Transcriptome analysis of the differences in gene expression between testis and ovary in green mud crab (Scylla paramamosain)

Whole transcriptome RNA sequencing provides novel insights into the molecular dynamics of ovarian development in mud crab, Scylla paramamosain after mating

Ovarian development in animals is a complicated biological process, requiring the simultaneous coordination among various genes and pathways. To understand the dynamic changes and molecular regulatory mechanisms of ovarian development in mud crab (Scylla paramamosain), both histological observation and whole transcriptome sequencing of ovarian tissues at different mating stages were implemented in this study. The histological results revealed that ovarian development was delayed in unmated females (60 days after courtship behavior but not mating), who exhibited an oocyte diameter of 56.38 ± 15.17 μm. Conversely, mated females exhibited accelerated the ovarian maturation process, with females reaching ovarian stage III (proliferative stage) 23 days after mating and attained an average oocyte diameter of 132.19 ± 15.07 μm. Thus, mating process is essential in promoting the rapid ovarian development in mud crab. Based on the whole transcriptome sequencing analysis, a total of 518 mRNAs, 1502 lncRNAs, 18 circRNAs and 151 miRNAs were identified to be differentially expressed between ovarian tissues at different mating stages. Notably, six differentially expressed genes (DEGs) associated with ovarian development were identified, including ovary development-related protein, red pigment concentrating hormone receptor, G2/mitotic-specific cyclin-B3-like, lutropin-chorio gonadotropic hormone receptor, renin receptor, and SoxB2. More importantly, both DEGs and targets of differentially expressed non-coding RNAs (DEncRNAs) were enriched in renin-angiotensin system, TGF-β signaling, cell adhesion molecules, MAPK signaling pathway, and ECM-receptor interaction, suggesting that these pathways may play significant roles in the ovarian development of mud crabs. Moreover, competition endogenous RNA (ceRNA) networks were constructed while mRNAs were differentially expressed between mating stages were involved in Gene Ontology (GO) biological processes such as developmental process, reproduction, and growth. These findings could provide solid foundations for the future development of female mud crab maturation enhancement strategy, and improve the understanding of the ovarian maturation process in crustaceans.

Identification and function analysis of steroid hormone synthesis pathway-related gene-Hsd3b in Scylla paramamosain

Mud crab (Scylla paramamosain) has become an important mariculture crab along the southeast coast of China due to its strong adaptability, delicious taste, and rich nutrition. Several vertebrate steroid hormones and their synthesis-related genes and receptors have been found in crustaceans, but there are few reports on their synthesis process and mechanism. 3-beta-hydroxysteroid dehydrogenase (HSD3B) is a member of the Short-chain Dehydrogenase/Reductase (SDR) family, and an indispensable protein in vertebrates' steroid hormone synthesis pathway. In this study, the SpHsd3b gene sequence was obtained from the transcriptome data of S. paramamosain, and its full-length open reading frame (ORF) was cloned. The spatial and temporal expression pattern of SpHsd3b was performed by quantitative real-time PCR (qRT-PCR). SpHsd3b dsRNA interference (RNAi) and HSD3B inhibitor (trilostane) were used to analyze the function of SpHSD3B. The results showed that the SpHsd3b gene has an 1113 bp ORF encoding 370 amino acids with a 3β-HSD domain. SpHSD3B has lower homology with HSD3B of vertebrates and higher homology with HSD3B of crustaceans. SpHsd3b was expressed in all examined tissues in mature crabs, and its expression was significantly higher in the testes than in the ovaries. SpHsd3b expression level was highest in the middle stage of testicular development, while its expression was higher in the early and middle stages of ovarian development. RNAi experiment and trilostane injection results showed that SpHSD3B had regulatory effects on several genes related to gonadal development and steroid hormone synthesis. 15-day trilostane suppression could also inhibit ovarian development and progesterone level of hemolymph. According to the above results, crustaceans may have steroid hormone synthesis pathways like vertebrates, and the Hsd3b gene may be involved in the gonadal development of crabs. This study provides further insight into the function of genes involved in steroid hormone synthesis in crustaceans.

Gonadal Transcriptomic Analysis Reveals Novel Sex-Related Genes in Bactrocera dorsalis

Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) is one of the most devastating agricultural pests worldwide due to its high reproductive and invasive abilities. The elucidation of its gonadal developmental characteristics and the identification of sex-related genes will provide a useful genetic basis for reproductive-based pest control. Here, the gonadal transcriptome of B. dorsalis was sequenced, and novel gonad-specific expressed genes were analyzed. A total of 1338, 336, 35, and 479 differentially expressed genes (DEGs) were found in the testis (TE), ovary (OV), female accessory gland (FAG), and male accessory gland (MAG), respectively. Furthermore, 463 highly expressed gonad-specific genes were identified, with the TE having the highest number of specific highly expressed genes, at 402, followed by 51 in the OV, 9 in the MAG, and only 1 in the FAG. Strikingly, approximately half of highly expressed gonad-specific genes were uncharacterized. Then, it was found that 35, 17, 3, 2, and 1 of 202 uncharacterized highly expressed TE-specific genes encoded proteins that contained transmembrane domains, signal peptides, high-mobility group boxes, the zinc finger domain, and the BTB/POZ domain, respectively. Interestingly, approximately 40% of uncharacterized highly expressed gonad-specific genes encoding proteins were not predicted to possess functional motifs or domains. Finally, the spatiotemporal expression and sequence characterization of six novel highly expressed gonad-specific genes were analyzed. Altogether, our findings provide a valuable dataset for future functional analyses of sex-related genes and potential target sites for pest control.

Comparative transcriptome analysis of ovaries and testes reveals sex-biased genes and pathways in zebrafish

Zebrafish (Danio rerio) is a widely recognized and extensively studied model organism in scientific research. The regulatory mechanism of gonadal development and differentiation of this species has aroused considerable attention. Nonetheless, the major sex-biased genes and pathways associated with gonadal development remain elusive. Therefore, to comprehend this intricate process, gonadal transcriptome sequencing was carried out to identify differentially expressed genes (DEGs) between the testes and ovaries of adult zebrafish. The preliminary assessment yielded a total of 23,529,272 and 23,521,368 clean reads from the cDNA libraries of ovaries and testes. Afterward, a comparative analysis of the transcriptome revealed 3,604 upregulated and 11,371 downregulated DEGs in the ovaries compared to the testes. Of these genes, 428 were exclusively expressed in females, while 3,516 were exclusively expressed in males. Additionally, further assessments were conducted to explore the functions associated with these DEGs in various biological processes. The data revealed their involvement in sex-biased pathways, such as progesterone-mediated oocyte maturation, oocyte meiosis, cytokine-cytokine receptor interaction, and cardiac muscle contraction. Finally, the expression levels of 14 sex-biased DEGs (cdc20, ccnb1, ypel3, chn1, bmp15, rspo1, tnfsf10, egfra, acta2, cox8a, gsdf, dmrt1, star, and cyp17a1) associated with the enriched pathways were subjected to further validation through qRT-PCR. The data acquired from these investigations offer valuable resources to support further exploration of the mechanisms governing sexual dimorphism and gonadal development in zebrafish.

Gut diazotrophs in lagomorphs are associated with season but not altitude and host phylogeny

Invertebrates such as termites feeding on nutrient-poor substrate receive essential nitrogen by biological nitrogen fixation of gut diazotrophs. However, the diversity and composition of gut diazotrophs of vertebrates such as Plateau pikas living in nutrient-poor Qinghai-Tibet Plateau remain unknown. To fill this knowledge gap, we studied gut diazotrophs of Plateau pikas (Ochotona curzoniae) and its related species, Daurian pikas (Ochotona daurica), Hares (Lepus europaeus) and Rabbits (Oryctolagus cuniculus) by high-throughput amplicon sequencing methods. We analyzed whether the gut diazotrophs of Plateau pikas are affected by season, altitude, and species, and explored the relationship between gut diazotrophs and whole gut microbiomes. Our study showed that Firmicutes, Spirochaetes, and Euryarchaeota were the dominant gut diazotrophs of Plateau pikas. The beta diversity of gut diazotrophs of Plateau pikas was significantly different from the other three lagomorphs, but the alpha diversity did not show a significant difference among the four lagomorphs. The gut diazotrophs of Plateau pikas were the most similarly to that of Rabbits, followed by Daurian pikas and Hares, which was inconsistent with gut microbiomes or animal phylogeny. The dominant gut diazotrophs of the four lagomorphs may reflect their living environment and dietary habits. Season significantly affected the alpha diversity and abundance of dominant gut diazotrophs. Altitude had no significant effect on the gut diazotrophs of Plateau pikas. In addition, the congruence between gut microbiomes and gut diazotrophs was low. Our results proved that the gut of Plateau pikas was rich in gut diazotrophs, which is of great significance for the study of ecology and evolution of lagomorphs.

De novo transcriptional analysis of the response to starvation stress in the white ridgetail prawn, Exopalaemon carinicauda

To study the mechanism of the biomolecular response in Exopalaemon carinicauda to starvation stress, we subjected muscle tissue RNA samples from four stress points, including 0 d(control group), 10 d, 20 d, and 30 d, to starvation stress on white ridgetail prawn with a body weight of 1.41 + 0.42 g, aquaculture water temperature of 23-25 °C, salinity of 26, dissolved oxygen ≥5 mg/L, and pH 8-8.5, Then performed de novo transcriptome assembly and gene expression analysis using BGISEQ-500 with a tag-based digital gene expression (DGE) system. By de novo assembling at the four times, we obtained 28,167, 21,115, 24,497, and 27,080 reads, respectively. The results showed that the stress at 10 d led to no significant difference in the expressed genes, while the stress at 20 d and 30 d showed a significant increase (or decrease) in the expression of 97 (276) and 143 (410) genes, respectively, which were involved in 8 different metabolic pathways. In addition, we detected 2647 unigene transcription factors. Eleven upregulated and sixteen downregulated genes from the different starvation stress groups were choose to verify the reliability of the transcriptome data, and the results showed that the expression trends of these genes were consistent with the results shown by the transcriptome. The analysis of the experimental data and our discussion of the response mechanism of white ridgetail prawn under starvation stress provides a foundation for further screening of the key genes of starvation stress and may help to elucidate their functions.

Testis cell pyroptosis mediated by CASP1 and CASP4: possible sertoli cell-only syndrome pathogenesis

BACKGROUND

Sertoli cell-only syndrome (SCOS) is the most serious pathological type of non-obstructive azoospermia. Recently, several genes related to SCOS have been identified, including FANCM, TEX14, NR5A1, NANOS2, PLK4, WNK3, and FANCA, but they cannot fully explain the pathogenesis of SCOS. This study attempted to explain spermatogenesis dysfunction in SCOS through testicular tissue RNA sequencing and to provide new targets for SCOS diagnosis and therapy.

METHODS

We analyzed differentially expressed genes (DEGs) based on RNA sequencing of nine patients with SCOS and three patients with obstructive azoospermia and normal spermatogenesis. We further explored the identified genes using ELISA and immunohistochemistry.

RESULTS

In total, 9406 DEGs were expressed (Log2|FC|≥ 1; adjusted P value < 0.05) in SCOS samples, and 21 hub genes were identified. Three upregulated core genes were found, including CASP4, CASP1, and PLA2G4A. Thus, we hypothesized that testis cell pyroptosis mediated by CASP1 and CASP4 might be involved in SCOS occurrence and development. ELISA verified that CASP1 and CASP4 activities in the testes of patients with SCOS were significantly higher than those in patients with normal spermatogenesis. Immunohistochemical results showed that CASP1 and CASP4 in the normal spermatogenesis group were mainly expressed in the nuclei of spermatogenic, Sertoli, and interstitial cells. CASP1 and CASP4 in the SCOS group were mainly expressed in the nuclei of Sertoli and interstitial cells because of the loss of spermatogonia and spermatocytes. CASP1 and CASP4 expression levels in the testes of patients with SCOS were significantly higher than those in patients with normal spermatogenisis. Furthermore, the pyroptosis-related proteins GSDMD and GSDME in the testes of patients with SCOS were also significantly higher than those in control patients. ELISA also showed that inflammatory factors (IL-1 β, IL-18, LDH, and ROS) were significantly increased in the SCOS group.

CONCLUSIONS

For the first time, we found that cell pyroptosis-related genes and key markers were significantly increased in the testes of patients with SCOS. We also observed many inflammatory and oxidative stress reactions in SCOS. Thus, we propose that testis cell pyroptosis mediated by CASP1 and CASP4 could participate in SCOS occurrence and development.

Eyestalk neuropeptide identification in the female red deep-sea crab, Chaceon quinquedens

Eyestalk-derived neuropeptides, primarily the crustacean hyperglycemic hormone (CHH) neuropeptide family, regulate vitellogenesis in decapod crustaceans. The red deep-sea crab, Chaceon quinquedens, a cold-water species inhabiting depths between 200 and 1800 m, has supported a small fishery, mainly harvesting adult males in the eastern US for over 40 years. This study aimed to understand the role of eyestalk-neuropeptides in vitellogenesis in C. quinquedens with an extended intermolt stage. Chromatography shows two CHH and one MIH peak in the sinus gland, with a CHH2 peak area four times larger than CHH1. The cDNA sequence of MIH and CHH of C. quinquedens is isolated from the eyestalk ganglia, and the qPCR assay shows MIH is significantly higher only at ovarian stages 3 than 4 and 5. However, MIH transcript and its neuropeptides do differ between stages 1 and 3. While CHH transcripts remain constant, its neuropeptide levels are higher at stages 3 than 1. Additionally, transcriptomic analysis of the de novo eyestalk ganglia assembly at ovarian stages 1 and 3 found 28 eyestalk neuropeptides. A GIH/VIH or GSH/VSH belonging to the CHH family is absent in the transcriptome. Transcripts per million (TPM) values of ten neuropeptides increase by 1.3 to 2.0-fold at stage 3 compared to stage 1: twofold for Bursicon α, followed by CHH, AKH/corazonin-like, Pyrokinin, CCAP, Glycoprotein B, PDH1, and IDLSRF-like peptide, and 1.3-fold of allatostatin A and short NP-F. WXXXRamide, the only downregulated neuropeptide, decreases TPM by ∼ 2-fold at stage 3, compared to stage 1. Interestingly, neuroparsin with the highest TPM values remains the same in stages 1 and 3. The mandibular organ-inhibiting hormone is not found in de novo assembly. We report that CHH, MIH, and eight other neuropeptides may play a role in vitellogenesis in this species.

Insulin-like Peptide Receptor (ILPR) in the Cuttlefish Sepiella japonica: Characterization, Expression, and Regulation of Reproduction

Insulin-like peptide receptor (ILPR) can effectively regulate ovarian development in invertebrates, but its effect in cuttlefish has not been reported. We isolated and characterized a ILPR gene from Sepiella japonica, referred to as SjILPR. This gene displayed significant homologies to Octopus bimaculoides ILPR, and contained all typical features of insulin receptors and tyrosine kinase domain structure. SjILPR is expressed in all detected tissues, with the highest expression in the ovary. During ovarian development stages, its expression levels in the ovary, pancreas, and liver were correlated to the female reproductive cycle. After the silencing of SjILPR in vivo, comparative transcriptome analysis identified 4314 differentially expressed genes (DEGs) in the injected group, including 2586 down-regulated genes and 1728 up-regulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that 832 DEGs were assigned to 222 pathways, many pathways of which were related to gonadal development. Four down-regulated genes relevant to ovarian development (Vitellogenin 1, Vitellogenin 2, Cathepsin L1-like, and Follistatin) were selected to confirm the accuracy of RNA-seq data by qRT-PCR. These results showed that SjILPR might regulate ovarian development to control reproduction by affecting the expression of the relevant genes in female S. japonica.

Effects of berberine hydrochloride on immune response in the crab Charybdis japonica

Berberine hydrochloride is the main effective component of Coptis spp. used in Chinese herbal medicine and its underlying molecular mechanisms, responsible for inducing effects in crustacean species, are not fully understood. In this study, the molecular response of the crab Charybdis japonica to berberine hydrochloride exposure was studied using transcriptome sequencing. The survival rate, gene expression and activities of several immune enzymes were measured after berberine hydrochloride treatments, with or without injection of the pathogenic bacterium Aeromonas hydrophila. A total of 962 differentially expressed genes (464 up-regulated and 498 down-regulated) were observed during exposure to 100 mg/L of berberine hydrochloride and in the control group after 48 h. Enrichment analysis revealed that these genes are involved in metabolism, cellular processes, signal transduction and immune functions, indicating that exposure to berberine hydrochloride activated the immune complement system. This bioactive compound simultaneously activated fibrinogen beta (FGB), fibrinogen alpha (FGA), alpha-2-macroglobulin (A2M), kininogen (KNG), fibrinogen gamma chain (FGB), alpha-2-HS-glycoprotein (AHSG), caspase-8 (CASP8), cathepsin L (CTSL), adenylate cyclase 3 (Adcy3) and MMP1. Its action could significantly increase the survival rate of the crabs injected with A. hydrophila and promote the activity of LZM, Caspas8, FGA, ACP and AKP in the hepatopancreas. When A. hydrophila was added, the neutralization of 300 mg/L berberine hydrochloride maximized the activities of Caspas8, LZM, ACP and AKP. Our results provide a new understanding of the potential effects of berberine hydrochloride on the immune system mechanisms in crustaceans.

Comparative Transcriptome Analysis Reveals the Process of Ovarian Development and Nutrition Metabolism in Chinese Mitten Crab, Eriocheir Sinensis

Ovarian development is a key physiological process that holds great significance in the reproduction of the Chinese mitten crab (Eriocheir sinensis), which is an economically important crab species for aquaculture. However, there is limited knowledge for the regulatory mechanisms of ovarian development. To study the molecular mechanisms of its ovarian development, transcriptome analysis was performed in the ovary and hepatopancreas of E. sinensis during ovarian stages I (oogonium proliferation), II (endogenous vitellogenesis), and III (exogenous vitellogenesis). The results showed that 5,520 and 226 genes were differentially expressed in the ovary and hepatopancreas, respectively. For KEGG enrichment analysis, the differentially expressed genes in the ovary were significantly clustered in phototransduction-fly, phagosome, and ECM-receptor interaction. Significantly enriched pathways in the hepatopancreas included fatty acid biosynthesis, fatty acid metabolism, and riboflavin metabolism. Further analysis showed that 25 genes and several pathways were mainly involved in oogenesis, including the ubiquitin-proteasome pathway, cyclic AMP-protein kinase A signaling pathway, and mitogen-activated protein kinase signaling pathway. Twenty-five candidate genes involved in vitellogenesis and endocrine regulation were identified, such as vitellogenin, vitellogenin receptor, estrogen sulfotransferase, ecdysone receptor, prostaglandin reductase 1, hematopoietic prostaglandin D synthase and juvenile hormone acid O-methyltransferase. Fifty-six genes related to nutritional metabolism were identified, such as fatty acid synthase, long-chain-fatty-acid-CoA ligase 4, 1-acyl-sn-glycerol-3-phosphate acyltransferase 4, fatty acid-binding protein, and glycerol-3-phosphate acyltransferase 1. These results highlight the genes involved in ovarian development and nutrition deposition, which enhance our understanding of the regulatory pathways and physiological processes of crustacean ovarian development.

Female reproduction-specific proteins, origins in marine species, and their evolution in the animal kingdom

The survival of a species largely depends on the ability of individuals to reproduce, thus perpetuating their life history. The advent of metazoans (i.e. pluricellular animals) brought about the evolution of specialized tissues and organs, which in turn led to the development of complex protein regulatory pathways. This study sought to elucidate the evolutionary relationships between female reproduction-associated proteins by analyzing the transcriptomes of representative species from a selection of marine invertebrate phyla. Our study identified more than 50 reproduction-related genes across a wide evolutionary spectrum, from Porifera to Vertebrata. Among these, a total of 19 sequences had not been previously reported in at least one phylum, particularly in Porifera. Moreover, most of the structural differences between these proteins did not appear to be determined by environmental pressures or reproductive strategies, but largely obeyed a distinguishable evolutionary pattern from sponges to mammals.

Two genes related to reproductive development in the juvenile prawn, Macrobrachium nipponense: Molecular characterization and transcriptional response to nanoplastic exposure

Plastic pollution in the form of nanoplastics poses a global threat to aquatic ecosystems and the organisms inhabiting them. However, few studies have been conducted on the effects of nanoplastic exposure on reproductive development in crustaceans. In order to address this issue, juvenile oriental river prawns (Macrobrachium nipponense) were exposed to different concentrations of 75-nm polystyrene nanoplastics (0, 5, 10, 20, 40 mg/L) for 28 days. In order to study the regulation of reproduction-related genes in the presence of nanoplastics, the Wee1 protein kinase gene (Wee1) and OTU domain ubiquitin aldehyde binding protein gene (OTUB) were selected. In this study, for the first time, the full-length cDNA of Mn-Wee1 and Mn-OTUB were cloned from M. nipponense. Homologous alignments revealed that Mn-Wee1 had a highly conserved function-critical sequence, and that Mn-OTUB was more closely related to OTUB1 than OTUB2. With increasing concentration of nanoplastics, the expression of both genes increased initially, then decreased. The inhibition of expression of Wee1 and OTUB occurred in 40 mg/L group, respectively. Analysis of the data also indicated that nanoplastic exposure might have differing effects on gene expression in M. nipponense male and female reproductive organs.

Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across sites of varying climate profiles

Background

The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab juveniles from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response.

Results

We present the first ever transcriptome assembly of S. serrata obtained from a data set containing 66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Our assembly contains many almost full-length transcripts – 5229 shrimp and 3049 fruit fly proteins have alignments that cover >80% of their sequence lengths to a contig. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat-stress response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis showed that between Cagayan and Bataan, there were 389 genes associated with 48 signaling and stress-response pathways, for which there was an effect of site in the response to heat; and between Cagayan and Bicol, there were 101 such genes affecting 8 pathways.

Conclusion

In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

Supplementary Information

The online version contains supplementary material available at (10.1186/s12864-021-07891-w).

Comparative proteomics elucidates the dynamics of ovarian development in the Chinese mitten crab Eriocheir sinensis

Ovarian development is a complex physiological process for crustacean reproduction that is divided into the oogonium proliferation stage, endogenous vitellogenic stage, exogenous vitellogenic stage, and oocyte maturation stage. Proteomics analysis offers a feasible approach to reveal the proteins involved in the complex physiological processes of any organism. Therefore, this study performed a comparative proteomics analysis of the ovary and hepatopancreas at three key ovarian stages, including stages I (oogonium proliferation), II (endogenous vitellogenesis) and IV (exogenous vitellogenesis), of the Chinese mitten crab Eriocheir sinensis using a label-free quantitative approach. The results showed that a total of 2,224 proteins were identified, and some key proteins related to ovarian development and nutrition metabolism were differentially expressed. The 26 key proteins were mainly involved in the ubiquitin/proteasome pathway (UPP), cyclic AMP-protein kinase A (cAMP-PKA) signaling pathway, and mitogen-activated protein kinase (MAPK) signaling pathway during oogenesis. Fifteen differentially abundant proteins (DAPs) were found to participate in vitellogenesis and oocyte development, such as vitelline membrane outer layer protein 1 homolog, vitellogenin, vitellogenin receptor, heat shock 70 kDa protein cognate 3 and farnesyl pyrophosphate synthase. Forty-seven DAPs related to nutrition metabolism were identified, including the protein digestion, fatty acid metabolism, prostaglandin metabolism, lipid digestion and transportation, i.e. short-chain specific acyl-CoA dehydrogenase, acyl-CoA desaturase, fatty acid-binding protein, long-chain fatty acid CoA ligase 4, and hematopoietic prostaglandin D synthase. These results not only indicate proteins involved in ovarian development and nutrient deposition but also enhance the understanding of the regulatory pathways and physiological processes of crustacean ovarian development.

Characterization of the foxl2 gene involved in the vtg expression in mud crab (Scylla paramamosain)

Forkhead box protein L2 (Foxl2) is involved in multiple physiological processes, such as ovarian development, granulosa cell differentiation, ovarian follicle development, and oocyte growth. In this study, a Spfoxl2 gene encoded 530 amino acid protein with characteristic forkhead (FH) domain was identified from transcriptome data of mud crab Scylla paramamosain and validated the accuracy by PCR technology. Meanwhile, the orthologues of the Spfoxl2 gene in other 14 crustacean species were identified with the same method. Further multiple sequence alignment analysis revealed the Foxl2 was highly conserved, especially in the FH domain, even completely identical in several species. Besides, the semi-quantitative PCR (Sq-PCR) result showed Spfoxl2 gene was mainly expressed in the gonad (testis and ovary). Further quantitative real-time PCR (qRT-PCR) result demonstrated its expression level in the testis was significantly higher than that in the ovary (p < 0.01). In addition, the qRT-PCR result showed that in zoea V, megalopa, and larval I, the expression level of Spfoxl2 in megalopa is the highest. In addition, a putative Foxl2 binding site was identified on the promoter region of Spvtg, and knockdown of Spfoxl2 mediated by RNAi technology increased the expression of Spvtg in the ovary, suggesting Spfoxl2 might be the upstream negative regulator of Spvtg. Overall, this study provided new insights into the role of Spfoxl2 in ovary development through regulating Spvtg expression in S. paramamosain.

Hypoxia-induced oxidative stress and transcriptome changes in the mud crab (Scylla paramamosain)

Mud crab (Scylla paramamosain) is an economically important cultured species in China. Hypoxia is a major environmental stressor during mud crab culture. In the present study, we investigated the oxidative stress and transcriptome changes in the gills of mud crab after intermediate hypoxia stress with dissolved oxygen (DO) 3.0 ± 0.2 mg/L (named as "DO3") and acute hypoxia stress with DO 1.0 ± 0.2 mg/L (named as "DO1") for 0, 3, 6, 12 and 24 h. The superoxide dismutase (SOD) activity of DO1 increased significantly at 3, 6 and 24 h after hypoxia stress, while SOD activity of DO3 increased significantly at 6 and 24 h. The total antioxidant capacity (T-AOC) increased significantly at 6, 12 and 24 h after hypoxia stress. The malondialdehyde (MDA) concentration of DO1 increased significantly at 6, 12 and 24 h after hypoxia stress, while MDA concentration of DO3 only increased significantly at 6 h. The lactate dehydrogenase (LDH) activity of DO1 increased significantly at 3, 6, 12 and 24 h after hypoxia stress, while LDH activity of DO3 increased significantly at 12 and 24 h. Transcriptomic analysis was conducted at 24 h of gill tissues after hypoxia stress. A total of 1052 differentially expressed genes (DEGs) were obtained, including 394 DEGs between DO1 and DO3, 481 DEGs between DO1 and control group, 177 DEGs between DO3 and control group. DEGs were enriched in the pathways related to metabolism, immune functions, ion transport, and signal transduction. Transcriptional analysis showed that glycolysis and tricarboxylic acid cycle genes were the key factors in regulating the adaptation of mud crab to hypoxia stress.

Identification of Sex-Related Genes from the Three-Spot Swimming Crab Portunus sanguinolentus and Comparative Analysis with the Crucifix Crab Charybdis feriatus

Simple Summary

Crabs within the family Portunidae are important marine species in both aquaculture and fishery sectors. The current aquaculture status of most portunids still relies on wild-caught fisheries due to the lack of essential knowledge regarding their reproductive biology and underlying governing mechanism. In the present study, we compared the differentially expressed genes (DEGs) between the different sexes of Portunus sanguinolentus based on their gonadal transcriptome profiles and subsequently contrasted them with the gonadal DEGs of Charybdis feriatus, the other member of the family Portunidae. In total, 40,964 DEGs between the ovaries and testes of P. sanguinolentus were uncovered, with 27,578 up-regulated and 13,386 down-regulated in females. After comparison, C. feriatus has approximately 63.5% of genes in common with P. sanguinolentus, with 62.6% showing similar expression patterns. Interestingly, the DMRT gene was specifically expressed in male P. sanguinolentus, while its homologous gene—doublesex (DSX)—was specifically expressed in male C. feriatus. The DEGs obtained from the gonadal transcriptome of P. sanguinolentus are a beneficial resource for future genetic and genomic research in P. sanguinolentus and its close species. The transcriptomic comparison analysis might provide references for better understanding the sex determination and differentiation mechanisms among portunids.

Abstract

Crabs within the family Portunidae are important marine species in both aquaculture and fishery sectors. The current aquaculture status of most portunids, however, still relies on wild-caught fisheries due to the lack of essential knowledge regarding their reproductive biology and underlying governing mechanism. With the advancement of sequencing technology, transcriptome sequencing has been progressively used to understand various physiological processes, especially on non-model organisms. In the present study, we compared the differentially expressed genes (DEGs) between sexes of Portunus sanguinolentus based on their gonadal transcriptome profiles and subsequently contrasted them with the gonadal DEGs of Charybdis feriatus, the other member of Family Portunidae. In total, 40,964 DEGs between ovaries and testes were uncovered, with 27,578 up- and 13,386 down-regulated in females. Among those, some sex-related DEGs were identified, including a dmrt-like (DMRT) gene which was specifically expressed in males. C. feriatus has approximately 63.5% of genes common with P. sanguinolentus, with 62.6% showing similar expression patterns. Interestingly, the DMRT gene was specifically expressed in male P. sanguinolentus while its homologous gene—doublesex (DSX)—was specifically expressed in male C. feriatus. The DEGs obtained from the gonadal transcriptome of P. sanguinolentus are a beneficial resource for future genetic and genomic research in P. sanguinolentus and its close species. The transcriptomic comparison analysis might provide references for better understanding the sex determination and differentiation mechanisms among portunids.

Differential expression analysis and identification of sex-related genes by gonad transcriptome sequencing in estradiol-treated and non-treated Ussuri catfish Pseudobagrus ussuriensis

The Ussuri catfish (Pseudobagrus ussuriensis) has an XX/XY sex determination system but its sex determination gene(s) remain unknown. To better understand the molecular sex determination mechanism, transcriptome analysis was conducted to obtain sex-related gene expression profiles. Transcriptome analyses were made of male and female developing/differentiating gonads by high-throughput RNA sequencing, including gonads from fish given an estradiol-induced sex reversal treatment. A total of 81,569 unigenes were assembled and 39,904 were significantly matched to known unique proteins by comparison with public databases. Twenty specifically expressed and 142 differentially expressed sex-related genes were extracted from annotated data by comparing the treatment groups. These genes are involved in spermatogenesis (e.g., Dnali1, nectin3, klhl10, mybl1, Katnal1, Eno4, Mns1, Spag6, Tsga10, Septin7), oogenesis (e.g., Lagr5, Fmn2, Npm2, zar1, Fbxo5, Fbxo43, Prdx4, Nrip1, Lfng, Atrip), gonadal development/differentiation (e.g., Cxcr4b, Hmgb2, Cftr, Ch25h, brip1, Prdm9, Tdrd1, Star, dmrt1, Tut4, Hsd17b12a, gdf9, dnd, arf1, Spata22), and estradiol response (e.g., Mmp14, Lhcgr, vtg1, vtg2, esr2b, Piwil1, Aifm1, Hsf1, gdf9). Dmrt1 and gdf9 may play an essential role in sex determination in P. ussuriensis. The expression patterns of six random genes were validated by quantitative real-time PCR, which confirmed the reliability and accuracy of the RNA-seq results. These data provide a valuable resource for future studies of gene expression and for understanding the molecular mechanism of sex determination/differentiation and gonadal development/differentiation (including hormone-induced sexual reversal) in Ussuri catfish. This has the potential to assist in producing monosex Ussuri catfish to increase aquacultural productivity.

Discovery of the Dmrt gene family members based on transcriptome analysis in mud crab Scylla paramamosain

Doublesex and mab-3 related transcription factors (Dmrts) play crucial roles in sex determination/differentiation and gonad development. The information on Dmrts and their functions are still scarce in mud crab Scylla paramamosain. In this study, 12 published transcriptome data of S. paramamosain were retrieved, pooled, and assembled. From the assembly, 7 Dmrt gene family members were identified and consisted of Spdmrt-like, Spdmrt-1a, Spdmrt-3, Spdmrt-11E, Spidmrt-1, Spdoublesex (Spdsx), and Spidmrt-2. These dmrt genes were predicted to encode 224 aa, 465 aa, 435 aa, 276 aa, 520 aa, 552 aa, and 266 aa protein precursors, respectively. The expression patterns of the dmrt genes were characterized by semi-quantitative PCR. The Spdmrt-like and Spdmrt-1a were exclusively detected in gonads, of which both expression levels in the testis were higher than that in the ovary. The Spdmrt-3, Spdmrt-11E, Spidmrt-1, Spdsx, and Spidmrt-2 were observed in various tissues; all these genes were sexually dimorphic except for dmrt-11E. Specifically, the expression level of Spdmrt-3 and Spidmrt-2 were higher in the testis than that in the ovary. On the contrary, the Spdsx and Spidmrt-1 expression level were higher in ovary than that in testis. The present study's findings provided a fundamental understanding of Dmrt gene family members involving sex determination/differentiation and gonad development in the S. paramamosain.

Comparison between cultured and wild Pacific white shrimp (Penaeus vannamei) vitellogenesis: next-generation sequencing and relative expression of genes directly and indirectly related to reproduction

Shrimp fisheries are among the most important fisheries worldwide, and shrimp culture has increased considerably in recent years. Most current studies on reproduction-related genes have been conducted on cultured shrimp. However, gene expression is intimately linked to physiological and environmental conditions, and therefore an organism’s growth environment has a great influence on reproduction. Thus, gene expression profiling, should be applied in fisheries studies. Here, we identified the expression patterns of 76 reproduction-related genes in P. vannamei via the analysis of pooled transcriptomes from a time-series experiment encompassing a full circadian cycle. The expression patterns of genes associated both directly (Vtg, ODP, and ProR) and indirectly (FAMet, CruA1, and CruC1) with reproduction were evaluated, as these genes could be used as molecular markers of previtellogenic and vitellogenic maturation stages. The evaluated genes were prominently upregulated during vitellogenic stages, with specific expression patterns depending on the organism’s environment, diet, and season. Vtg, ProR, ODP, and FaMet could serve as molecular markers for both wild and cultured organisms.

miR-9 and miR-263 Regulate the Key Genes of the ERK Pathway in the Ovary of Mud Crab Scylla paramamosain

Mud crab Scylla paramamosain is one of the most important economic crabs in China. The molecular regulatory mechanism of ovarian development has received considerable attention in recent years. Some studies found that ERK (extracellular signal-regulated protein kinase) signaling pathway plays an important role in ovarian development and is negatively regulated by microRNAs (miRNAs). However, the study about the regulation of miRNA on the ERK pathway in crustacean's ovary remains unknown. In this study, the target genes of the ERK signaling pathway regulated by selected miRNAs identified from the ovary of mud crab in our previous research were predicted by using bioinformatics tools. The results showed that the ERK2 might be a target gene of miR-9c, miR-263a, and miR-263b; MEK2 may be a target gene of miR-263a; and Rap-1b may be a target gene of miR-9, miR-9c, and miR-263a. Results of in vitro dual-luciferase reporter assay showed that the relative luciferase activities were significantly lower in HEK293T cells co-transfected with the combination of miRNA mimics and pmir-RB-REPORTTM-target gene-3'UTR than those with the combination of mimics NC and pmir-RB-REPORTTM-target gene-3'UTR. In contrast, the relative luciferase activities were significantly higher in HEK293T cells co-transfected with miRNA inhibitor than those with inhibitor NC. To further validate in vitro results, the miRNA reagents were injected into the living female mud crabs, and the expression levels of miRNAs and target genes after the injection were analyzed by quantitative real-time PCR. The in vivo experimental results showed that miRNAs (miR-9c/miR-263a) agomir (enhancers)/antagomir (inhibitors) can enhance/decrease the expression of two miRNAs, respectively, and the expression of target genes in the ovary was declined/increased after injection of agomir/antagomir reagent. In conclusion, miR-9/miR-263 can negatively regulate the expression of the ERK pathway genes (ERK2, MEK2, and Rap-1b) in the ovary of mud crab.

Expression dynamics of solute carrier family 15 member 4 (SLC15A4) and its potential regulatory role in ovarian development of the Indian white shrimp, Penaeus indicus

Solute carrier proteins (SLC) are essential membrane transport proteins responsible for transporting lipids, amino acids, sugars, neurotransmitters, and drugs across the biological membranes. Dysfunction of these carrier proteins may lead to an imbalance of biological mechanisms and also in the failure of the transporting pathways of several signaling neurotransmitters. In the present study, a 646 bp of a solute carrier protein (SLC15A4) was cloned and sequenced from the Indian white shrimp, Penaeus indicus. Multiple sequence alignment using ClustalW and phylogenetic analysis of putative SLC15A4 fragment from P. indicus (PiSLC15A4) was performed using Mega X tool. Tissue distribution analysis was carried out using real-time PCR. The differential expressions of PiSLC15A4 were also analyzed in the ovaries and brain tissues of wild-caught female shrimps at different maturation stages and in the brain tissues of captive females subjected to induce maturation by eyestalk ablation. Significant diversity in SLC15A4 sequence obtained from P. indicus was observed when compared to the other species. Tissue distribution analysis confirmed the ubiquitous expression of PiSLC15A4 in all the tissues examined. The differential expressions of PiSLC15A4 indicated higher expression of the gene in brain tissue of females at the vitellogenic stage, while the expressions in ovaries were significantly higher in the immature stage. The differential expressions of PiSLC15A4 in the brain tissues were substantially higher in eyestalk ablated shrimps compared to the eyestalk intact females. The study suggests a role for SLC15A4 in the endocrine signaling pathways stimulating ovarian maturation in P. indicus.

Integrative analysis reveals pathways associated with sex reversal in Cynoglossus semilaevis

Sex reversal is a complex biological phenomenon exhibited by Cynoglossus semilaevis. Some genetic females may irreversibly convert to pseudomales, thus increasing aquaculture costs because males grow much more slowly than females. In this study, an integrative analysis of transcriptome and proteome was performed to compare differences in gene and protein expression in females and pseudomales after gonad differentiation in C. semilaevis. Based on RNA-Seq results, 1893 genes showed differences in expression at the transcript level between females and pseudomales. Of these differentially expressed genes (DEGs), zona pellucida sperm-binding protein 4-like (LOC103393374 , ZP4), zona pellucida sperm-binding protein 4-like (LOC103396071, ZP4) and forkhead box L2 (foxl2) were highly expressed in females and doublesex and mab-3 related transcription factor 1(dmrt1) and doublesex and mab-3 related transcription factor 3 (dmrt3) were highly expressed in pseudomales. GO enrichment analysis results indicate that wnt signaling pathways and oocyte maturation are two terms enriched in female. At the protein level, Tandem Mass Tags analysis revealed that 324 proteins differed in their relative abundance between pseudomales and females. KEGG analysis found that pseudo-highly expressed proteins were enriched in the ubiquitin mediated proteolysis pathway. For integrative analysis, the Spearman correlation coefficient between the transcriptome and proteome was 0.59. Among 52 related genes, 46 DEGs (88%) were well matched in their levels of change in protein abundance. These findings reveal major active pathways in female and pseudomale gonads after sex reversal and provide new insights into molecular mechanisms associated with sex reversal regulatory network.

Single-molecule real-time (SMRT) sequencing facilitates Tachypleus tridentatus genome annotation

Tachypleus tridentatus is a keystone species in marine ecosystems. Its hemolymph also provides the limulus amebocyte lysate (LAL) for detection of bacterial endotoxin in human medical service. Here we combined SMRT sequencing and Illumina RNA-seq to characterize the novel isoforms, novel genetic loci, fusion isoforms formation and transcriptome structure and further to unveil the transcriptome complexity of T. tridentatus. We identified 26,705 non-redundancy isoforms form 10,919 genetic loci, including 25,713 novel isoforms, 2403 novel genes and 170 fusion isoforms. In addition, 1578 novel genes and 23,172 novel isoforms were annotated in the NR, Pfam, KOG, COG, eggNOG, Swiss-Prot, KEGG and GO databases. Meanwhile, we have obtained 4671 gene family clustering based on genetic loci. Furthermore, there are 17,296, 4887, 1054, and 1435 APAs, AS events, lncRNAs, and TFs were identified in the T. tridentatus long-read transcriptome and the target genes of 1054 lncRNA sequences were also predicted. Overall, our work firstly provided the long-read transcriptome and these data are very necessary to improve the annotation information of T. tridentatus genome and optimize the boundaries of 12,342 original reference annotated genes. Furthermore, these information are a potential resource to study LAL secretion mechanisms in T. tridentatus.

Presence of serotonin and its receptor in the central nervous system and ovary and molecular cloning of the novel crab serotonin receptor of the blue swimming crab, Portunus pelagicus

Serotonin (5-HT) plays pivotal roles in many physiological processes including reproduction of crustaceans, which are mediated 5-HT receptors. The distributions of 5-HT and its receptor have never been explored in Portunus pelagicus. To validate the targets which indirectly indicate the roles of 5-HT in this crab, we have investigated the distribution of 5-HT in the central nervous system (CNS) and ovary using immunohistochemistry and tissue expression of its receptor by RT-PCR. In the brain, 5-HT immunoreactivity (-ir) was detected in clusters 6, 7, 8, 11, 14, 15 and the fibers. In the ventral nerve cord (VNC), 5-HT-ir was detected in pairs of neurons and the fibers connected to the neurons. In the ovary, 5-HT-ir was intense in the oocyte step 1 (Oc1) and Oc2, and its intensity was slightly decreased in Oc3 and Oc4. The 5-HT receptor was molecularly characterized to be type 7, and it was strongly expressed in the eyestalk, brain, VNC, mature ovary and muscle. Due to the presence of 5-HT receptor we suggest that 5-HT acts primarily at the CNS and ovary, thus implicating its role in reproduction especially in the development of oocytes though its exact function in this crab needed to be explored further.

Comparative transcriptome reveals the potential modulation mechanisms of estradiol affecting ovarian development of female Portunus trituberculatus

Estradiol is an important sex steroid hormone that is involved in the regulation of crustacean ovarian development. However, the molecular regulatory mechanisms of estradiol on ovarian development are largely unknown. This study performed transcriptome sequencing of ovary, hepatopancreas, brain ganglion, eyestalk, and mandibular organ of crabs after estradiol treatment (0.1μg g^-1 crab weight). A total of 23, 806 genes were annotated, and 316, 1300, 669, 142, 383 genes were expressed differently in ovary, hepatopancreas, brain ganglion, eyestalk, and mandibular organ respectively. Differentially expressed gene enrichment analysis revealed several crucial pathways including protein digestion and absorption, pancreatic secretion, insect hormone biosynthesis, drug metabolism-cytochrome P450 and signal transduction pathway. Through this study, some key genes in correlation with the ovarian development and nutrition metabolism were significantly affected by estradiol, such as vitelline membrane outer layer 1-like protein, heat shock protein 70, Wnt5, JHE-like carboxylesterase 1, cytochrome P302a1, crustacean hyperglycemic hormone, neuropeptide F2, trypsin, carboxypeptidase B, pancreatic triacylglycerol lipase-like, and lipid storage droplet protein. Moreover, RT-qPCR validation demonstrated that expression of transcripts related to ovarian development (vitelline membrane outer layer 1-like protein and cytochrome P302a1) and nutrition metabolism (trypsin, glucose dehydrogenase and lipid storage droplet protein) were significantly affected by estradiol treatment. This study not only has identified relevant genes and several pathways that are involved in estradiol regulation on ovarian development of P. trituberculatus, but also provided new insight into the understanding of the molecular function mechanisms of estradiol in crustacean.

De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BACKGROUND

The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns.

RESULTS

A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species.

CONCLUSIONS

This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

De Novo Transcriptome Analysis Reveals Abundant Gonad-specific Genes in the Ovary and Testis of Henosepilachna vigintioctopunctata

Henosepilachna vigintioctopunctata (Coleoptera: Coccinellidae) is a major pest affecting Solanaceae plants in Asian countries. In this study, we sequenced the ovary and testis transcriptomes of H. vigintioctopunctata to identify gonad-related genes. Comparison of the unigene sequences in ovary and testis libraries identified 1,421 and 5,315 ovary- and testis-specific genes, respectively. Among the ovary-specific genes, we selected the RC2-like and PSHS-like genes to investigate the effects of gene silencing on the mortality, percentage infertility, pre-oviposition period, fecundity, daily number of eggs laid, and hatching rate in female adults. Although the percentage mortality and infertility of females did not differ significantly among dsRNA treatments, fecundity was significantly reduced in the dsRC2-like and dsPSHS-like treatment groups. Moreover, the pre-oviposition period was markedly prolonged in response to dsPSHS-like treatment. This is the first reported RNA sequencing of H. vigintioctopunctata. The transcriptome sequences and gene expression profiles of the ovary and testis libraries will provide useful information for the identification of gonad-related genes in H. vigintioctopunctata and facilitate further research on the reproductive biology of this species. Moreover, the gonad-specific genes identified may represent candidate target genes for inhibiting the population growth of H. vigintioctopunctata.

High-Density Genetic Linkage Maps Provide Novel Insights Into ZW/ZZ Sex Determination System and Growth Performance in Mud Crab (Scylla paramamosain)

Mud crab, Scylla paramamosain is one of the most important crustacean species in global aquaculture. To determine the genetic basis of sex and growth-related traits in S. paramamosain, a high-density genetic linkage map with 16,701 single nucleotide polymorphisms (SNPs) was constructed using SLAF-seq and a full-sib family. The consensus map has 49 linkage groups, spanning 5,996.66 cM with an average marker-interval of 0.81 cM. A total of 516 SNP markers, including 8 female-specific SNPs segregated in two quantitative trait loci (QTLs) for phenotypic sex were located on LG32. The presence of female-specific SNP markers only on female linkage map, their segregation patterns and lower female: male recombination rate strongly suggest the conformation of a ZW/ZZ sex determination system in S. paramamosain. The QTLs of most (90%) growth-related traits were found within a small interval (25.18–33.74 cM) on LG46, highlighting the potential involvement of LG46 in growth. Four markers on LG46 were significantly associated with 10–16 growth-related traits. BW was only associated with marker 3846. Based on the annotation of transcriptome data, 11 and 2 candidate genes were identified within the QTL regions of sex and growth-related traits, respectively. The newly constructed high-density genetic linkage map with sex-specific SNPs, and the identified QTLs of sex- and growth-related traits serve as a valuable genetic resource and solid foundation for marker-assisted selection and genetic improvement of crustaceans.

Genome survey, high-resolution genetic linkage map construction, growth-related quantitative trait locus (QTL) identification and gene location in Scylla paramamosain

Scylla paramamosain is one of the most economically important crabs in China. In this study, the first genome survey sequencing of this crab was performed, and the results revealed that the estimated genome size was 1.21 Gb with high heterozygosity (1.3%). Then, RAD technology was used to construct a high-resolution linkage map for this species. A total of 24,444 single nucleotide polymorphism (SNP) makers were grouped into 47 linkage groups. The total length of the linkage groups was 3087.53 cM with a markers interval of 0.92 cM. With the aid of transcriptome and genome scaffold data, 4,271 markers were linked to genes, including several important growth-related genes such as transforming growth factor-beta regulator I, immune related-gene C-type lectin and ecdysone pathway gene broad-complex-like protein. Further, 442 markers, representing 279 QTLs, associated with 24 traits were identified, and of these markers, 78 were linked to genes. Some interesting genes, such as dedicator of cytokinesis protein 3, tenascin-X and DNA helicase MCM8, were believed to have important relationship with specific traits and merit further exploration. The results of this study will accelerate the genetic improvement and genome sequencing analysis of the mud crab.

Fibroblast growth factor-5 promotes spermatogonial stem cell proliferation via ERK and AKT activation

Background

Sertoli cells are the most important somatic cells contributing to the microenvironment (named niche) for spermatogonial stem cells (SSCs). They produce amounts of crucial growth factors and structure proteins that play essential roles in the complex processes of male SSCs survival, proliferation, and differentiation. It has been suggested that Sertoli cell abnormalities could result in spermatogenesis failure, eventually causing azoospermia in humans. However, to the end, the gene expression characteristics and protein functions of human Sertoli cells remained unknown. In this study, we aimed to evaluate the effect of fibroblast growth factor-5 (FGF5), a novel growth factor downregulated in Sertoli cells from Sertoli cell-only syndrome (SCOS) patients compared to Sertoli cells from obstructive azoospermia (OA) patients, on SSCs.

Methods

We compared the transcriptome between Sertoli cell from SCOS and OA patients. Then, we evaluated the expression of FGF5, a growth factor which is downregulated in SCOS Sertoli cells, in human primary cultured Sertoli cells and testicular tissue. Also, the proliferation effect of FGF5 in mice SSCs was detected using EDU assay and CCK-8 assay. To investigate the mechanism of FGF5, Phospho Explorer Array was performed. And the results were verified using Western blot assay.

Results

Using RNA-Seq, we found 308 differentially expressed genes (DEGs) between Sertoli cells from SCOS and OA patients. We noted and verified that the expression of fibroblast growth factor-5 (FGF5) was higher in Sertoli cells of OA patients than that of SCOS patients at both transcriptional and translational levels. Proliferation assays showed that rFGF5 enhanced the proliferation of mouse SSCs line C18-4 in a time- and dose-dependent manner. Moreover, we demonstrated that ERK and AKT were activated and the expression of Cyclin A2 and Cyclin E1 was enhanced by rFGF5.

Conclusion

The distinct RNA profiles between Sertoli cells from SCOS and OA patients were identified using RNA-Seq. Also, FGF5, a growth factor that downregulated in SCOS Sertoli cells, could promote SSCs proliferation via ERK and AKT activation.

Female-specific SNP markers provide insights into a WZ/ZZ sex determination system for mud crabs Scylla paramamosain, S. tranquebarica and S. serrata with a rapid method for genetic sex identification

BACKGROUND

Mud crabs, Scylla spp., are commercially important large-size marine crustaceans in the Indo-West Pacific region. As females have the higher growth rate and economic value, the production of all female stocks is extremely essential in aquaculture. However, the sex determination mechanism is still unclear. Development of sex-specific genetic markers based on next-generation sequencing proved to be an effective tool for discovering sex determination system in various animals.

RESULTS

Restriction-site associated DNA sequencing (RAD-seq) was employed to isolate sex-specific SNP markers for S. paramamosain. A total of 335.6 million raw reads were obtained from 20 individuals, of which 204.7 million were from 10 females and 130.9 million from 10 males. After sequence assembly and female-male comparison, 20 SNP markers were identified to be sex-specific. Furthermore, ten SNPs in a short sequence (285 bp) were confirmed heterozygous in females and homozygous in males in a large population by PCR amplification and sequencing. Subsequently, a female-specific primer was successfully designed according to the female-specific nucleotide which could amplify an expected band from females but not from males. Thus, a rapid and effective method for molecular sexing in S. paramamosain was developed, meanwhile, this method could successfully identify the sex of S. tranquebarica and S. serrata. Finally, nine and four female-specific SNP markers were detected in S. tranquebarica and S. serrata, respectively.

CONCLUSIONS

Sex-specific SNP markers were firstly identified in crab species and showed female heterogamety and male homogamety, which provided strong genetic evidence for a WZ/ZZ sex determination system in mud crabs S. paramamosain, S. tranquebarica and S. serrata. These findings will lay a solid foundation for the study of sex determination mechanism, sex chromosome evolution, and the development of mono-sex population in crustaceans.

Dimorphism of sex and gonad-development-related genes in male and female lined seahorse, Hippocampus erectus, based on transcriptome analyses

Seahorse is characterized by its male pregnancy and sex-role reversal. To better understand the sexual dimorphism of male and female seahorses based on essential genes, we performed systematic transcriptome studies for both genders. A total of 157,834,590 cleaned reads were obtained and assembled into 129,268 transcripts and 31,764 could be annotated. Results showed that 176 up-regulated and 391 down-regulated transcripts were identified in the male seahorses compared with those in females. Genes involved in sex differentiation, such as dmrt1, sox9, fem1 and vasa, were identified and characterized. Moreover, the essential genes involved in reproductive molecular pathway were identified and analyzed in seahorses. In conclusion, the present study provides an archive for the future systematic research on seahorse sex differentiation.

miR-34 regulates reproduction by inhibiting the expression of MIH, CHH, EcR, and FAMeT genes in mud crab Scylla paramamosain

Mud crab Scylla paramamosain is a commercially important species widely cultured in China. It is well known that the eyestalk regulates reproductive activities in crustaceans. In our previous research, we found that the miR-34 expression level in male eyestalk was significantly higher than that in females. Thus, we assumed that it may play an important role in regulating reproduction. In this study, we used bioinformatic tools to identify the target genes of miR-34 in eyestalk. Six reproduction-related genes with an intact 3'-untranslated region (UTR), including molt-inhibiting hormone (MIH), crustacean hyperglycemic hormone (CHH), vitellogenesis-inhibiting hormone, red pigment concentrating hormone, ecdysone receptor (EcR), and farnesoic acid methyltransferase (FAMeT) were identified. When the 3'-UTR plasmid vectors of the six genes were cotransfected with miR-34 mimics into 293FT cells, respectively, the luciferase activities of four genes (MIH, CHH, EcR, and FAMeT) were significantly decreased compared with that in the control group; on the contrary, when the six plasmid vectors were cotransfected with the miR-34 inhibitor respectively, the luciferase activities of four genes (MIH, CHH, EcR, and FAMeT) were significantly higher than that in the control group. When agomiR-34 and antagomiR-34 were injected into the eyestalk respectively in vivo, the expression levels of the MIH, CHH, EcR, and FAMeT genes were detected by a quantitative real-time polymerase chain reaction. The results showed that agomiR-34 suppressed the expression of the four genes, whereas antagomiR-34 enhanced their expression. These experimental results confirmed our hypothesis that miR-34 may indirectly regulate reproduction via binding to the 3'-UTRs of MIH, CHH, EcR, and FAMeT genes and suppressing their expression.

Comparative transcriptomic analysis of crab hemocytes in response to white spot syndrome virus or Vibrio alginolyticus infection

To assess the immune response of hemocytes to white spot syndrome virus (WSSV) or Vibrio alginolyticus infection in the mud crab Scylla paramamosain, a transcriptome analysis was performed. We report the analysis of 45131 transcripts from S. paramamosain hemocytes by de novo assembly. A comparison with GenBank protein and nucleotide sequences identified 33699 genes as previously known. The length distribution of the genes was 8147 genes ≥200 bp, 4714 genes ≥300 bp, and 3517 genes ≥2000 bp. A total of 21579 simple sequence repeats (SSRs) were found in the transcriptomic dataset, including 9% monomers, 53.34% dimers and 32.55% trimers. A total of 13172 and 5087 differentially expressed transcripts were found in the V. alginolyticus-infected group and WSSV-infected group, respectively. Of these, 5920 transcripts were up-regulated and 7252 were down-regulated in the V. alginolyticus-infected crabs and 2302 transcripts were up-regulated and 2785 were down-regulated in the WSSV-infected crabs. Additionally, 3096 transcripts were differentially expressed simultaneously in the V. alginolyticus-infected crabs and the WSSV-infected crabs. Several known immune-related genes such as heat shock protein, Janus kinase, STAT, relish, caspase, Ca²⁺-transporting ATPase and lysosomal alpha-mannosidase were found among the differentially expressed transcripts. Transcription and its regulation were significant biological processes, and ATP binding and zinc ion binding were significant molecular functions. This is the first report of comparative transcriptomic analysis of crab hemocytes in response to WSSV or V. alginolyticus infection. These findings will contribute to our understanding of the immune response to WSSV and V. alginolyticus infection in crustaceans.

Transcriptome analysis for identification of candidate genes related to sex determination and growth in Charybdis japonica

Charybdis japonica is an important cultured crab in China and it exhibits sex differences in their growth. Growth is an important economic trait that is controlled by many genes. In order to discover the growth-related regulatory mechanisms, whole-body transcriptomic sequencing and comparative analyses in different genders of C. japonica were conducted based on Illumina RNA-seq technology. In the present study, we obtained 62,879,204 and 60,226,334 clean reads in female and male libraries, respectively. 25,000,000 clean reads of every library were randomly selected and compared with Nt database to examine the possible contamination. Results showed that all clean reads were distributed among C. japonica or other species that were closely relative to this species, indicating no-pollution. De novo assembly was performed and a total of 32,543 and 44,174 unigenes were produced in female and male of C. japonica, respectively. Among all the unigenes, 12,591 and 14,455 unigenes of female and male crabs were annotated based on protein databases. Moreover, a total of 33,926 unigenes were found to contain ORFs and 52,839 SSRs were detected. The contrast between male and female C. japonica identifying 1939 unigenes were significantly differentially expressed. In addition, we specifically discussed some gene functions and pathways potentially associated with sex determination and growth. This is the first systematic report of whole transcriptome in C. japonica. The transcriptome information provides a basic resource for further studies on understanding the molecular basis of biological processes in C. japonica and other crustaceans.

Transcriptome sequencing and molecular markers discovery in the gonads of Portunus sanguinolentus

Crab culture has gained prominence in the last decade due to the large global market demand for live crabs and crab products. Portunus sanguinolentus is one of the economically important crab species in the Indo-Pacific region, with distinct differences in growth and size between male and female crabs, thus, leading to huge difference in their market values. The culture of P. sanguinolentus is still in its infancy, with crab supplies heavily dependent on wild catch. In order to unravel the molecular differences between male and female crabs, we generated a comprehensive transcriptomic dataset for P. sanguinolentus by sequencing the gonads of both sexes using the Illumina Hiseq 2500 system. Transcriptomes were assembled using Trinity de novo assembly followed by annotation. This transcriptomic data set for P. sanguinolentus would serve as an important reference data for genomic and genetic studies in this crab and related species.

Transcriptome-seq provides insights into sex-preference pattern of gene expression between testis and ovary of the crucifix crab (Charybdis feriatus)

The crucifix crab, Charybdis feriatus, which mainly inhabits Indo-Pacific region, is regarded as one of the most high-potential species for domestication and incorporation into the aquaculture sector. However, the regulatory mechanisms of sex determination and differentiation of this species remain unclear. To identify candidate genes involved in sex determination and differentiation, high throughput sequencing of transcriptome from the testis and ovary of C. feriatus was performed by the Illumina platform. After removing adaptor primers, low-quality sequences and very short (<50 nt) reads, we obtained 80.9 million and 66.2 million clean reads from testis and ovary, respectively. A total of 86,433 unigenes were assembled, and ~43% (37,500 unigenes) were successfully annotated to the NR, NT, Swiss-Prot, KEGG, COG, GO databases. By comparing the testis and ovary libraries, we obtained 27,636 differentially expressed genes. Some candidate genes involved in the sex determination and differentiation of C. feriatus were identified, such as vasa, pgds, vgr, hsp90, dsx-f, fem-1, and gpr. In addition, 88,608 simple sequence repeats were obtained, and 61,929 and 77,473 single nucleotide polymorphisms from testis and ovary were detected, respectively. The transcriptome profiling was validated by quantitative real-time PCR in 30 selected genes, which showed a good consistency. The present study is the first high-throughput transcriptome sequencing of C. feriatus. These findings will be useful for future functional analysis of sex-associated genes and molecular marker-assisted selections in C. feriatus.

De novo transcriptome analysis and differentially expressed genes in the ovary and testis of the Japanese mantis shrimp Oratosquilla oratoria by RNA-Seq

The mantis shrimp Oratosquilla oratoria is a widely distributed, commercially important crustacean species. Although its conservation and the development of successful artificial breeding technologies have recently received considerable attention, there are currently no available data regarding the molecular mechanisms in controlling reproduction. In this study, we performed transcriptome sequencing of the testis, ovary, female and male eyestalks and the androgenic gland of O. oratoria, and compared the expression pattern of transcripts from the testis and ovary libraries to identify genes involved in gonadal development. A total of 147,130,937 clean reads were retrieved after removing the adapters in reads and filtering out low-quality data. All the reads were assembled into 94,990 unigenes (23,133 in testis and ovary) with an average length of 783 base pairs (bp) and N50 of 1502 bp. A search of all-unigenes against COG, GO, KEGG, KOG, Pfam, Swiss-Prot and Nr databases resulted in a total of 19,404 annotated unigenes. Comparison of the sequences in the ovary and testis libraries revealed that 1188 unigenes were up-regulated in the ovary and 2732 were up-regulated in the testis. Twenty ovary-up-regulated and 21 testis-up-regulated unigenes were confirmed by quantitative real-time PCR. Additionally, 13,437 simple sequence repeats (SSRs) and 275,799 putative single nucleotide polymorphisms (SNPs) were identified. The important functional genes and pathways identified here provide a valuable dataset for understanding the molecular mechanisms controlling gonad development in O. oratoria, and the numerous (13,437 SSRs and 275,799 SNPs) molecular markers obtained here will provide fundamental basis for functional genomic and population genetic studies of O. oratoria.

Analysis of Annotation and Differential Expression Methods used in RNA-seq Studies in Crustacean Systems

In the field of crustacean biology, usage of RNA-seq to study gene expression is rapidly growing. Major advances in sequencing technology have contributed to the ability to examine complex patterns of genome activity in a wide range of organisms that are extensively used for comparative physiology, ecology and evolution, environmental monitoring, and commercial aquaculture. Relative to insect and vertebrate model organisms, however, information on the organization of crustacean genomes is virtually nonexistent, making de novo transcriptome assembly, annotation and quantification problematic and challenging. We present here a summary of the methodologies and software analyses employed in 23 recent publications, which describe de novo transcriptome assembly, annotation, and differential gene expression in a variety of crustacean experimental systems. We focus on establishing a series of best practices that will allow for investigators to produce datasets that are understandable, reproducible, and of general utility for related analyses and cross-study comparisons.

Effects of Organotins on Crustaceans: Update and Perspectives

Organotins (OTs) are considered some of the most toxic chemicals introduced into aquatic environments by anthropogenic activities. They are widely used for agricultural and industrial purposes and as antifouling additives on boat hull's paints. Even though the use of OTs was banned in 2008, elevated levels of OTs can still be detected in aquatic environments. OTs' deleterious effects upon wildlife and experimental animals are well documented and include endocrine disruption, immunotoxicity, neurotoxicity, genotoxicity, and metabolic dysfunction. Crustaceans are key members of zooplankton and benthic communities and have vital roles in food chains, so the endocrine-disrupting effects of tributyltin (TBT) on crustaceans can affect other organisms. TBT can disrupt carbohydrate and lipid homeostasis of crustaceans by interacting with retinoid X receptor (RXR) and crustacean hyperglycemic hormone (CHH) signaling. Moreover, it can also interact with other nuclear receptors, disrupting methyl farnesoate and ecdysteroid signaling, thereby altering growth and sexual maturity, respectively. This compound also interferes in cytochrome P450 system disrupting steroid synthesis and reproduction. Crustaceans are also important fisheries worldwide, and its consumption can pose risks to human health. However, some questions remain unanswered. This mini review aims to update information about the effects of OTs on the metabolism, growth, and reproduction of crustaceans; to compare with known effects in mammals; and to point aspects that still needs to be addressed in future studies. Since both macrocrustaceans and microcrustaceans are good models to study the effects of sublethal TBT contamination, novel studies should be developed using multibiomarkers and omics technology.

Comparative Transcriptome Analysis Provides Insights into Differentially Expressed Genes and Long Non-Coding RNAs between Ovary and Testis of the Mud Crab (Scylla paramamosain)

The molecular mechanism underlying sex determination and gonadal differentiation of the mud crab (Scylla paramamosain) has received considerable attention, due to the remarkably biological and economic differences between sexes. However, sex-biased genes, especially non-coding genes, which account for these differences, remain elusive in this crustacean species. In this study, the first de novo gonad transcriptome sequencing was performed to identify both differentially expressed genes and long non-coding RNAs (lncRNAs) between male and female S. paramamosain by using Illumina Hiseq2500. A total of 79,282,758 and 79,854,234 reads were generated from ovarian and testicular cDNA libraries, respectively. After filtrating and de novo assembly, 262,688 unigenes were produced from both libraries. Of these unigenes, 41,125 were annotated with known protein sequences in public databases. Homologous genes involved in sex determination and gonadal development pathways (Sxl-Tra/Tra-2-Dsx/Fru, Wnt4, thyroid hormone synthesis pathway, etc.) were identified. Three hundred and sixteen differentially expressed unigenes were further identified between both transcriptomes. Meanwhile, a total of 233,078 putative lncRNAs were predicted. Of these lncRNAs, 147 were differentially expressed between sexes. qRT-PCR results showed that nine lncRNAs negatively regulated the expression of eight genes, suggesting a potential role in sex differentiation. These findings will provide fundamental resources for further investigation on sex differentiation and regulatory mechanism in crustaceans.

Molecular Characterization and Expression Profiles of Sp-uchl3 and Sp-uchl5 during Gonad Development of Scylla paramamosain

Ubiquitin C-terminal hydrolases (UCHLs) are a subset of deubiquitinating enzymes, and are involved in numerous physiological processes. However, the role of UCHLs during gonad development has not been studied in crustaceans. In this study, we have first cloned and analyzed expression profiling of Sp-uchl3 and Sp-uchl5 genes from mud crab Scylla paramamosain. The full-length cDNA of Sp-uchl3 is of 1804 bp. Its expression level in the ovary was significantly higher than in other tissues (p < 0.01), and during gonadal development, its expression in both O1 and O5 stages was significantly higher than in the other three stages of ovaries (p < 0.05), while in T3 it was higher than in the former two stages of testes (p < 0.05). Meanwhile, the full-length cDNA of Sp-UCHL5 is 1217 bp. The expression level in the ovary was significantly higher than in other tissues (p < 0.01). Its expression in ovaries was higher than in testes during gonadal development (p < 0.05). The expression level in the O5 stage was the highest, followed by the O3 stage in ovarian development, and with no significant difference in the testis development (p > 0.05). These results provide basic data showing the role of Sp-UCHL3 and Sp-UCHL5 in the gonad development of the crab.

De novo transcriptome sequencing and analysis of male and female swimming crab (Portunus trituberculatus) reproductive systems during mating embrace (stage II)

Background

The swimming crab Portunus trituberculatus is one of the most commonly farmed crustaceans in China. As one of the most widely known and high-value edible crabs, it crab supports large crab fishery and aquaculture in China. Only large and sexually mature crabs can provide the greatest economic benefits, suggesting the considerable effect of reproductive system development on fishery. Studies are rarely conducted on the molecular regulatory mechanism underlying the development of the reproductive system during the mating embrace stage in this species. In this study, we used high-throughput sequencing to sequence all transcriptomes of the P. trituberculatus reproductive system.

Results

Transcriptome sequencing of the reproductive system produced 81,688,878 raw reads (38,801,152 and 42,887,726 reads from female and male crabs, respectively). Low-quality (quality <20) reads were trimmed and removed, leaving only high-quality reads (37,020,664 and 41,021,030 from female and male crabs, respectively). A total of 126,188 (female) and 164,616 (male) transcripts were then generated by de novo transcriptome assembly using Trinity. Functional annotation of the obtained unigenes revealed that a large number of key genes and some important pathways may participate in cell proliferation and signal transduction. On the basis of our transcriptome analyses and as confirmed by quantitative real-time PCR, a number of genes potentially involved in the regulation of gonadal development and reproduction of P. trituberculatus were identified: ADRA1B, BAP1, ARL3, and TRPA1.

Conclusion

This study is the first to report on the whole reproductive system transcriptome information in stage II of P. trituberculatus gonadal development and provides rich resources for further studies to elucidate the molecular basis of the development of reproductive systems and reproduction in crabs. The current study can be used to further investigate functional genomics in this species.

Electronic supplementary material

The online version of this article (10.1186/s12863-017-0592-5) contains supplementary material, which is available to authorized users.

VIH from the mud crab is specifically expressed in the eyestalk and potentially regulated by transactivator of Sox9/Oct4/Oct1

Vitellogenesis-inhibiting hormone (VIH) is known to regulate ovarian maturation by suppressing the synthesis of vitellogenin (Vtg) in crustaceans, which belongs to a member of crustacean hyperglycemic hormone (CHH) family synthesized and secreted from the X-organ/sinus gland complex of eyestalks. In this study, the cDNA, genomic DNA (gDNA) and the 5'-upstream regulatory (promoter region) sequences of VIH gene were obtained by conventional PCR, genome walker and tail-PCR techniques according to our transcriptomic database of Scylla paramamosain. The full-length cDNA of SpVIH is 634bp including 105bp 5'UTR, 151bp 3'UTR and 378bp ORF that encodes a peptide of 125 amino acids. The full length gDNA of SpVIH is 790bp containing two exons and one intron. The 5'-flanking promoter regions of SpVIH we isolated are 3070bp from the translation initiation (ATG) and 2398bp from the predicted transcription initiation (A), which consists of putative core promoter region and multiple potential transcription factor binding sites. SpVIH was only expressed in eyestalk. The expression level of SpVIH in eyestalk of female crab decreased gradually along with the development of ovary. As there is not cell line of crabs available, we chose the mature transfection system HEK293FT cell lines to explore the mechanism of transcription regulation of SpVIH in crabs. Sequential deletion assays using luciferase reporter gene in HEK293FT cells revealed that the possible promoter activity regions (including positive and negative transcription factors binding sites simultaneously) presented between pSpVIH-4 and pSpVIH-6. In order to further identify the crucial transcription factors binding site in this region, the site-directed mutagenesis of Sox9/Oct4/Oct1 binding site of pSpVIH-4 was created. The results demonstrated that the transcriptional activity of pSpVIH-4△ decreased significantly (p<0.05). Thus, it is reasonable to deduce that the Sox9/Oct4/Oct1 may be the essential positive transcription factors which regulate the expression of SpVIH.

Transcriptome profiling of claw muscle of the mud crab (Scylla paramamosain) at different fattening stages

In crustaceans, muscle growth and development is complicated, and to date substantial knowledge gaps exist. In this study, the claw muscle, hepatopancreas and nervous tissue of the mud crab (Scylla paramamosain) were collected at three fattening stages for sequence by the Illumina sequencing. A total of 127.87 Gb clean data with no less than 3.94 Gb generated for each sample and the cycleQ30 percentages were more than 86.13% for all samples. De Bruijn assembly of these clean data produced 94,853 unigenes, thereinto, 50,059 unigenes were found in claw muscle. A total of 121 differentially expressed genes (DEGs) were revealed in claw muscle from the three fattening stages with a Padj value < 0.01, including 63 genes with annotation. Functional annotation and enrichment analysis showed that the DEGs clusters represented the predominant gene catalog with roles in biochemical processes (glycolysis, phosphorylation and regulation of transcription), molecular function (ATP binding, 6-phosphofructokinase activity, and sequence-specific DNA binding) and cellular component (6-phosphofructokinase complex, plasma membrane, and integral component of membrane). qRT-PCR was employed to further validate certain DEGs. Single nucleotide polymorphism (SNP) analysis obtained 159,322, 125,963 and 166,279 potential SNPs from the muscle transcriptome at stage B, stage C and stage D, respectively. In addition, there were sixteen neuropeptide transcripts being predicted in the claw muscle. The present study provides a comprehensive transcriptome of claw muscle of S. paramamosain during fattening, providing a basis for screening the functional genes that may affect muscle growth of S. paramamosain.