The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation

New genes helped acorn barnacles adapt to a sessile lifestyle

Barnacles are the only sessile lineages among crustaceans, and their sessile life begins with the settlement of swimming larvae (cyprids) and the formation of protective shells. These processes are crucial for adaptation to a sessile lifestyle, but the underlying molecular mechanisms remain poorly understood. While investigating these mechanisms in the acorn barnacle, Amphibalanus amphitrite, we discovered a new gene, bcs-6, which is involved in the energy metabolism of cyprid settlement and originated from a transposon by acquiring the promoter and cis-regulatory element. Unlike mollusks, the barnacle shell comprises alternate layers of chitin and calcite and requires another new gene, bsf, which generates silk-like fibers that efficiently bind chitin and aggregate calcite in the aquatic environment. Our findings highlight the importance of exploring new genes in unique adaptative scenarios, and the results will provide important insights into gene origin and material development.

Effects of different salinity reduction intervals on osmoregulation, anti-oxidation and apoptosis of Eriocheir sinensis megalopa

Eriocheir sinensis megalopa has a special life history of migrating from seawater to freshwater. In order to investigate how the megalopa adapt themselves to the freshwater environment, we designed an experiment to reduce the salinity of water from 30 ppt to 0 at rates of 30 ppt, 15 ppt, 10 ppt, and 5 ppt per 24 h to evaluate the effects of different degrees of hyposaline stress on the osmotic regulation ability and antioxidant system of the megalopa. Experimental results related to osmotic pressure regulation show that the gill tissue of megalopa in the treatment group of 30 ppt/24 h rapid reduction of salinity was damaged, while in the treatment group of 5 ppt/24 h it was intact. At the same time, the experiment also found that in each treatment group with different salinity reduction rates, compared with the control salinity, the NKA activity of megalopa increased significantly after the salinity was reduced to 20 ppt (p < 0.05). In addition, two genes involved in chloride ion transmembrane absorption have different expression patterns in the treatment groups with different salinity reduction rates. Among them, Clcn2 was significantly highly expressed only in the rapid salinity reduction intervals of 30 ppt/24 h and 15 ppt/24 h (p < 0.05). Slc26a6 was significantly highly expressed only in the slow salinity reduction intervals of 10 ppt/24 h and 5 ppt/24 h (p < 0.05). On the other hand, the results of antioxidant and apoptosis related experiments showed that in all treatment groups with different rates of salinity reduction, the activities of T-AOC, GSH-PX, and CAT basically increased significantly after salinity reduction compared to the control salinity. Moreover, the activities of T-AOC and CAT were significantly higher in the 10 ppt/24 h and 5 ppt/24 h treatment groups than in the 30 ppt/24 h and 15 ppt/24 h treatment groups. Finally, the experimental results related to apoptosis showed that the expression trends of Capase3 and Bax-2 were basically the same in the treatment groups with different salinity reduction rates, and their expressions were significantly higher in the 10 ppt/24 h and 5 ppt/24 h treatment groups than in the 30 ppt/24 h and 15 ppt/24 h treatment groups. In summary, the present study found that megalopa had strong hyposaline tolerance and were able to regulate osmolality at different rates of salinity reduction, but the antioxidant capacity differed significantly between treatment groups, with rapid salinity reduction leading to oxidative damage in the anterior gills and reduced antioxidant enzyme activity and apoptosis levels.

Genome assemblies of two species of porcelain crab, Petrolisthes cinctipes and Petrolisthes manimaculis (Anomura: Porcellanidae)

Crabs are a large subtaxon of the Arthropoda, the most diverse and species-rich metazoan group. Several outstanding questions remain regarding crab diversification, including about the genomic capacitors of physiological and morphological adaptation, that cannot be answered with available genomic resources. Physiologically and ecologically diverse Anomuran porcelain crabs offer a valuable model for investigating these questions and hence genomic resources of these crabs would be particularly useful. Here, we present the first two genome assemblies of congeneric and sympatric Anomuran porcelain crabs, Petrolisthes cinctipes and Petrolisthes manimaculis from different microhabitats. Pacific Biosciences high-fidelity sequencing led to genome assemblies of 1.5 and 0.9 Gb, with N50s of 706.7 and 218.9 Kb, respectively. Their assembly length difference can largely be attributed to the different levels of interspersed repeats in their assemblies: The larger genome of P. cinctipes has more repeats (1.12 Gb) than the smaller genome of P. manimaculis (0.54 Gb). For obtaining high-quality annotations of 44,543 and 40,315 protein-coding genes in P. cinctipes and P. manimaculis, respectively, we used RNA-seq as part of a larger annotation pipeline. Contrarily to the large-scale differences in repeat content, divergence levels between the two species as estimated from orthologous protein-coding genes are moderate. These two high-quality genome assemblies allow future studies to examine the role of environmental regulation of gene expression in the two focal species to better understand physiological response to climate change, and provide the foundation for studies in fine-scale genome evolution and diversification of crabs.

Adaptation of Glucose Metabolism to Limb Autotomy and Regeneration in the Chinese Mitten Crab

Limb autotomy and regeneration represent distinctive responses of crustaceans to environmental stress. Glucose metabolism plays a pivotal role in energy generation for tissue development and regeneration across various species. However, the relationship between glucose metabolism and tissue regeneration in crustaceans remains elusive. Therefore, this study is aimed at analyzing the alterations of glucose metabolic profile during limb autotomy and regeneration in Eriocheir sinensis, while also evaluating the effects of carbohydrate supplementation on limb regeneration. The results demonstrated that limb autotomy triggered a metabolic profile adaption at the early stage of regeneration. Hemolymph glucose levels were elevated, and multiple glucose catabolic pathways were enhanced in the hepatopancreas. Additionally, glucose and ATP levels in the regenerative limb were upregulated, along with increased expression of glucose transporters. Furthermore, the gene expression and activity of enzymes involved in gluconeogenesis were repressed in the hepatopancreas. These findings indicate that limb regeneration triggers metabolic profile adaptations to meet the elevated energy requirements. Moreover, the study observed that supplementation with corn starch enhanced limb regeneration capacity by promoting wound healing and blastema growth. Interestingly, dietary carbohydrate addition influenced limb regeneration by stimulating gluconeogenesis rather than glycolysis in the regenerative limb. Thus, these results underscore the adaptation of glucose metabolism during limb autotomy and regeneration, highlighting its essential role in the limb regeneration process of E. sinensis.

Genome-Wide Identification of Vitellogenin Gene Family and Comparative Analysis of Their Involvement in Ovarian Maturation in Exopalaemon carinicauda

Vitellogenin (Vtg) is a precursor of yolk proteins in egg-laying vertebrates and invertebrates and plays an important role in vitellogenesis and embryonic development. However, the Vtg family remains poorly characterized in Exopalaemon carinicauda, a major commercial mariculture species found along the coasts of the Yellow and Bohai Seas. In this study, 10 Vtg genes from the genomes of E. carinicauda were identified and characterized. Phylogenetic analyses showed that the Vtg genes in crustaceans could be classified into four groups: Astacidea, Brachyra, Penaeidae, and Palaemonidae. EcVtg genes were unevenly distributed on the chromosomes of E. carinicauda, and a molecular evolutionary analysis showed that the EcVtg genes were primarily constrained by purifying selection during evolution. All putative EcVtg proteins were characterized by the presence of three conserved functional domains: a lipoprotein N-terminal domain (LPD_N), a domain of unknown function (DUF1943), and a von Willebrand factor type D domain (vWD). All EcVtg genes exhibited higher expression in the female hepatopancreas than in other tissues, and EcVtg gene expression during ovarian development suggested that the hepatopancreas is the main synthesis site in E. carinicauda. EcVtg1a, EcVtg2, and EcVtg3 play major roles in exogenous vitellogenesis, and EcVtg3 also plays a major role in endogenous vitellogenesis. Bilateral ablation of the eyestalk significantly upregulates EcVtg mRNA expression in the female hepatopancreas, indicating that the X-organ/sinus gland complex plays an important role in ovarian development, mostly by inducing Vtg synthesis. These results could improve our understanding of the function of multiple Vtg genes in crustaceans and aid future studies on the function of EcVtg genes during ovarian development in E. carinicauda.

Exoskeleton protein repertoires in decapod crustaceans revealed distinct biomineralization evolution with molluscs

Crustaceans are the champions of mineral mobilization and deposition in the animal kingdom due to their unique ability to rapidly and periodically mineralize and demineralize their exoskeletons. They are commonly covered with mineralized exoskeletons for protection and regularly molt throughout their lives. Mineralized crustacean exoskeletons are formed under the control of macromolecules especially matrix proteins but the types of matrix proteins are understudied compared to those in molluscan shells. This gap hinders our understanding of their evolutionary paths compared with those of molluscs. Here, we comprehensively analyzed matrix proteins in the exoskeleton of two crabs, one shrimp, and one crayfish and resulted in a major improvement (∼10-fold) in the identification of biomineralization proteins compared to conventional methods for decapod crustaceans. By a comparison with well-studied molluscan biomineralization proteins, we found that decapod crustaceans evolved novel proteins to form mineralized exoskeletons while sharing some proteins with those of molluscs. Our study sheds light on their evolution and adaption to different environment for exoskeleton formation and provides a foundation for further studies of mineralization in crustaceans under normal and climate-changed conditions. SIGNIFICANCE: Most crustaceans have mineralized exoskeletons as protection. How they form these hierarchical structures is still unclear. This is due partially to the understudied matrix proteins in the minerals. This study filled such a gap by using proteomic analysis of matrix proteins from four decapod crustacean exoskeletons. Many novel proteins were discovered which enabled a solid comparison with those of molluscs. By comparison, we proposed that crustaceans evolved novel proteins to form mineralized exoskeletons while sharing some proteins with those of molluscs. This is useful for us to understand the evolution of two major biomineralized phylum.

Hedgehog signaling is essential in the regulation of limb regeneration in the Chinese mitten crab, Eriocheir sinensis

Tissue autotomy is a unique adaptive response to environmental stress, followed by regeneration process compensating for the loss of body parts. The crustaceans present remarkable activity of appendage autotomy and regeneration, however, the molecular mechanism is still unclear. In this study, the Eriocheir sinensis Hedgehog (EsHH) and Smoothened (EsSMO) were identified in the regenerative limbs, and the function of Hedgehog signaling pathway on limb regeneration was evaluated. At the blastema growth stage of limb regeneration, the expression of EsHH and EsSMO was up-regulated in response to limb autotomy stress, and down-regulated at blastema differentiation stage. To clarify the effect of Hedgehog pathway during limb regeneration, the regenerative efficiency was evaluated with Smoothened inhibitor cyclopamine or RNAi (ds-HH) injection. We observed that the regenerative efficiency was significantly repressed with blockage of Hedgehog pathway at both the basal growth stage and the proecdysial growth stage, which was indicated by the delay of wound healing and blastema growth, as well as a decrease in the size of newly formed limbs. In addition, gene expression and BrdU incorporation assay showed that the proliferation and myogenic differentiation of blastema cells were suppressed with either cyclopamine or ds-HH injection. Thus, these results suggest that Hedgehog signaling pathway is essential for the establishment of limb regeneration in E. sinensis through promoting the proliferation and myogenic differentiation of blastema cells.

Eriocheir sinensis feminization-1c (Fem-1c) and Its Predicted miRNAs Involved in Sexual Development and Regulation

Feminization-1c (Fem-1c) is important for sex differentiation in the model organism Caenorhabditis elegans. In our previous study, the basic molecular characteristics of the Fem-1c gene (EsFem-1c) in Eriocheir sinensis (Henri Milne Edwards, 1854) were cloned to determine the relationship with sex differentiation. In this study, the genomic sequence of EsFem-1c contained five exons and four introns, with an exceptionally long 3'UTR sequence. The qRT-PCR results of EsFem-1c demonstrated lower tissue expression in the androgenic gland of the intersex crab than the normal male crab, implying that EsFem-1c plays a role in crab AG development. RNA interference experiments and morphological observations of juvenile and mature crabs indicated that EsFem-1c influences sexual development in E. sinensis. A dual-luciferase reporter assay disclosed that tcf-miR-315-5p effectively inhibits the translation of the EsFem-1c gene, influencing male development. An intriguing finding was that miRNA tcf-miR-307 could increase EsFem-1c expression by binding to the alternative splicing region with a length of 248 bp (ASR-248) in the 3'UTR sequence. The present research contributes to a better understanding of the molecular regulation mechanism of EsFem-1c and provides a resource for future studies of the miRNA-mediated regulation of sexual development and regulation in E. sinensis.

Analyses of the Dmrt family in a decapod crab, Eriocheir sinensis uncover new facets on the evolution of DM domain genes

DM domain genes are a group of transcription factors that are integral to sexual development and its evolution in metazoans. Their functions and regulatory mechanisms are not well understood in Malacostraca (crabs and crayfish) while these sex regulators have been widely identified in the past decade. In this study, the Dmrt family was investigated in the decapod crab, Eriocheir sinensis. We find that most members of the EsDmrt family begin to enrich around the juvenile 1 stage. In reproductive organs, EsDsx1, EsDsx2, EsiDMY and EsiDmrt1a highly express in the male-specific androgenic gland (AG), while EsDmrt-like, EsDsx-like, EsDmrt11E, and EsiDmrt1b show relatively high expression in testis. Also, we find the highly aberrant expression of EsiDMY and EsiDmrt1a in the chimeric AG, strongly indicating their function in AG development. Moreover, RNA interference of EsDsx1, EsiDMY, and EsiDmrt1a results in a significant decrease in transcription of the Insulin-like androgenic hormone (IAG), respectively. Our findings suggest that Dmrt genes in E. sinensis primarily function in male sexual differentiation, especially in AG development. Besides, this study identifies two unique groups of Dmrt genes in Malacostraca: Dsx and iDmrt1. In Malacostraca Dsx, we uncover a cryptic mutation in the eight zinc motif-specific residues, which were firmly believed to be invariant across the Dmrt family. This mutation sets the Malacostraca Dsx apart from all the other Dmrt genes and implies a different way of transcriptional regulation. Genes from the iDmrt1 group show phylogenetical limitation to the malacostracan species and underwent positive selection, suggesting their highly specialized gene function to this class. Based on these findings, we propose that Dsx and iDmrt1 in Malacostraca have developed unique transcriptional regulation mechanisms to facilitate AG development. We hope that this study would contribute to our understandings of sexual development in Malacostraca and provide new insights into the evolutionary history of the Dmrt family.

Whole genome evaluation analysis and preliminary Assembly of Oratosquilla oratoria (Stomatopoda: Squillidae)

BACKGROUND

As the dominant species of Stomatopoda, Oratosquilla oratoria has not been fully cultivated artificially, and the fishery production mainly depends on marine fishing. Due to the lack of stomatopod genome, the development of molecular breeding of mantis shrimps still lags behind.

METHODS AND RESULTS

A survey analysis was performed to obtain the genome size, GC content and heterozygosity ratio in order to provide a fundation for subsequent whole-genome sequencing. The results showed that the estimated genome size of the O. oratoria was about 2.56 G, and the heterozygosity ratio was 1.81%, indicating that it is a complex genome. Then the sequencing data was preliminarily assembled with k-mer = 51 by SOAPdenovo software to obtain a genome size of 3.01G and GC content of 40.37%. According to ReapeatMasker and RepeatModerler analysis, the percentage of repeats in O. oratoria was 45.23% in the total genome, similar to 44% in Survey analysis. The MISA tool was used to analyze the simple sequence repeat (SSR) characteristics of genome sequences including Oratosquilla oratoria, Macrobrachium nipponense, Fenneropenaeus chinensis, Eriocheir japonica sinensis, Scylla paramamosain and Paralithodes platypus. All crustacean genomes showed similar SSRs characteristics, with the highest proportion of di-nucleotide repeat sequences. And AC/GT and AGG/CCT repeats were the main types of di-nucleotide and tri-nucleotide repeats in O. oratoria.

CONCLUSION

This study provided a reference for the genome assembly and annotation of the O. oratoria, and also provided a theoretical basis for the development of molecular markers of O. oratoria.

Hippo Signaling Regulates Blastema Formation During Limb Regeneration in Chinese Mitten Crab (Eriocheir sinensis)

Limb autotomy and regeneration are specific adaptations of crustaceans in response to external stress and attacks, which make them a suitable model to investigate the mechanism of organ regeneration in invertebrates. In this study, the Hippo gene of Eriocheir sinensis (EsHPO) was identified, and the effects of Hippo signaling on limb regeneration were evaluated. The expression of EsHPO and other key components of Hippo signaling was down-regulated during the basal growth phase in response to limb autotomy stress and then up-regulated during the proecdysial growth phase. The descending expression patterns of Hippo signal components were correlated with transcriptional activation of YKI and downstream target genes during the blastema formation stage, which suggested that Hippo signaling plays a key role during limb regeneration in E. sinensis. To further test the hypothesis, the transcription factor YKI was blocked via verteporfin injection after autotomy, which disrupted limb regeneration by repressing wound healing and preventing blastema emergence. Furthermore, our experiments revealed that the proliferation of blastema cells was blocked by verteporfin. In addition, the expression of genes related to ECM remodeling, cell cycle progression, and apoptosis resistance was down-regulated following the injection of verteporfin. Our findings therefore indicate that Hippo signaling is essential for successful wound healing and limb regeneration in E. sinensis by inducing ECM remodeling, as well as promoting the proliferation and repressing the apoptosis of blastema cells.

Comparative transcriptome, digital gene expression and proteome profiling analyses provide insights into the brachyurization from the megalopa to the first juvenile in Eriocheir sinensis

Eriocheir sinensis larva normally experiences 11 stages. The reduced abdomen folded beneath the thorax is the most prominent characteristic of morphological alteration from megalopa to juvenile crab. Up to date, the molecular mechanisms of brachyurization remain a mystery. Here, transcriptome library, digital gene expression (DGE) libraries and proteome libraries at two developmental stages [the megalopa stage of E. sinensis (stage M) and the first stage of juvenile crab (stage J1)] of the Chinese mitten crab larva were constructed for RNA sequencing and iTRAQ approaches followed by bioinformatics analysis, respectively. In total, 1106 genes and 871 proteins were differentially expressed between the stage M and stage J1. Moreover, several important pathways were identified, including biosynthesis of secondary metabolites, metabolic pathways, focal adhesion, and some disease pathways. Besides, muscle contraction, oxidative phosphorylation, calcium signaling, PI3K-Akt, DNA replication pathway, and integrin signaling pathway also had important functions in brachyurization process. Furthermore, the components, actin, actin-related protein, collagens, filamin-A/B, laminin, integrins, paxillin, and fibronectin had up-regulated expression levels in M stage compared to J1 stage.

Dietary T-2 toxin induces transcriptomic changes in hepatopancreas of Chinese mitten crab (Eriocheir sinensis) via nutrition metabolism and apoptosis-related pathways

Long-term feed route exposure to T-2 toxin was proved to elicit growth retarding effects and induction of oxidative stress and apoptosis in Chinese mitten crab (Eriocheir sinensis). However, no study with a holistic perspective has been conducted to date to further describe the in-depth toxicological mechanism of T-2 toxin in E.sinensis. In this study, an RNA-Sequencing (RNA-seq) was used in this study to investigate the effects of feed supplementation with 0 mg/kg and 4 mg/kg T-2 toxin on the hepatopancreas transcriptome of E.sinensis and establish a hepatopancreas transcriptome library of T-2 toxin chronically exposed crabs after five weeks, where 14 differentially expressed genes (DEGs) were screened out across antioxidant, apoptosis, autophagy, glucolipid metabolism and protein synthesis. The actual expression of all the DEGs (Caspase, ATG4, PERK, ACSL, CAT, BIRC2, HADHA, HADHB, ACOX, PFK, eEFe1, eIF4ɑ, RPL13Ae) was also analyzed by real-time quantitative PCR (RT-qPCR). It was demonstrated that long-term intake of large amounts of T-2 toxin could impair antioxidant enzyme activity, promote apoptosis and protective autophagy, disrupt lipid metabolism and inhibit protein synthesis in the hepatopancreas of E.sinensis. In conclusion, this study explored the toxicity mechanism of T-2 toxin on the hepatopancreas of E.sinensis at the mRNA level, which lays the foundation for further investigation of the molecular toxicity mechanism of T-2 toxin in aquatic crustaceans.

Potential toxicity and dietary risk of tricyclazole to Chinese mitten crab (Eriocheir sinensis) in the rice-crab co-culture model

Tricyclazole is used as a common fungicide to control rice blast. However, studies on the toxicity of tricyclazole to crabs in the rice-crab co-culture system are still extremely rare. Here, the environmental dissipation of tricyclazole was monitored in this model, and the potential toxicity of tricyclazole to E. sinensis at environmental concentrations as well as the dietary risk was evaluated. The results showed that tricyclazole had no significant acute toxicity to E. sinensis (LC₅₀ > 100 mg/L), while it promoted body weight gain. Tricyclazole in the hepatopancreas had a higher persistent bioaccumulation risk than in the muscle. Tricyclazole suppressed the immune response of E. sinensis under prolonged exposure and there should be gender differences, with females being more sensitive. Lipid metabolism enzymes were also significantly inhibited. While tricyclazole stimulated males molting but prolonged molting duration, both molting and duration of females were also disturbed. The dietary risk assessment indicated that tricyclazole intake from current crab consumption was low risk. This evidence demonstrated that tricyclazole may have potential risks to individual development, nutritional quality, and economic value on E. sinensis and should be used with caution in rice-crab co-culture system whenever possible.

Effects of triazole plant growth regulators on molting mechanism in Chinese mitten crab (Eriocheir sinensis)

Rice crab co-culture is a new integrated farming model in China. The application of triazole plant growth regulators (PRGs) is often used as an advantageous option to combat rice lodging. However, there is still a gap regarding the toxicity of these PRGs on the growth and development of the Chinese mitten crab (Eriocheir sinensis, E. sinensis). Here the effect of triazoles (paclobutrazol and uniconazole) on the molting mechanism of E. sinensis was investigated. Monitoring of regulatory genes associated with molting showed that the two PRGs were found to inhibit the expression of ecdysteroid hormone (EH), ecdysteroid receptors gene (EcR), and retinoid X receptors gene (RXR) and induce secretion of molt-inhibiting hormone (MIH) gene. In addition, the activities of chitinase (CHIA) and N-acetyl-β-d-aminoglucosidase (β-NAGase) were also inhibited by exposure to PRGs. Exposure to PRGs also elevated the mRNA expression of the growth-related myostatin gene (MSTN). These results revealed that there is a long-term risk of exposure to triazoles PRGs that may inhibit molting and affect normal development and immune system of E. sinensis.

MEK homologue is involved in immune response by regulating antimicrobial peptides expression in Chinese mitten crab Eriocheir sinensis

MEK activates the phosphorylation of downstream molecules involved in various immune responses. In this study, an MEK homologue gene in Chinese mitten crab Eriocheir sinensis (designated as EsMEK) was investigated. EsMEK mRNA was constitutively expressed in all tissues with higher expression in hepatopancreas, hemocytes, and gills. EsMEK protein was mainly localized in the cytoplasm. Lipopolysaccharide (LPS) and Aeromonas hydrophila challenge significantly increased the mRNA levels of EsMEK in hemocytes. In addition, the mRNA expression level of some antimicrobial peptides (AMPs), including EsWAP, EsDWD1, and EsALF decreased significantly due to the inhibition of EsMEK by specific dsRNA in LPS-challenged crabs. Downstream pathway analysis revealed that the phosphorylation of EsERK decreased prominently after EsMEK inhibition. These results suggested that EsMEK played an important role in regulating the expression of antimicrobial peptides in E. sinensis through MEK-ERK pathway.

New insights for the regulatory feedback loop between type 1 crustacean female sex hormone (CFSH-1) and insulin-like androgenic gland hormone (IAG) in the Chinese mitten crab (Eriocheir sinensis)

To clarify the hormone control on sex determination and differentiation, we studied the Chinese mitten crab, Eriocheir sinensis (Henri Milne Edwards, 1854), a species with importantly economic and ecological significance. The crustacean female sex hormone (CFSH) and the insulin-like androgenic gland hormone (IAG) have been found to be related to the sex determination and/or differentiation. CFSH-1 of E. sinensis (EsCFSH-1) encoded a 227 amino-acid protein including a signal peptide, a CFSH-precursor-related peptide, and a mature CFSH peptide. Normally, EsCFSH-1 was highly expressed in the eyestalk ganglion of adult female crabs, while the expression was declined in the intersex crabs (genetic females). The intersex crabs had the androgenic glands, and the expression level of EsIAG was close to that of male crabs. During the embryogenesis and larval development, the changes of EsCFSH-1 and EsIAG genes expression in male and female individuals were shown after the zoea IV stage. Next, we confirmed the existence of the regulatory feedback loop between EsCFSH-1 and EsIAG by RNA interference experiment. The feminization function of EsCFSH-1 was further verified by examining the morphological change of external reproductive organs after EsCFSH-1 knockdown. The findings of this study reveal that the regulatory interplay between CFSH and IAG might play a pivotal role in the process of sex determination and/or differentiation in decapod crustaceans.

Identification and Expression Analysis of Dsx and Its Positive Transcriptional Regulation of IAG in Black Tiger Shrimp (Penaeus monodon)

Doublesex (Dsx) is a polymorphic transcription factor of the DMRTs family, which is involved in male sex trait development and controls sexual dimorphism at different developmental stages in arthropods. However, the transcriptional regulation of the Dsx gene is largely unknown in decapods. In this study, we reported the cDNA sequence of PmDsx in Penaeus monodon, which encodes a 257 amino acid polypeptide. It shared many similarities with Dsx homologs and has a close relationship in the phylogeny of different species. We demonstrated that the expression of the male sex differentiation gene Dsx was predominantly expressed in the P. monodon testis, and that PmDsx dsRNA injection significantly decreased the expression of the insulin-like androgenic gland hormone (IAG) and male sex-determining gene while increasing the expression of the female sex-determining gene. We also identified a 5′-flanking region of PmIAG that had two potential cis-regulatory elements (CREs) for the PmDsx transcription. Further, the dual-luciferase reporter analysis and truncated mutagenesis revealed that PmDsx overexpression significantly promoted the transcriptional activity of the PmIAG promoter via a specific CRE. These results suggest that PmDsx is engaged in male reproductive development and positively regulates the transcription of the PmIAG by specifically binding upstream of the promoter of the PmIAG. It provides a theoretical basis for exploring the sexual regulation pathway and evolutionary dynamics of Dmrt family genes in P. monodon.

"Omics" data unveil early molecular response underlying limb regeneration in the Chinese mitten crab, Eriocheir sinensis

Limb regeneration is a fascinating and medically interesting trait that has been well preserved in arthropod lineages, particularly in crustaceans. However, the molecular mechanisms underlying arthropod limb regeneration remain largely elusive. The Chinese mitten crab Eriocheir sinensis shows strong regenerative capacity, a trait that has likely allowed it to become a worldwide invasive species. Here, we report a chromosome-level genome of E. sinensis as well as large-scale transcriptome data during the limb regeneration process. Our results reveal that arthropod-specific genes involved in signal transduction, immune response, histone methylation, and cuticle development all play fundamental roles during the regeneration process. Particularly, Innexin2-mediated signal transduction likely facilitates the early stage of the regeneration process, while an effective crustacean-specific prophenoloxidase system (ProPo-AS) plays crucial roles in the initial immune response. Collectively, our findings uncover novel genetic pathways pertaining to arthropod limb regeneration and provide valuable resources for studies on regeneration from a comparative perspective.

Identification of Hox genes and their expression profiles during embryonic development of the emerging model organism, Macrobrachium olfersii

Hox genes encode transcription factors that specify the body segment identity during development, including crustaceans, such as amphipods and decapods, that possess a remarkable diversity of segments and specialized appendages. In amphipods, alterations of specialized appendages have been obtained using knockout experiment of Hox genes, which suggests that these genes are involved in the evolution of morphology within crustaceans. However, studies of Hox genes in crustaceans have been limited to a few species. Here, we identified the homeodomain of nine Hox genes: labial (lab), proboscipedia (pb), Deformed (Dfd), Sex combs reduced (Scr), fushi tarazu (ftz), Antennapedia (Antp), Ultrabithorax (Ubx), abdominal-A (abdA), and Abdominal-B (AbdB), and evaluated their expression by RT-qPCR and RT-PCR in the ovary, during embryonic development, and at the first larval stage (Zoea I) of the decapod Macrobrachium olfersii. The transcript levels of lab, Dfd, and ftz decreased and transcripts of pb, Scr, Antp, Ubx, abdA, and AbdB increased during embryonic development. Hox genes were expressed in mature ovaries and Zoea I larval stages, except Scr and ftz, respectively. In addition, isoforms of Dfd, Scr, Ubx, and abdA, which have been scarcely reported in crustaceans, were described. New partial sequences of 87 Hox genes from other crustaceans were identified from the GenBank database. Our results are interesting for future studies to determine the specific function of Hox genes and their isoforms in the freshwater prawn M. olfersii and to contribute to the understanding of the diversity and evolution of body plans and appendages in Crustaceans.

Microcystin-LR induces apoptosis in Juvenile Eriocheir sinensis via the mitochondrial pathway

Microcystin-LR (MC-LR), the toxic substance of cyanobacteria secondary metabolism, widely exists in water environments and poses great risks to living organisms. Some toxicological assessments of MC-LR have performed at physiological and biochemical levels. However, plenty of blanks about the potential mechanism in aquatic crustacean remains. In this study, we firstly assessed the exposure toxicity of MC-LR to juvenile E. sinensis and clarified that the 96 h LD50 of MC-LR was 73.23 μg/kg. Then, hepatopancreas transcriptome profiles of MC-LR stressed crabs were constructed at 6 h post-injection and 37 differential expressed genes (DEGs) were identified. These DEGs were enriched in cytoskeleton, peroxisome and apoptosis pathways. To further reveal the toxicity of MC-LR, oxidative stress parameters (SOD, CAT, GSH-px and MDA), apoptosis genes (caspase 3, bcl-2 and bax) and apoptotic cells were detected. Significant accumulated MDA and rise-fall enzyme activities verified the oxidative stress caused by MC-LR. It is noteworthy that quantitative real-time PCR and TUNEL assay indicated that MC-LR stress-induced apoptosis via the mitochondrial pathway. Interestingly, activator protein-1 may play a crucial role in mediating the hepatotoxicity of MC-LR by regulating apoptosis and oxidative stress. Taken together, our study investigated the toxic effects and the potential molecular mechanisms of MC-LR on juvenile E. sinensis. It provided useful data for exploring the toxicity of MC-LR to aquatic crustaceans at molecular levels.

Rational Design of High-Performance Keratin-Based Hemostatic Agents

Keratins are considered ideal candidates as hemostatic agents, but the development lags far behind their potentials due to the poorly understood hemostatic mechanism and structure-function relations, owing to the composition complexity in protein extracts. Here, it is shown that by using a recombinant synthesis approach, individual types of keratins can be expressed and used for mechanism investigation and further high-performance keratin hemostatic agent design. In the comparative evaluation of full-length, rod-domain, and helical segment keratins, the α-helical contents in the sequences are identified to be directly proportional to keratins' hemostatic activities, and Tyr, Phe, and Gln residues at the N-termini of α-helices in keratins are crucial in fibrinopeptide release and fibrin polymerization. A feasible route to significantly enhance the hemostatic efficiency of helical keratins by mutating Cys to Ser in the sequences for enhanced water wettability through soluble expression is then further presented. These results provide a rational strategy to design high-efficiency keratin hemostatic agents with superior performance over clinically used gelatin sponge in multiple animal models.

Genetic and morphological evidence indicates the persistence of Japanese mitten crab mitochondrial DNA in Europe for over 20 years and its introgression into Chinese mitten crabs

Cryptic biological invasions are largely unrecognised, leading to an underestimation of the number of invading taxa and their potential impacts. The Chinese mitten crab, Eriocheir sinensis, is a highly invasive species with serious economic and ecological impacts in Europe. Recently, mitochondrial DNA (mtDNA) of the Japanese mitten crab, E. japonica, has been discovered in populations from The Netherlands, Poland and Germany, but the taxonomic status and time of introduction of specimens carrying this mtDNA are uncertain. To this end, we investigated the morphology and variation of the mitochondrial cytochrome c oxidase subunit I (COI) gene of mitten crabs collected in central-western Europe between 1998 and 2020. Mitten crabs from Belgium harboured a Japanese mitten crab COI haplotype in 33% to 65% of individuals, even in our earliest samples from 1998. All other studied populations carried only Chinese mitten crab COI haplotypes. Morphologically, many of the juvenile Belgian mitten crabs showed intermediate traits between the two species, while all investigated adult mitten crabs, regardless of their mitochondrial haplotype or country of origin, were morphologically assigned to E. sinensis. This intermediate morphology of the juveniles and genetic-morphological discrepancy of adults suggests that Japanese mitten crabs introgressed with Chinese mitten crabs, which could have happened both before and after the introduction of mitten crabs to Europe. A specific Chinese mitten crab COI haplotype, found in Belgium, was previously only known from Vladivostok (Russia), where Chinese and Japanese mitten crab hybrids naturally occur. This Far East region is, therefore, a plausible source for at least part of the mitten crab mitochondrial diversity in Belgium.

Genome of a giant isopod, Bathynomus jamesi, provides insights into body size evolution and adaptation to deep-sea environment

Background

The deep-sea may be regarded as a hostile living environment, due to low temperature, high hydrostatic pressure, and limited food and light. Isopods, a species-rich group of crustaceans, are widely distributed across different environments including the deep sea and as such are a useful model for studying adaptation, migration, and speciation. Similar to other deep-sea organisms, giant isopods have larger body size than their shallow water relatives and have large stomachs and fat bodies presumably to store organic reserves. In order to shed light on the genetic basis of these large crustaceans adapting to the oligotrophic environment of deep-sea, the high-quality genome of a deep-sea giant isopod Bathynomus jamesi was sequenced and assembled.

Results

B. jamesi has a large genome of 5.89 Gb, representing the largest sequenced crustacean genome to date. Its large genome size is mainly attributable to the remarkable proliferation of transposable elements (84%), which may enable high genome plasticity for adaptive evolution. Unlike its relatives with small body size, B. jamesi has expanded gene families related to pathways of thyroid and insulin hormone signaling that potentially contribute to its large body size. Transcriptomic analysis showed that some expanded gene families related to glycolysis and vesicular transport were specifically expressed in its digestive organs. In addition, comparative genomics and gene expression analyses in six tissues suggested that B. jamesi has inefficient lipid degradation, low basal metabolic rate, and bulk food storage, suggesting giant isopods adopt a more efficient mechanism of nutrient absorption, storage, and utilization to provide sustained energy supply for their large body size.

Conclusions

Taken together, the giant isopod genome may provide a valuable resource for understanding body size evolution and adaptation mechanisms of macrobenthic organisms to deep-sea environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01302-6.

Lipid metabolism, immune and apoptosis transcriptomic responses of the hepatopancreas of Chinese mitten crab to the exposure to microcystin-LR

Global warming is favouring the incidence, intensity and duration of harmful cyanobacterial blooms. Microcystin-LR (MC-LR), a hepatotoxic agent, is produced during cyanobacterial blooms. To understand the molecular mechanisms of acute hepatotoxic effect of low doses of MC-LR in crab, we examined differentially expressed genes in samples of the hepatopancreas of Chinese mitten crab (Eriocheir sinensis) collected in 48 h after injections of MC-LR at doses of 0, 25, 50, and 75 µg/kg. The results revealed that MC-LR induced changes in corresponding gene led to the accumulation of triglycerides. MC-LR exposure affected sterol metabolism. Apoptosis-related genes such as Fas-L, Bcl-XL, Cytc, AiF, p53, PERK, calpain, CASP2, CASP7, α-tubulin, PARP, GF, G12, and PKC were upregulated. Conversely, expression levels of CASP10 and ASK1 were downregulated. Genes related to the regulation of actin cytoskeleton (Rho, ROCK, MLCP, MLC, PAK, and PFN) were upregulated. Further, expression levels of genes encoding fatty acid elongation-related enzymes were upregulated, but the expression of genes related to fatty acid synthesis was slightly down regulated. Taken together, these results demonstrated the hepatic toxicity and molecular mechanisms of changes in lipid metabolism, immune and apoptosis in Chinese mitten crab under the MC-LR-induced stress, which is the first report on crabs and performs a comprehensive analysis and a new insight of the molecular toxicological responses in crabs.

Insulin-like signaling promotes limb regeneration in the Chinese mitten crab (Eriocheir sinensis)

In the pond culture of Chinese mitten crabs, limb autotomy seriously affects the feeding efficiency, immunity and survival. Therefore, it is crucial to understand the mechanism of limb regeneration of mitten crabs, so that culture strategies could be developed to reduce the limb impairment rate. The insulin-like signaling (ILS) pathway is evolutionarily conserved, and plays key roles in the growth and immunity of various species. In this study, a full-length cDNA of insulin-like receptor (EsInR) was identified from Eriocheir sinensis, and its mRNA expression patterns during limb regeneration was evaluated. The cDNA of EsInR includes a 4326 bp ORF encoding a protein of 1441 amino acids, with conserved α-and β-subunits. The EsInR and genes related to ILS were found to be upregulated during limb regeneration, which indicated that ILS plays a key role in limb regeneration of E. sinensis. Our experiment revealed that inhibition of ILS through injection of the InR inhibitor GSK1838705A at the blastema formation stage significantly reduced the limb regeneration rate compared to control group. In addition, injection of GSK1838705A also reduced the size of newly formed limbs after the molting cycle. Furthermore, we found that genes related to myogenesis were downregulated following injection of InR inhibitor both before and after molting. The results also indicated that cyclins and CDK1 were downregulated, while CKIs were upregulated following treatment with the InR inhibitor. These results suggest that ILS regulates limb regeneration in E. sinensis by promoting muscle growth and regeneration in response to autotomy stress. Thus, we identified a conserved insulin-like receptor in E. sinensis, and provide new evidence for the involvement of ILS in the regulation of limb autotomy and regeneration in crustaceans.

Full-Length Transcriptome of Red Swamp Crayfish Hepatopancreas Reveals Candidate Genes in Hif-1 and Antioxidant Pathways in Response to Hypoxia-Reoxygenation

Red swamp crayfish is particularly prone to exposure to hypoxia-reoxygenation stress on account of the respiration and rhythmic, light-dependent photosynthetic activity of the algae and aquatic grass. Up to now, the regulation mechanisms of the adverse effects of hypoxia-reoxygenation for this species were still unknown, especially the roles of the antioxidant enzymes in reducing oxidative damage during reoxygenation. To screen for vital genes or pathways upon hypoxic-reoxygenation stress, hepatopancreas gene expression profiles were investigated by using a strategy combining second and third generation sequencing. Five groups of samples, including hypoxia for 1 and 6 h with DO of 1.0 mg/L, reoxygenation for 1 and 12 h with DO of 6.8 mg/L, and the samples under normoxia condition, were used for transcriptome sequencing. Twenty Illumina cDNA libraries were prepared to screen for the differentially expressed genes (DEGs) among the 5 groups of samples. Based on the assembled reference full-length transcriptome, 389 and 533 significantly DEGs were identified in the groups under severe hypoxia treatment for 1 and 6 h, respectively. The top three enriched pathways for these DEGs were "protein processing in endoplasmic reticulum," "MAPK signaling pathway," and "endocytosis." Among these DEGs, hypoxia-inducible factor 1α (Hif-1α) and some Hif-1 downstream genes, such as Ugt-1, Egfr, Igfbp-1, Pk, and Hsp70, were significant differentially expressed when exposed to hypoxia stress. A series of antioxidant enzymes, including two types of superoxide dismutase (Cu/ZnSOD and MnSOD), catalase (CAT), and glutathione peroxidase (GPx), were identified to be differentially expressed during hypoxia-reoxygenation treatment, implying their distinct modulation roles on reoxygenation-induced oxidative stress. The full-length transcriptome and the critical genes characterized should contribute to the revelation of intrinsic molecular mechanism being associated with hypoxia/reoxygenation regulation and provide useful foundation for future genetic breeding of the red swamp crayfish.

A chromosome-level genome of Portunus trituberculatus provides insights into its evolution, salinity adaptation and sex determination

Portunus trituberculatus (Crustacea: Decapoda: Brachyura), commonly known as the swimming crab, is of major ecological importance, as well as being important to the fisheries industry. P. trituberculatus is also an important farmed species in China due to its rapid growth rate and high economic value. Here, we report the genome sequence of the swimming crab, which was assembled at the chromosome scale, covering ~1.2 Gb, with 79.99% of the scaffold sequences assembled into 53 chromosomes. The contig and scaffold N50 values were 108.7 kb and 15.6 Mb, respectively, with 19,981 protein-coding genes. Based on comparative genomic analyses of crabs and shrimps, the C2H2 zinc finger protein family was found to be the only gene family expanded in crab genomes, suggesting it was closely related to the evolution of crabs. The combination of transcriptome and bulked segregant analysis provided insights into the genetic basis of salinity adaptation and rapid growth in P. trituberculatus. In addition, the specific region of the Y chromosome was located for the first time in the genome of P. trituberculatus, and three genes were preliminarily identified as candidate genes for sex determination in this region. Decoding the swimming crab genome not only provides a valuable genomic resource for further biological and evolutionary studies, but is also useful for molecular breeding of swimming crabs.