Identification of Neuropeptides Using Long-Read RNA-Seq in the Swimming Crab Portunus trituberculatus, and Their Expression Profile Under Acute Ammonia Stress.
Ontology highlight
ABSTRACT:
SUBMITTER: Wang D
PROVIDER: S-EPMC9149262 | biostudies-literature | 2022
REPOSITORIES: biostudies-literature
Publications
Identification of Neuropeptides Using Long-Read RNA-Seq in the Swimming Crab <i>Portunus trituberculatus</i>, and Their Expression Profile Under Acute Ammonia Stress.
Wang Daixia D Liu Xiaochen X Zhang Jingyan J Gao Baoquan B Liu Ping P Li Jian J Meng Xianliang X
Frontiers in physiology 20220516
Similar Datasets
Project description:Neuropeptides and their G protein-coupled receptors (GPCRs) regulate multiple physiological processes. Currently, little is known about the identity of native neuropeptides and their receptors in Portunus trituberculatus. This study employed RNA-sequencing and reverse transcription-polymerase chain reaction (RT-PCR) techniques to identify neuropeptides and their receptors that might be involved in regulation of reproductive processes of P. trituberculatus. In the central nervous system transcriptome data, 47 neuropeptide transcripts were identified. In further analyses, the tissue expression profile of 32 putative neuropeptide-encoding transcripts was estimated. Results showed that the 32 transcripts were expressed in the central nervous system and 23 of them were expressed in the ovary. A total of 47 GPCR-encoding transcripts belonging to two classes were identified, including 39 encoding GPCR-A family and eight encoding GPCR-B family. In addition, we assessed the tissue expression profile of 33 GPCRs (27 GPCR-As and six GPCR-Bs) transcripts. These GPCRs were found to be widely expressed in different tissues. Similar to the expression profiles of neuropeptides, 20 of these putative GPCR-encoding transcripts were also detected in the ovary. This is the first study to establish the identify of neuropeptides and their GPCRs in P. trituberculatus, and provide information for further investigations into the effect of neuropeptides on the physiology and behavior of decapod crustaceans.
| S-EPMC8449533 | biostudies-literature
Project description:BackgroundMyogenic factor 6 (Myf6) plays an important role in muscle growth and differentiation. In aquatic animals and livestock, Myf6 contributes to improving meat quality and strengthening the accumulation of muscle flavor substances. However, studies on Myf6 gene polymorphisms in crustaceans have not been reported.ResultsIn the current study, we characterized the Myf6 gene for Portunus trituberculatus to better understand its biological function. The full-length cDNA of Myf6 was 4,101 bp, with a 915 bp open reading frame encoding 304 amino acids. In addition, Myf6 included a conservative bHLH domain. Homology analysis showed that Myf6 shared the highest identity with Penaeus vannamei. Expression pattern analysis of Myf6 in fast- and slow-growing groups revealed that the expression level of the latter was significantly higher than that of the former (P < 0.05). qPCR studies revealed that Myf6 was expressed in various tissues with the highest level in muscle. Nineteen single nucleotide polymorphisms (SNPs) of Myf6 were identified and five of them were significantly associated with growth-related traits of P. trituberculatus (P < 0.05), including full carapace width, carapace length, body height, and body weight. The AG and GG genotypes of g.1,187,834 A > G exhibited superior growth-related traits than the AA genotype. In the combined genotypes of g.1,187,324 C > T and g.1,187,834 A > G, the average body weight of diplotype D5 (CT-GG) was higher than that of diplotype D1 (CC-AA), D2 (CC-AG), and D3 (CC-GG) in a cultivated population. A haploblock was generated by three significant SNPs (g.1187834 A > G, g.1188616 A > G, and g.1189024 C > A), containing four haplotypes (AAA, AAC, AGC, and GGC), among which GGC haplotype exhibited superior growth traits (full carapace width and body weight) than the AAA haplotype.ConclusionsTo our knowledge, this is the first report on Myf6 in crustaceans. The results of this study would contribute to elucidating multiple functions of the Myf6 gene in crustaceans and exploring the potential as a candidate gene in selective breeding programs of P. trituberculatus.
| S-EPMC11684091 | biostudies-literature
Project description:The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking. Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with an N50 length of 21.80 Mb by Hi-C technology. We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction.
| S-EPMC6944217 | biostudies-literature
Project description:The neuropeptide corazonin (Crz) exerts diverse physiological effects in insects, yet its role in crustaceans remains elusive. The abundant expression of Crz receptor (CrzR) in the Y-organs of several crustaceans suggests a potential involvement of Crz in regulating ecdysteroid synthesis. In this study, we examined the effects of PtCrz on ecdysteroid synthesis during the molting period of Portunus trituberculatus through PtCrz treatments and PtCrzR silencing. Our results showed that PtCrz peptide stimulates ecdysteroid levels and the gene expression involved in ecdysteroidogenesis both in vitro and in vivo, whereas dsPtCrzR treatments had opposite effects on ecdysteroid levels and associated gene expression. Thus, our study suggests that PtCrz may modulate ecdysteroid synthesis via Y-organ-expressed PtCrzR. Furthermore, we also discovered the involvement of PtCrz/PtCrzR signaling in regulating PtETH expression. Notably, the inhibitory effect of dsPtCrzR on ecdysteroid synthesis or PtETH expression can be reversed by PtCrz treatment, suggesting the potential existence of multiple receptors for PtCrz. This study provides new insights into the function of crustacean Crz and, for the first time, elucidates the presence of a neuropeptide that can stimulate ecdysteroid synthesis in crustaceans.
| S-EPMC11352189 | biostudies-literature
Project description:BackgroundTemperature is an important environment factor that is critical to the survival and growth of crustaceans. However, the mechanisms by which crustaceans detect changes in temperature are still unclear. The transient receptor potential (TRP) channels are non-selective cation channels well known for properties in temperature sensation. However, comprehensive understandings on TRP channels as well as their temperature sensing functions are still lacking in crustaceans.ResultsIn this study, a total of 26 TRP genes were identified in the swimming crab, Portunus trituberculatus, which can be classified into TRPA, TRPC, TRPP, TRPM, TRPML, TRPN and TRPV. Tissue expression analysis revealed a wide distribution of these TRP genes in P. trituberculatus, and antennules, neural tissues, and ovaries were the most commonly expressed tissues. To investigate the responsiveness of TRP genes to the temperature change, 18 TRPs were selected to detect their expression after high and low temperature stress. The results showed that 12 TRPs showed induced gene expression in both high and low temperature groups, while 3 were down-regulated in the low temperature group, and 3 showed no change in expression in either group.ConclusionsThis study characterized the TRP family genes in P. trituberculatus, and explored their involvement in response to temperature stress. Our results will enhance overall understanding of crustacean TRP channels and their possible functions.
| S-EPMC10795286 | biostudies-literature
Project description:Molting is one of the most important biological processes of crustacean species, and a number of molecular mechanisms facilitate this complex procedure. However, the understanding of the immune mechanisms underlying crustacean molting cycle remains very limited. This study performed transcriptome sequencing in hemolymph and hepatopancreas of the swimming crab (Portunus trituberculatus) during the four molting stages: post-molt (AB), inter-molt (C), pre-molt (D), and ecdysis (E). The results showed that there were 78,572 unigenes that were obtained in the hemolymph and hepatopancreas of P. trituberculatus. Further analysis showed that 98 DEGs were involved in immunity response of hemolymph and hepatopancreas, and most of the DEGs participated in the process of signal transduction, pattern recognition proteins/receptors, and antioxidative enzymes system. Specifically, the key genes and pathway involved in signal transduction including the GPCR126, beta-integrin, integrin, three genes in mitogen-activated protein kinase (MAPK) signaling cascade (MAPKKK10, MAPKK4, and p38 MAPK), and four genes in Toll pathway (Toll-like receptor, cactus, pelle-like kinase, and NFIL3). For the pattern recognition proteins/receptors, the lowest expression level of 11 genes was found in the E stage, including C-type lectin receptor, C-type lectin domain family 6 member A and SRB3/C in the hemolymph, and hepatopancreatic lectin 4, C-type lectin, SRB, Down syndrome cell adhesion molecule homolog, Down syndrome cell adhesion molecule isoform, and A2M. Moreover, the expression level of copper/zinc superoxide dismutase isoform 4, glutathione peroxidase, glutathione S-transferase, peroxiredoxin, peroxiredoxin 6, and dual oxidase 2 in stage C or stage D significantly higher than that of stage E or stage AB. These results fill in the gap of the continuous transcriptional changes that are evident during the molting cycle of crab and further provided valuable information for elucidating the molecular mechanisms of immune regulation during the molting cycle of crab.
| S-EPMC9659622 | biostudies-literature
Project description:Transcription activator proteins are regulatory proteins that bind to the promoter regions of target genes. Transcription activator protein-1 (AP-1) regulates numerous genes related to the immune system, apoptosis, and proliferation. In this study, the full-length cDNA of AP-1 from Portunus trituberculatus (PtAP-1) was identified by expressed sequence tag analysis and cDNA-end rapid amplification. The gene is 1183 bp and encodes a 256-amino acid protein with a predicted molecular mass and isoelectric point of 28.96 kDa and 8.90, respectively. PtAP-1 showed the highest expression level in the gonad tissue and the lowest expression level in blood, hemocyte, muscle, hepatopancreas, and gill, during the first 6 h of low-salinity stimulation (10%). Additionally, we observed steady decreases in PtAP-1 mRNA expression in the gill, but at 12 h, expression was initially upregulated, followed by a significant decrease until restoration to baseline levels at 48 h. Additionally, Vibrio alginolyticus challenge resulted in significant upregulation of PtAP-1 expression in the first 6 h, which was maintained at high levels for 48 h. From 48 to 72 h, we observed decreases in PtAP-1 levels, although they remained significantly higher than those detected at baseline. These results suggested that PtAP-1 is involved in the immune response and osmoregulation of crustaceans.
| S-EPMC6237694 | biostudies-literature
Project description:The quality of crustacean aquatic products is affected by feed. Cholesterol (CHO), an essential element for crustacean growth, has been widely supplemented in diet, but its food quality regulation remains unclear. The study aimed to investigate the effects of different dietary CHO levels (0.12%, 1.00%, and 2.50%) on the nutritional value and flavor quality in the edible parts of female swimming crabs (Portunus trituberculatus). Results showed that dietary CHO levels significantly increased lipid content in the hepatopancreas and promoted the accumulation of n-3 long-chain polyunsaturated fatty acids (LC-PUFA) in the hepatopancreas and muscle by activating the gene expression related to biosynthesis pathways. However, with dietary CHO levels increased, protein content in muscle decreased significantly. This may be related to dietary CHO supplementation (especially 2.50% CHO level) suppressed amino acid accumulation in the hepatopancreas and muscle by downregulating the target of the rapamycin pathway and upregulating amino acid catabolism-related genes. Moreover, 1.00% CHO treatment had higher relative levels of volatiles, producing grassy, fruity, and fatty odors in muscle, which may be due to the upregulation of the branched-chain amino acid transaminase (bcat) expression level. Dietary CHO weakened nucleotide and free amino acid accumulation in hepatopancreas and muscle. Overall, this study suggests that dietary 1.00% CHO level had higher LC-PUFA and pleasing flavor substances in muscle but was not conducive to hepatopancreatic protein and flavor nucleotide deposition of swimming crab.
| S-EPMC11324362 | biostudies-literature
Project description:Portunus trituberculatus holds significant economic value. The spermatogenesis is regulated by numerous signaling pathways. Among them, the TGF-β signaling pathway plays an important role in the development of testes and spermatogenesis. Smad4 is a Co-Smad protein that forms a complex with R-Smad to regulate the expression of target genes. The sperm structure in crustaceans differs greatly from that in mammals, with mature sperm lacking tails. Our previous studies have reported the function of R-Smad in the spermatogenesis of P. trituberculatus. In this study, we cloned the full-length cDNA sequence of PTSMAD4; immunofluorescence technology revealed that PTSMAD4 is expressed throughout all stages of spermatogenesis. We knocked down the expression of PTSMAD4 in P. trituberculatus using RNAi technology, and the immunofluorescence results show abnormal co-localization and weakened signals of PTSMAD4 and PTSMAD2. Additionally, transcriptome sequencing results enriched functional genes and pathways related to spermatogenesis. This study indicates that PTSMAD4 may participate in the spermatogenesis process through its involvement in signal transduction. This research not only lays the foundation for further study of the function of the TGF-β signaling pathway in spermatogenesis but also provides a theoretical basis for further investigation of the spermatogenesis mechanism in crustaceans.
| S-EPMC11642582 | biostudies-literature
Project description:Carbohydrate is the cheapest source of energy among the three major nutrient groups, an appropriate amount of carbohydrates can reduce feed cost and improve growth performance, but carnivorous aquatic animals cannot effectively utilize carbohydrates. The objectives of the present study are aimed at exploring the effects of dietary corn starch levels on glucose loading capacity, insulin-mediated glycemic responses, and glucose homeostasis for Portunus trituberculatus. After two weeks of feeding trial, swimming crabs were starved and sampled at 0, 1, 2, 3, 4, 5, 6, 12, and 24 hours, respectively. The results indicated that crabs fed diet with 0% corn starch exhibited lower glucose concentration in hemolymph than those fed with the other diets, and glucose concentration in hemolymph remained low with the extension of sampling time. The glucose concentration in hemolymph of crabs fed with 6% and 12% corn starch diets reached the peak after 2 hours of feeding; however, the glucose concentration in hemolymph of crabs fed with 24% corn starch attained the highest value after 3 hours of feeding, and the hyperglycemia lasted for 3 hours and decreased rapidly after 6 hours of feeding. Enzyme activities in hemolymph related to glucose metabolism such as pyruvate kinase (PK), glucokinase (GK), and phosphoenolpyruvate carboxykinase (PEPCK) were significantly influenced by dietary corn starch levels and sampling time. Glycogen content in hepatopancreas of crabs fed with 6% and 12% corn starch first increased and then decreased; however, the glycogen content in hepatopancreas of crabs fed with 24% corn starch significantly increased with the prolongation of feeding time. In the 24% corn starch diet, insulin-like peptide (ILP) in hemolymph reached a peak after 1 hour of feeding and then significantly decreased, whereas crustacean hyperglycemia hormone (CHH) was not significantly influenced by dietary corn starch levels and sampling time. ATP content in hepatopancreas peaked at 1 h after feeding and then decreased significantly in different corn starch feeding groups, while the opposite trend was observed in NADH. The activities of mitochondrial respiratory chain complexes I, II, III, and V of crabs fed with different corn starch diets significantly increased first and then decreased. In addition, relative expressions of genes related to glycolysis, gluconeogenesis, glucose transport, glycogen synthesis, insulin signaling pathway, and energy metabolism were significantly affected by dietary corn starch levels and sampling time. In conclusion, the results of the present study reveal glucose metabolic responses were regulated by different corn starch levels at different time points and play an important role in clearing glucose through increased activity of insulin, glycolysis, and glycogenesis, along with gluconeogenesis suppression.
| S-EPMC9973156 | biostudies-literature