg/L and potassium ions under 533 mg/L are biologically acceptable. However, magnesium ions require adjustment to a narrow optimal range to ensure survival and physiological performance. Full article

Tussah immunoreactive pupa powder (IPP) is composed of various active substances. We speculated that it has the potential to improve key economic traits of sea urchins. Therefore, we conducted a 60-day experiment to examine the effects of IPP on growth, antioxidant capacity, gonad quality, and gut microbiota of sea urchins (Strongylocentrotus intermedius). The experiment involved the preparation of a kelp group and four types of feed containing 0% (the control group), 0.5%, 1.0%, and 1.5% IPP. The results indicated that IPP had no significant impact on the survival of sea urchins (p > 0.05). Firstly, adding IPP promoted the growth of sea urchins. The 1.0% IPP group showed the highest weight gain rate among the feed group, significantly higher than that of the control group (p < 0.05). Secondly, compared with the kelp group, the addition of IPP significantly improved the growth and quality of sea urchin gonads (p < 0.05), which demonstrated certain industrial value. Thirdly, following the addition of IPP, the activities of SOD, CAT, and POD significantly increased in comparison to the control group (p < 0.05). Lastly, added IPP increased the abundance of Firmicutes, Bacteroidetes, and Rhodobacteraceae, while reducing the abundance of Ralstonia and Vibrio. This indicates that added IPP may improve the digestive function and gut health of sea urchins. Overall, added IPP can improve certain economic traits and antioxidant capacity of sea urchins. This manuscript provides a theoretical reference for the healthful aquaculture of S. intermedius. Full article

This study aims to clarify the dose–response relationship between dietary β-carotene levels and gonadal pigment deposition and regulation mechanisms related to the carotenoid synthesis of Strongylocentrotus intermedius based on a 60-day feeding trial and subsequent transcriptome analysis. Adult sea urchins (initial weight: 9.33 ± 0.21 g) of three cages were given one of the dry feeds with different doses of β-carotene (0 mg/kg, 150 mg/kg, 300 mg/kg) or fresh kelp (Saccharina japonica). The results indicated that the weight gain rate (WGR) of sea urchins increased with the addition of β-carotene, with that of the C300 group being markedly higher than that of the C0 group. The addition of β-carotene significantly improved the redness (a*) and yellowness (b*) values of the gonads, with sea urchins in the C300 group exhibiting closest gonad coloration to those in the kelp-fed group. Meanwhile, β-carotene and echinenone in the gonads of the C300 group showed the highest contents, reaching 1.96 μg/kg and 11.97 μg/kg, respectively. Several differential genes, enriched in the pathways of steroid biosynthesis, oxidative phosphorylation, and ubiquitination, were screened based on transcriptome analysis. Real-time PCR further demonstrated that β-carotene significantly upregulated the expression of cholesterol 25-hydroxylase (CH25H), NADH dehydrogenase subunit 1 (ND1), NADH dehydrogenase subunit 2 (ND2), and NADH dehydrogenase subunit 4 (ND4) while it downregulated the expression of 24-dehydrocholesterol reductase (DHCR24). These results showed that 300 mg/kg β-carotene significantly increased the WGR, redness, and yellowness values, as well as the contents of β-carotene and echinenone in the gonads of S. intermedius. On the one hand, dietary β-carotene increased NADH enzyme activity, which participates in echinenone synthesis by donating electrons for the transformation of β-carotene to echinenone synthesis. On the other hand, the addition of β-carotene inhibited cholesterol synthesis by increasing the expression of CH25H and decreasing the expression of DHCR24, which could in turn increase the fluidity and permeability of the cell membranes and the transport efficiency of β-carotene and echinenone from the digestive tract to the gonads. These results provided fundamental insights into the production of sea urchin gonads with market-favored colors. Full article

To identify effective strategies for preserving the genetic diversity of Strongylocentrotus intermedius populations, this study employed 15 SSR loci and SSR-seq technology to construct three parental mating groups based on different genetic distances: relatively distant (0.33640), relatively close (0.13051), and mixed (0.29916). These mating groups were used to produce three corresponding offspring populations: the distant group (D), the close group (C), and the mixed group (M). A total of 150 offspring from these populations were genotyped to analyze the effects of parental genetic distance on the genetic diversity of their offspring. The results showed that the observed allele number (Na) in the D and M groups was 4.200 and 4.733, respectively, both lower than the parental family population (FP) group (5.000) but higher than the C group (3.571). The effective allele number (Ne) in the D and M groups was 2.782 and 2.728, respectively, slightly below that of the parental FP group (2.816) but greater than the C group (2.211). Similarly, the observed heterozygosity (Ho) in the D and M groups was 0.496 and 0.488, respectively, both below that of the parental FP group (0.522) but above the C group (0.447). The expected heterozygosity (He) in the D and M groups was 0.586 and 0.579, respectively, slightly lower than the parental FP group (0.595) but higher than the C group (0.487). Additionally, the polymorphism information content (PIC) in the D and M groups was 0.530 and 0.531, respectively, indicating high polymorphism, although slightly lower than the parental FP group (0.546) and significantly higher than the C group (0.438). These findings indicate that the genetic diversity of all the three offspring populations declined to varying degrees compared to the parental population, with the C group experiencing the most severe reduction. In contrast, the D and M groups maintained comparably higher levels of genetic diversity, which were comparable to each other. This study underscores the importance of increasing the genetic distance between parents or adopting mixed mating strategies to sustain genetic diversity in breeding populations. These approaches are recommended for future breeding programs to ensure the long-term conservation and sustainability of genetic resources. Full article

Rapid and coordinated test growth is crucial for maintaining the normal body shape of Strongylocentrotus intermedius juveniles. In total, 270 S. intermedius (1.19 ± 0.01 g) were randomly assigned to 18 floating cages. Three cages of sea urchins were fed kelp (Saccharina japonica) (control diet) or one of five formulated feeds with different carbohydrate-to-lipid ratios (C/L) (1, 2, 4, 8, and 16) for 90 days. The results suggested that the weight gain rate of S. intermedius fed C/L4 was markedly greater than that fed C/L1 and C/L16 except for kelp, C/L2, and C/L8. The test diameter (TD) and test height (TH) gain rates of S. intermedius fed C/L4 were markedly greater than those fed other dry feeds except for C/L2. The TH/TD of S. intermedius fed kelp was markedly greater than that fed dry feeds, except for C/L1 and C/L2. Juvenile S. intermedius fed C/L2 showed higher test magnesium content, larger holes, and longer and thinner trabeculae than those fed other dry feeds. Overall, juvenile S. intermedius fed C/L4 had the highest body weight gain rate and test growth rate among the formulated feed groups. Juveniles fed C/L2 had the most coordinated test growth reflected by TD/TH, which is comparable to those fed kelp. Therefore, the optimal C/L for rapid and coordinated test growth of juvenile S. intermedius should be higher than 2 but lower than 4. Full article

Growth differentiation among farmed sea urchins (Strongylocentrotus intermedius) poses a significant challenge to aquaculture, with there being a limited understanding of the underlying molecular mechanisms. In this study, sea urchins with varying growth rates, reared under identical conditions, were analyzed for feeding behavior, gut microbiota, and transcriptomes. Large-sized sea urchins demonstrated significantly higher feeding ability and longer duration than smaller ones. The dominant phyla across all size groups were Campylobacterota, Proteobacteria, and Firmicutes, with Campylobacterota showing the highest abundance in small-sized sea urchins (82.6%). However, the families Lachnospiraceae and Pseudomonadaceae were significantly less prevalent in small-sized sea urchins. Transcriptome analysis identified 214, 544, and 732 differentially expressed genes (DEGs) in the large vs. medium, large vs. small, and medium vs. small comparisons, respectively. Gene Ontology and KEGG pathway analyses associated DEGs with key processes such as steroid biosynthesis, protein processing within the endoplasmic reticulum, and nucleotide sugar metabolism. Variations in phagosomes and signaling pathways indicated that size differences are linked to disparities in energy expenditure and stress responses. These findings provide a foundation for future investigations into the regulatory mechanisms underlying growth differences in S. intermedius and provide clues for the screening of molecular markers useful to improve sea urchin production. Full article

To screen for immune indicators closely related to disease resistance, two species of sea urchin susceptible to black mouth disease (Strongylocentrotus intermedius, S. intermedius ♀ × Heliocidaris crassispina ♂) and three species of sea urchin resistant to black mouth disease (H. crassispina, H. crassispina ♀ × S. intermedius ♂ and Mesocentrotus nudus) were artificially infected with the black mouth pathogen Vibrio echinoideorum. The phagocytosis-related immune indices of the five sea urchin species were compared at different time points post-infection. The results demonstrated that the parameters such as apoptotic rate of phagocytes, mean contribution value (MCV) of single effective phagocyte on Acid Phosphatase (ACP), Reactive Oxygen Species (ROS), and Total Antioxidant Capacity (T-AOC) of the five sea urchin species first increased and then decreased after infection. The key time points were 3 h to 6 h and 48 h post-infection when the black mouth disease-resistant and susceptible sea urchins demonstrated differences. At 3 h or 6 h post-infection, the up-regulation folds in MCV of ACP, ROS and T-AOC of black mouth disease-resistant sea urchins were considerably higher than that of the susceptible sea urchins. At 6 h post-infection, the apoptosis rate and the phagocytic index (PI) of the black mouth disease-resistant sea urchins were significantly higher than those of the susceptible sea urchins (p < 0.05). At 48 h post-infection, the necrosis rate of phagocytes, MCV of ACP and MCV of ROS of the black mouth disease-resistant sea urchins were significantly lower than those of the susceptible sea urchins (p < 0.05). The apoptosis and necrosis rate of phagocytes, PI, and MCV on ACP, ROS may be used as indicators of disease resistance in sea urchins. Disease resistance standards in immune indices can be summarized as phagocytosis increases greatly in the early infection stage and decreases timely to a normal level after killing the pathogen in a short period. Full article

To establish a parentage identification method for Strongylocentrotus intermedius, 15 microsatellite loci and simple sequence repeat sequencing (SSR-seq) technology were used to perform SSR sequencing and typing of the validation population with known pedigree information and the simulation population. Cervus v3.0 was used for gene frequency statistics, simulated analysis, and parentage identification analysis. The results showed that, in validation population, using 15 microsatellite loci, the highest success rate of parent pairs identification was 86%, the highest success rate of female parent identification was 93%, and the highest success rate of male parent identification was 90%. The simulated population was analyzed using 12–15 loci, and the identification rate was up to 90%. In cases where accurate parentage was not achieved, individuals could exhibit genetic similarities with 1–3 male or female parents. Individuals identified as lacking a genetic relationship can be selected as parents to prevent inbreeding. This study shows that parent pairs or single parents of most offspring can be identified successfully using these 15 selected loci. The results lay a foundation for the establishment of a parentage identification method for S. intermedius. Full article

A 90 d feeding experiment was conducted to investigate the effects of vitamin E (VE) on growth, intestinal microbiota, immune response, and related gene expression of juvenile sea urchin (Strongylocentrotus intermedius). Six dry feeds were made to contain graded levels of VE (78, 105, 152, 235, 302, and 390 mg/kg); these were named E78, E105, E152, E235, E302, and E390, respectively. Dry feed E50 and fresh kelp (HD) were used as the control diets. There were six replicates of cages in each dietary group, and each cage held 20 sea urchins with an initial body weight of approximately 1.50 g. Results exhibited that weight gain rate and gonadosomatic index (GSI) of the sea urchins were not significantly affected by dietary VE ranging from 78 to 390 mg/kg. Sea urchins in the dry feed groups showed poorer growth performance, but significantly higher GSI than those in the fresh kelp groups. The pepsin and lipase activities were not significantly promoted by low or moderate VE, but were inhibited by a high level of VE (302–390 mg/kg), while amylase and cellulase activities were significantly increased by low or moderate VE, with the highest values observed in the E105 and E235 groups, respectively. VE addition at a low dosage (105–152 mg/kg) showed inhibitory effects on immune and antioxidant enzyme activities and expression of inflammation-related genes, but showed no beneficial effects at moderate or high dosage (235–390 mg/kg), while a moderate or relatively higher level of VE (235–302 mg/kg) significantly increased the expression of several immune-related genes. The relative abundance of Proteobacteria, Actinobacteria, Ruegeria, and Maliponia in the intestine of the sea urchins increased with the increase in VE in the dry feeds. On the contrary, the relative abundance of the Firmicutes, Bacteroidetes, Escherichia-Shigella, Bacteroides, and Clostridium sensu stricto 1 gradually decreased as VE content increased. These results indicated that a moderate level of VE (172.5–262.4) can achieve ideal digestive enzyme activities and growth performance, but a relatively higher level of VE (235–302 mg/kg) was beneficial for maintaining the immune and antioxidant capacity of juvenile S. intermedius by regulating the expression of inflammation- and immune-related genes and abundance of some bacteria to a healthy state. Full article

Screening for chitinolytic activity in the bacterial strains from different Pacific Ocean regions revealed that the highly active representatives belong to the genera Microbulbifer, Vibrio, Aquimarina, and Pseudoalteromonas. The widely distributed chitinolytic species was Microbulbifer isolated from the sea urchin Strongylocentrotus intermedius. Among seventeen isolates with confirmed chitinolytic activity, only the type strain P. flavipulchra KMM 3630^T and the strains of putatively new species Pseudoalteromonas sp. B530 and Vibrio sp. Sgm 5, isolated from sea water (Vietnam mollusc farm) and the sea urchin S. intermedius (Peter the Great Gulf, the Sea of Japan), significantly suppressed the hyphal growth of Aspergillus niger that is perspective for the biocontrol agents’ development. The results on chitinolytic activities and whole-genome sequencing of the strains under study, including agarolytic type strain Z. galactanivorans Dji^T, found the new functionally active chitinase structures and biotechnological potential. Full article

The sea cucumber Apostichopus japonicus and the sea urchin Strongylocentrotus intermedius are two commercially important species and are widely cultured in China. Here, a laboratory experiment was conducted for 34 days to assess whether the survival, growth and behavior performances are better in the new commercially valuable integrated multi-trophic aquaculture (IMTA) system (group M, 90 S. intermedius and 37 A. japonicus/10,638 cm³ of stocking density) than those in the control group for sea urchins (group U, 90 S. intermedius/10,638 cm³ of stocking density) and the control group for sea cucumbers (group C, 37 A. japonicus/10,638 cm³ of stocking density). We found that feeding behavior, crawling behavior, body length and body weight of sea cucumbers were significantly greater in group M than those in group C. These results suggest that the new IMTA system improves fitness-related behaviors and consequently leads to a better growth in A. japonicus while maintaining a high biomass. We further found that group M showed significantly larger body size and Aristotle’s lantern reflex as well as significantly lower mortality and morbidity in sea urchins, compared to those in group U. This suggests that the new IMTA system greatly improves feeding behavior and body growth, and survival of cultured S. intermedius. This IMTA system is a promising candidate to promote the production efficiency of juvenile A. japonicus (as primary species) and S. intermedius (as subsidiary species) in China. Full article