Portunus pelagicus
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PROVIDER: PRJNA99275 | ENA |
REPOSITORIES: ENA
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Project description:BACKGROUND:Crustacean moulting is a complex process involving many regulatory pathways. A holistic approach to examine differential gene expression profiles of transcripts relevant to the moulting process, across all moult cycle stages, was used in this study. Custom cDNA microarrays were constructed for Portunus pelagicus. The printed arrays contained 5000 transcripts derived from both the whole organism, and from individual organs such as the brain, eyestalk, mandibular organ and Y-organ from all moult cycle stages. RESULTS:A total of 556 clones were sequenced from the cDNA libraries used to construct the arrays. These cDNAs represented 175 singletons and 62 contigs, resulting in 237 unique putative genes. The gene sequences were classified into the following biological functions: cuticular proteins associated with arthropod exoskeletons, farnesoic acid O-methyltransferase (FaMeT), proteins belonging to the hemocyanin gene family, lectins, proteins relevant to lipid metabolism, mitochondrial proteins, muscle related proteins, phenoloxidase activators and ribosomal proteins. Moult cycle-related differential expression patterns were observed for many transcripts. Of particular interest were those relating to the formation and hardening of the exoskeleton, and genes associated with cell respiration and energy metabolism. CONCLUSIONS:The expression data presented here provide a chronological depiction of the molecular events associated with the biological changes that occur during the crustacean moult cycle. Tracing the temporal expression patterns of a large variety of transcripts involved in the moult cycle of P. pelagicus can provide a greater understanding of gene function, interaction, and regulation of both known and new genes with respect to the moulting process.
2011-01-01 | S-EPMC3062621 | BioStudies
Project description:BACKGROUND: Crustaceans represent an attractive model to study biomineralization and cuticle matrix formation, as these events are precisely timed to occur at certain stages of the moult cycle. Moulting, the process by which crustaceans shed their exoskeleton, involves the partial breakdown of the old exoskeleton and the synthesis of a new cuticle. This cuticle is subdivided into layers, some of which become calcified while others remain uncalcified. The cuticle matrix consists of many different proteins that confer the physical properties, such as pliability, of the exoskeleton. RESULTS: We have used a custom cDNA microarray chip, developed for the blue swimmer crab Portunus pelagicus, to generate expression profiles of genes involved in exoskeletal formation across the moult cycle. A total of 21 distinct moult-cycle related differentially expressed transcripts representing crustacean cuticular proteins were isolated. Of these, 13 contained copies of the cuticle_1 domain previously isolated from calcified regions of the crustacean exoskeleton, four transcripts contained a chitin_bind_4 domain (RR consensus sequence) associated with both the calcified and un-calcified cuticle of crustaceans, and four transcripts contained an unannotated domain (PfamB_109992) previously isolated from C. pagurus. Additionally, cryptocyanin, a hemolymph protein involved in cuticle synthesis and structural integrity, also displays differential expression related to the moult cycle. Moult stage-specific expression analysis of these transcripts revealed that differential gene expression occurs both among transcripts containing the same domain and among transcripts containing different domains. CONCLUSION: The large variety of genes associated with cuticle formation, and their differential expression across the crustacean moult cycle, point to the complexity of the processes associated with cuticle formation and hardening. This study provides a molecular entry path into the investigation of the gene networks associated with cuticle formation.
2007-01-01 | S-EPMC2222620 | BioStudies
Project description:<h4>Background</h4>The swimming crab, Portunus trituberculatus, which is naturally distributed in the coastal waters of Asia-Pacific countries, is an important farmed species in China. Salinity is one of the most important abiotic factors that influence not only the distribution and abundance of crustaceans, it is also an important factor for artificial propagation of the crab. To better understand the interaction between salinity stress and osmoregulation, we performed a transcriptome analysis in the gills of Portunus trituberculatus challenged with salinity stress, using the Illumina Deep Sequencing technology.<h4>Results</h4>We obtained 27,696,835, 28,268,353 and 33,901,271 qualified Illumina read pairs from low salinity challenged (LC), non-challenged (NC), and high salinity challenged (HC) Portunus trituberculatus cDNA libraries, respectively. The overall de novo assembly of cDNA sequence data generated 94,511 unigenes, with an average length of 644 bp. Comparative genomic analysis revealed that 1,705 genes differentially expressed in salinity stress compared to the controls, including 615 and 1,516 unigenes in NC vs LC and NC vs HC respectively. GO functional enrichment analysis results showed some differentially expressed genes were involved in crucial processes related to osmoregulation, such as ion transport processes, amino acid metabolism and synthesis processes, proteolysis process and chitin metabolic process.<h4>Conclusion</h4>This work represents the first report of the utilization of the next generation sequencing techniques for transcriptome analysis in Portunus trituberculatus and provides valuable information on salinity adaptation mechanism. Results reveal a substantial number of genes modified by salinity stress and a few important salinity acclimation pathways, which will serve as an invaluable resource for revealing the molecular basis of osmoregulation in Portunus trituberculatus. In addition, the most comprehensive sequences of transcripts reported in this study provide a rich source for identification of novel genes in the crab.
2013-01-01 | S-EPMC3849447 | BioStudies
Project description:<h4>Background</h4>Molting is an essential biological process throughout the life history of crustaceans, which is regulated by many neuropeptide hormones expressed in the eyestalk. To better understand the molting mechanism in Portunus trituberculatus, we used digital gene expression (DGE) to analyze single eyestalk samples during the molting cycle by high-throughput sequencing.<h4>Results</h4>We obtained 14,387,942, 12,631,508 and 13,060,062 clean sequence reads from inter-molt (InM), pre-molt (PrM) and post-molt (PoM) cDNA libraries, respectively. A total of 1,394 molt-related differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analysis identified some important processes and pathways with key roles in molting regulation, such as chitin metabolism, peptidase inhibitor activity, and the ribosome. We first observed a pattern associated with the neuromodulator-related pathways during the molting cycle, which were up-regulated in PrM and down-regulated in PoM. Four categories of important molting-related transcripts were clustered and most of them had similar expression patterns, which suggests that there is a connection between these genes throughout the molt cycle.<h4>Conclusion</h4>Our work is the first molt-related investigation of P. trituberculatus focusing on the eyestalk at the whole transcriptome level. Together, our results, including DEGs, identification of molting-related biological processes and pathways, and observed expression patterns of important genes, provide a novel insight into the function of the eyestalk in molting regulation.
2017-01-01 | S-EPMC5386282 | BioStudies
Project description:A holistic approach to examine differential gene expression profiles of transcripts relevant to the moulting process, across all moult cycle stages, was used in this study. Custom cDNA microarrays were constructed for P. pelagicus. The printed arrays contained 5000 transcripts derived from both the whole organism, and from individual organs such as the brain, eyestalk, mandibular organ and Y-organ from all moult cycle stages. A total of 556 clones were sequenced from the cDNA libraries used to construct the arrays. These cDNAs represented 217 singlets and 62 contigs, resulting in 279 unique putative genes. Moult cycle-related differential expression patterns were observed for many transcripts. Keywords: cyclic moult stage comparison of the crab Portunus pelagicus Overall design: In order to identify differential gene expression across moult stages, two consecutive moult stages were compared on each array in a dual colour (Cy3 and Cy5) experiment. RNA samples were pooled across subjects in order to reduce the effect of biological variation (nine subjects were pooled across a total of three arrays) for each moult stage comparison. Equal amounts of total RNA from three crabs in one moult stage, were pooled, and compared against equal amounts of total RNA pooled from three crabs in another moult stage, on one array. This was repeated three times in total, the different moult stages were labelled with Cy3 or Cy5 respectively. Consecutive moult stages were compared in the following format; postmoult (Cy3) with intermoult (Cy5), intermoult (Cy3) with early premoult (Cy5), early premoult (Cy3) with late premoult (Cy5), late premoult (Cy3) with ecdysis (Cy5), and ecdysis (Cy3) with postmoult (Cy5).
2008-01-03 | GSE6997 | GEO
Project description:<h4>Background</h4>The swimming crab, Portunus trituberculatus, is an important farmed species in China, has been attracting extensive studies, which require more and more genome background knowledge. To date, the sequencing of its whole genome is unavailable and transcriptomic information is also scarce for this species. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive transcript dataset for major tissues of Portunus trituberculatus by the Illumina paired-end sequencing technology.<h4>Results</h4>Total RNA was isolated from eyestalk, gill, heart, hepatopancreas and muscle. Equal quantities of RNA from each tissue were pooled to construct a cDNA library. Using the Illumina paired-end sequencing technology, we generated a total of 120,137 transcripts with an average length of 1037 bp. Further assembly analysis showed that all contigs contributed to 87,100 unigenes, of these, 16,029 unigenes (18.40% of the total) can be matched in the GenBank non-redundant database. Potential genes and their functions were predicted by GO, KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literature, many putative genes with fundamental roles in growth and muscle development, including actin, myosin, tropomyosin, troponin and other potentially important candidate genes were identified for the first time in this specie. Furthermore, 22,673 SSRs and 66,191 high-confidence SNPs were identified in this EST dataset.<h4>Conclusion</h4>The transcriptome provides an invaluable new data for a functional genomics resource and future biological research in Portunus trituberculatus. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs. The molecular markers identified in this study will provide a material basis for future genetic linkage and quantitative trait loci analyses, and will be essential for accelerating aquaculture breeding programs with this species.
2014-01-01 | S-EPMC3983128 | BioStudies
Project description:Enhancing the production of aquatic animals is crucial for fishery management and aquaculture applications. Ovaries are specialized tissues that play critical roles in producing oocytes and hormones. Significant biochemical changes take place during the sexual maturation of Portunus trituberculatus, but the genetics of this process has not been extensively studied. Transcriptome sequencing can be used to determine gene expression changes within specific periods. In the current study, we used transcriptome sequencing to produce a comprehensive transcript dataset for the ovarian development of P. trituberculatus. Approximately 100 million sequencing reads were generated, and 126,075 transcripts were assembled. Functional annotation of the obtained transcripts revealed important pathways in ovarian development, such as those involving the vitellogenin gene. Also, we performed deep sequencing of ovaries in phases III and IV of sexual maturation in P. trituberculatus. Differential analysis of gene expression identified 506 significantly differentially expressed genes, which belong to 20 pathway, transporters, development, transcription factors, metabolism of other amino acids, carbohydrate and lipid, solute carrier family members, and enzymes. Taken together, our study provides the first comprehensive transcriptomic resource for P. trituberculatus ovaries, which will strengthen understanding of the molecular mechanisms underlying the sexual maturation process and advance molecular nutritional studies of P. trituberculatus.
2015-01-01 | S-EPMC4591999 | BioStudies
Project description:An 8-weeks feeding trial with swimming crab, Portunus trituberculatus, was conducted to investigate the effects of different dietary lipid sources on the lipid classes, lipid metabolism, and mitochondrial energy metabolism relevant genes expression. Six isonitrogenous and isolipidic experimental diets were formulated to contain fish oil (FO), krill oil (KO), palm oil (PO), rapeseed oil (RO), soybean oil (SO), and linseed oil (LO), respectively. A total of 270 swimming crab juveniles (initial weight 5.43 ± 0.03 g) were randomly divided into six diets with three replications, each consisted of 45 juvenile crabs. The results revealed that crabs fed KO had highest lipid content in hepatopancreas and free fatty acids in serum among all diets. The anabolic pathway relevant genes: fas and acc were up-regulated in KO diet. The catabolic pathway relevant genes, hsl, was up-regulated in LO diet, while cpt1 was up-regulated in KO diet. Whereas, the genes involved in the transport and uptake of fatty acids such as fabp1 and fatp4 were down-regulated in crab fed PO and RO diets. Furthermore, the gene expression levels of transcription factors: srebp-1 and hnf4? in KO and SO diets were the highest among all diets. FO and KO diets had significantly higher unsaturation index of mitochondrial membrane than others. The genes related to mitochondrial energy metabolism, such as Atpase6, sirt1, and sirt3 were significantly up-regulated in KO and SO diets. In summary, dietary KO and SO supplementation could improve the lipid metabolism, promote energy production for juvenile swimming crab and improve physiological process and function including molting. These findings could contribute to deepen the understanding of the physiological metabolism of dietary fatty acids for swimming crab.
2019-01-01 | S-EPMC6491875 | BioStudies
Project description:MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate gene expression in organisms. To understand the underlying mechanisms behind the molecular response of the crab to low salt-stress, high-throughput Illumina/Solexa deep sequencing technology was used to investigate the expression profiles of miRNAs under low salinity challenged. Two mixed RNA pool libraries of gill tissues from low salinity challenged (LC) and the control groups (NC) were sequenced on the Illumina platform. A total of 6,166,057 and 7,032,973 high-quality reads were obtained from the NC and LC libraries, respectively. Sixty-seven miRNAs consisting of 16 known and 51 novel ones were identified, among which, 12 miRNAs were differentially expressed in LC compared to NC. Thirty-four of the target genes predicted were differentially expressed in the opposite direction to the miRNAs, which were involved in crucial processes related to osmoregulation by gene ontology (GO) functional enrichment analysis, such as anion transport processes (GO:0006820) and chitin metabolic process (GO:0006030). These results provide a basis for further investigation of the miRNA-modulating networks in osmoregulation of Portunus trituberculatus.
2016-01-01 | S-EPMC4679733 | BioStudies
Project description:The swimming crab Portunus trituberculatus is a commercially important crab species in East Asia countries. Gonadal development is a physiological process of great significance to the reproduction as well as commercial seed production for P. trituberculatus. However, little is currently known about the molecular mechanisms governing the developmental processes of gonads in this species. To open avenues of molecular research on P. trituberculatus gonadal development, Illumina paired-end sequencing technology was employed to develop deep-coverage transcriptome sequencing data for its gonads. Illumina sequencing generated 58,429,148 and 70,474,978 high-quality reads from the ovary and testis cDNA library, respectively. All these reads were assembled into 54,960 unigenes with an average sequence length of 879 bp, of which 12,340 unigenes (22.45% of the total) matched sequences in GenBank non-redundant database. Based on our transcriptome analysis as well as published literature, a number of candidate genes potentially involved in the regulation of gonadal development of P. trituberculatus were identified, such as FAOMeT, mPR?, PGMRC1, PGDS, PGER4, 3?-HSD and 17?-HSDs. Differential expression analysis generated 5,919 differentially expressed genes between ovary and testis, among which many genes related to gametogenesis and several genes previously reported to be critical in differentiation and development of gonads were found, including Foxl2, Wnt4, Fst, Fem-1 and Sox9. Furthermore, 28,534 SSRs and 111,646 high-quality SNPs were identified in this transcriptome dataset. This work represents the first transcriptome analysis of P. trituberculatus gonads using the next generation sequencing technology and provides a valuable dataset for understanding molecular mechanisms controlling development of gonads and facilitating future investigation of reproductive biology in this species. The molecular markers obtained in this study will provide a fundamental basis for population genetics and functional genomics in P. trituberculatus and other closely related species.
2015-01-01 | S-EPMC4456094 | BioStudies