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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. [ABSTRACT FROM AUTHOR]

Polyploid breeding can produce new species with a faster growth rate, higher disease resistance, and higher survival rate, and has achieved significant economic benefits. This study investigated the protein differences in the body wall of triploid Apostichopus japonicus and diploid A. japonicus using isotope-labeled relative and absolute quantitative Tandem Mass Tag technology. A total of 21,096 independent peptides and 4621 proteins were identified. Among them, there were 723 proteins with significant expression differences, including 413 up-regulated proteins and 310 down-regulated proteins. The differentially expressed proteins (DEPs) were enriched in 4519 Gene Ontology enrichment pathways and 320 Kyoto Encyclopedia of Genes and Genomes enrichment pathways. Twenty-two key DEPs related to important functions such as growth and immunity of triploid A. japonicus were screened from the results, among which 20 were up-regulated, such as cathepsin L2 cysteine protease and fibrinogen-like protein A. Arylsulfatase A and zonadhesin were down-regulated. The up-regulated proteins were mainly involved in oxidative stress response, innate immune response, and collagen synthesis in triploid A. japonicus , and the down-regulated proteins were mainly associated with the sterility of triploid A. japonicus. In addition, the transcriptome and proteome were analyzed jointly to support proteome data. In this study, the differences in protein composition between triploid and diploid A. japonicus were analyzed for the first time, and the results revealed the underlying reasons for the growth advantage of triploid A. japonicus. [Display omitted] • The growth and development advantages of triploid A. japonicus were discussed. • The molecular mechanisms controlling the growth traits of triploid A. japonicus were analyzed. • The function of the screened differential proteins on triploid A. japonicus was thoroughly discussed. • The protein-protein interaction (PPI) network of the identified DEPs was examined. • The relationship between the transcriptome and proteome of triploid A. japonicus was examined. [ABSTRACT FROM AUTHOR]

Strongylocentrotus intermedius is one of the most economically valuable sea urchin species in China, and its growth and survival are severely constrained by ocean warming and the hypoxia that often accompanies high water temperatures. To elucidate the molecular mechanisms of S. intermedius that regulate gene expression in response to multi-causal environmental stresses. We performed a de novo transcriptome analysis of coelomocyte from S. intermedius to heat (25 °C), hypoxia (2 mg/L), and the combined stress. We identified 35,635, 29,107, and 29,440 differentially expressed genes (DEGs) in S. intermedius cultured under high temperature, low oxygen, and combined stress, respectively. Further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses revealed that these DEGs mainly enriched the functional categories of "Protein processing in endoplasmic reticulum," and "Glutathione metabolism" by heat stress, such as HSP70, GSTO1, PDIA4. After hypoxic stress, "Notch signaling pathway" and metabolism-related pathways such as "Glycerolipid metabolism", "Pyruvate metabolism" were significantly enriched. Exposure to combined stress resulted in a two-factor additive effect at the transcriptome level and have a more extensive impact on the immune correlated pathways in S. intermedius than single stress, the expression of related immune genes (C3, C5, and AIFM2) were up-regulated. Quantitative real-time PCR (qRT-PCR) analysis of the expression of 18 DEGs confirmed the RNA-Seq results. Observations in the present study will improve the understanding of the molecular mechanism of S. intermedius in response to multi-causal environmental stress. [Display omitted] • The transcriptome of S. intermedius under high temperature, hypoxia, and combined stresses was constructed. • A total of 35,635, 29,107, and 29,440 DEGs were identified under three stresses, respectively. • The transcriptome of S. intermedius showed a two-factor additive effect under combined stress. • S. intermedius demonstrated comprehensive transcriptional regulation in response to global climate change. [ABSTRACT FROM AUTHOR]

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. • The valuable database of miRNA was constructed for S. intermedius under V. harveyi infection. • A large number of miRANs and their targets, such as CALM1 , CAL1A2 , SPSB4 were response to V. harveyi infection. • The interaction of multiple mRNA-miRNAs in the immune-related process in S. intermedius. [ABSTRACT FROM AUTHOR]