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Scientific Data Apr 2023Red claw crayfish (Cherax quadricarinatus) is an aquatic crustacean with considerable potential for the commercial culture and an ideal model for studying the mechanism...
Red claw crayfish (Cherax quadricarinatus) is an aquatic crustacean with considerable potential for the commercial culture and an ideal model for studying the mechanism of sex determination. To provide better genomic resources, we assembled a chromosome-level genome with a size of 5.26 Gb and contig N50 of 144.33 kb. Nearly 90% of sequences were anchored to 100 chromosomes, which represents the high-quality crustacean genome with the largest number of chromosomes ever reported. The genome contained 78.69% repeat sequences and 20,460 protein-coding genes, of which 82.40% were functionally annotated. This chromosome-scale genome would be a valuable reference for assemblies of other complex genomes and studies of evolution in crustaceans.
Topics: Animals; Astacoidea; Chromosomes; Genome; Genomics; Phylogeny; Repetitive Sequences, Nucleic Acid
PubMed: 37062798
DOI: 10.1038/s41597-023-02124-z -
PLoS Genetics Dec 2023Clonal genome evolution is a key feature of asexually reproducing species and human cancer development. While many studies have described the landscapes of clonal genome...
Clonal genome evolution is a key feature of asexually reproducing species and human cancer development. While many studies have described the landscapes of clonal genome evolution in cancer, few determine the underlying evolutionary parameters from molecular data, and even fewer integrate theory with data. We derived theoretical results linking mutation rate, time, expansion dynamics, and biological/clinical parameters. Subsequently, we inferred time-resolved estimates of evolutionary parameters from mutation accumulation, mutational signatures and selection. We then applied this framework to predict the time of speciation of the marbled crayfish, an enigmatic, globally invasive parthenogenetic freshwater crayfish. The results predict that speciation occurred between 1986 and 1990, which is consistent with biological records. We also used our framework to analyze whole-genome sequencing datasets from primary and relapsed glioblastoma, an aggressive brain tumor. The results identified evolutionary subgroups and showed that tumor cell survival could be inferred from genomic data that was generated during the resection of the primary tumor. In conclusion, our framework allowed a time-resolved, integrated analysis of key parameters in clonally evolving genomes, and provided novel insights into the evolutionary age of marbled crayfish and the progression of glioblastoma.
Topics: Animals; Humans; Glioblastoma; Genome; Astacoidea; Genomics; Biological Evolution; Mutation
PubMed: 38096267
DOI: 10.1371/journal.pgen.1011085 -
Integrative and Comparative Biology Aug 2020Invasive species represent a serious ecological threat for many ecosystems worldwide and provide a unique opportunity to investigate rapid adaptation and evolution.... (Review)
Review
Invasive species represent a serious ecological threat for many ecosystems worldwide and provide a unique opportunity to investigate rapid adaptation and evolution. Genetic variation allows populations of organisms to be both robust and adaptable to different environmental conditions over evolutionary timeframes. In contrast, invasive animals can rapidly adapt to new environments, with minimal genetic diversity. Thus, the extent to which environmental effects can trigger epigenetic responses is particularly interesting for understanding the role of epigenetics in rapid adaptation. In this review, we provide a brief overview of the different epigenetic mechanisms that control gene expression, and emphasize the importance of epigenetics for environmental adaptation. We also discuss recent publications that provide important examples for the role of epigenetic mechanisms in environmental adaptation. Furthermore, we present an overview of the current knowledge about epigenetic modulation as an adaptive strategy for invasive species. A particularly interesting example is provided by the marbled crayfish, a novel, monoclonal freshwater crayfish species that has colonized diverse habitats within a few years. Finally, we address important limitations of current approaches and highlight the potential importance of less well-known mechanisms for non-genetic organismal adaptation.
Topics: Adaptation, Biological; Animals; Astacoidea; Ecosystem; Epigenesis, Genetic; Introduced Species
PubMed: 32333755
DOI: 10.1093/icb/icaa023 -
Ecotoxicology and Environmental Safety Jan 2023Microplastic pollution has attracted a lot of attention in recent years. Not only can it be ingested by animals, but it can easily become a carrier of other pollutants,...
Microplastic pollution has attracted a lot of attention in recent years. Not only can it be ingested by animals, but it can easily become a carrier of other pollutants, forming a composite pollutant with potentially toxic effects on organisms. We investigated the effect of Cu on the accumulation of polystyrene microplastics (PS) in the gills of Procambarus clarkii and whether PS exacerbated the immune toxicity of Cu to P. clarkii were exposed to Cu, PS and PS+Cu for 48 h, the accumulation of PS in gill and hepatopancreas immune and antioxidant indices were analyzed. The objective was to investigate the toxic effects of Ps and Cu compound pollutants on P. clarkii and whether the accumulated pollutants would cause food safety problems. The results showed that microplastic particles adhered to each other and aggregated in the PS+Cu group, and the number of microplastic particles in gill in the PS+Cu group was significantly lower than that in the PS group. Compared with the other two treatment groups, SOD, CAT, GPx activities and MDA content increased significantly in the PS+Cu group and were relatively delayed. At 12 h, 24 h, 36 h and 48 h, the SOD mRNA expression levels in the PS+Cu group were all significantly lower than those in the Cu group (P < 0.05). At 24 h and 48 h, CAT mRNA expression in the PS+Cu group was significantly higher than that in the Cu group (P < 0.05). Crustin 4 mRNA expressions in the PS+Cu group was significantly higher than that in the Cu group at 12 h and 36 h (P < 0.05). The results demonstrate that the PS and Cu compound reduced the accumulation of microplastic particles in the gill. PS particles delayed Cu entry into P. clarkii for a short time (12 h) and reduced the toxic effect, but with the increase of exposure time (24 h and 48 h), the toxic effect of PS and Cu complexes on P. clarkii increases, and the large accumulation of PS and Cu complexes may cause food safety problems.
Topics: Animals; Copper; Plastics; Microplastics; Astacoidea; Polystyrenes; Water Pollutants, Chemical; Superoxide Dismutase; RNA, Messenger
PubMed: 38321696
DOI: 10.1016/j.ecoenv.2022.114432 -
Chemosphere Dec 2023This study investigated the toxicity of polyethylene microplastics (MPs; <0.02 mm) and CuSO4, alone and in combination, on the freshwater crayfish Pontastacus...
Single and combined effects of CuSO and polyethylene microplastics on biochemical endpoints and physiological impacts on the narrow-clawed crayfish Pontastacusleptodactylus.
This study investigated the toxicity of polyethylene microplastics (MPs; <0.02 mm) and CuSO4, alone and in combination, on the freshwater crayfish Pontastacus leptodactylus. In this study, the crayfish were exposed to PE-MPs (0.0, 0.5, and 1 mg L) and CuSO4·5H2O (0.0, 0.5, and 1 mg L) for a period of 28 days. Next, multi-biomarkers, including biochemical, immunological, and oxidative stress indicators were analyzed. Results showed that co-exposure to PE-MPs and CuSO4 resulted in increased aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), and decreased alkaline phosphatase (ALP), butyrylcholinesterase (BChE), and gamma-glutamyl-transferase (GGT). Triglycerides, cholesterol, glucose, and albumin content also increased. Although no significant change was observed in lysozyme and phenoloxidase activities in crayfish co-exposed to 0.5 mg L MPs and 0.5 mg L CuSO4, their activities were significantly decreased in other experimental groups. Oxidative stress parameters in hepatopancreas indicated increased superoxide dismutase (SOD), glutathione peroxidase (GPx), and in malondialdehyde (MDA) levels, but decreased catalase (CAT), glucose 6-phosphate dehydrogenase (G6PDH), and cellular total antioxidant (TAC). Results showed that the sub-chronic toxicity of CuSO4 was confirmed. The study confirmed the toxicity of CuSO4 and found that higher concentrations led to more severe effects. Co-exposure to PE-MPs and CuSO4 primarily compromised the endpoints, showing increased toxicity when both pollutants were present in higher concentrations. The activities of POX, LYZ, ALP, GGT, LDH, and CAT were suppressed by both CuSO4 and MPs. However, a synergistic increase was observed in other measured biomarkers in crayfish co-exposed to CuSO4 and MPs.
Topics: Animals; Microplastics; Polyethylene; Plastics; Astacoidea; Butyrylcholinesterase; Antioxidants; Oxidative Stress; Glucose; Biomarkers
PubMed: 37865200
DOI: 10.1016/j.chemosphere.2023.140478 -
Journal of Microbiological Methods Nov 2022Field-ready qPCR assays with extended shelf-life support monitoring programs for emerging aquatic pathogens and enable quick conservation and management decisions. Here,...
Field-ready qPCR assays with extended shelf-life support monitoring programs for emerging aquatic pathogens and enable quick conservation and management decisions. Here, we developed, validated, and tested the shelf-life of qPCR assays targeting Gyrodactylus salaris and Aphanomyces astaci with lyophilization and air-drying.
Topics: Animals; Astacoidea; Aphanomyces; Real-Time Polymerase Chain Reaction
PubMed: 36241007
DOI: 10.1016/j.mimet.2022.106594 -
Communications Biology Sep 2021The marbled crayfish (Procambarus virginalis) is a triploid and parthenogenetic freshwater crayfish species that has colonized diverse habitats around the world....
The marbled crayfish (Procambarus virginalis) is a triploid and parthenogenetic freshwater crayfish species that has colonized diverse habitats around the world. Previous studies suggested that the clonal marbled crayfish population descended as recently as 25 years ago from a single specimen of P. fallax, the sexually reproducing parent species. However, the genetic, phylogeographic, and mechanistic origins of the species have remained enigmatic. We have now constructed a new genome assembly for P. virginalis to support a detailed phylogeographic analysis of the diploid parent species, Procambarus fallax. Our results strongly suggest that both parental haplotypes of P. virginalis were inherited from the Everglades subpopulation of P. fallax. Comprehensive whole-genome sequencing also detected triploid specimens in the same subpopulation, which either represent evolutionarily important intermediate genotypes or independent parthenogenetic lineages arising among the sexual parent population. Our findings thus clarify the geographic origin of the marbled crayfish and identify potential mechanisms of parthenogenetic speciation.
Topics: Animals; Astacoidea; Biological Evolution; Genetic Speciation; Genome; Genotype; Parthenogenesis; Phylogeography
PubMed: 34535758
DOI: 10.1038/s42003-021-02609-w -
Parasitology Sep 2022Human autochthonous infections with the trematode are increasingly being reported in North America, but the true prevalence and geographic distribution are unknown.... (Review)
Review
Human autochthonous infections with the trematode are increasingly being reported in North America, but the true prevalence and geographic distribution are unknown. Ingestion of raw crayfish is reported in most human cases, typically in the context of alcohol intoxication. Risk of infection varies depending on what part of the crayfish is ingested as metacercariae of (>50% mature to adults) localize to the heart and pericardium of the crayfish. Reported human cases have manifested primarily in otherwise healthy young adults presenting with severe eosinophilic pneumonia, pleuritis, systemic symptoms, dermatologic lesions and cerebral involvement. However, it is likely that many infections go unreported due to lack of awareness, mild illness or the absence of rapid commercially available diagnostic tests. Promising advances have been made related to novel diagnostic targets. Conservation of these antigen targets among at least four species could make these antigens viable for diagnostic testing of specifically as well as other species, but additional studies and funding investments are required. Public and physician awareness may have improved due to targeted education campaigns, but ongoing activities to raise awareness are needed, particularly in areas where cases have not been frequently reported to date.
Topics: Animals; Astacoidea; Humans; Metacercariae; North America; Paragonimiasis; Paragonimus
PubMed: 35965058
DOI: 10.1017/S0031182021001359 -
Journal of the American Association For... May 2022Crayfish (Decapoda: Astacoidea and Parastacoidea) are among the few animals that have stem cells in hemolymph, with the capacity to continuously produce differentiated...
Crayfish (Decapoda: Astacoidea and Parastacoidea) are among the few animals that have stem cells in hemolymph, with the capacity to continuously produce differentiated neuronal structures throughout life. As the use of crayfish and other invertebrates increases in biomedical research, we must develop laboratory standards and guidelines for performing clinical procedures. This manuscript presents introductory protocols for anesthesia in crayfish during diagnostic imaging. Five anesthetic protocols were evaluated: immersion in buffered tricaine methanesulfonate (MS222; 50 mg/L); immersion in buffered MS222 (150 mg/L); immersion in propofol (65 mg/L); injection of propofol (50 mg/kg); and injection of propofol (100 mg/kg) into the ventral surface of an abdominal somite. MS222 immersion (50 and 150 mg/L) had no observable effect on crayfish. After an extended period of time, immersion in propofol (65 mg/L) created a sedative effect suitable for short-term handling. Propofol injection (50 mg/kg) into the ventral surface of an abdominal somite created an effective plane of anesthesia without adverse effects during or after recovery. Propofol injection at 100 mg/kg had adverse effects and is not recommended for use in crayfish. CT imaging was performed successfully as proof of concept for handling anesthetized crayfish. These findings provide initial data for the anesthetization of crayfish used in research settings.
Topics: Aminobenzoates; Anesthesia; Anesthetics, Local; Animals; Astacoidea; Mesylates; Propofol; Tomography; Tomography, X-Ray Computed
PubMed: 35537819
DOI: 10.30802/AALAS-JAALAS-21-000133 -
Frontiers in Immunology 2023In invertebrates, hemocytes are the key factors in innate immunity. However, the types of invertebrate immune hemocytes are unclassified due to the limitation of...
In invertebrates, hemocytes are the key factors in innate immunity. However, the types of invertebrate immune hemocytes are unclassified due to the limitation of morphological classification. To determine the immune hemocytes of crustaceans, the heterogeneity of hemocytes of shrimp and crayfish , two representative crustacean species, were characterized in this study. The results of single-cell RNA sequencing indicated that shrimp and crayfish contained 11 and 12 types of hemocytes, respectively. Each of different types of hemocytes specifically expressed the potential marker genes. Based on the responses of shrimp and crayfish to the infection of white spot syndrome virus (WSSV) and the challenge of lipopolysaccharide (LPS), four types of immune hemocytes of crustaceans were classified, including semi-granular hemocytes involved in antimicrobial peptide production, granular hemocytes responsible for the production of antimicrobial peptides, hemocytes related to cell proliferation and hemocytes in immunity-activated state. Therefore, our study provided the first classification of crustacean hemocytes as well as of immune hemocytes of crustaceans at the single-cell resolution, which would be helpful to understand the innate immunity of invertebrates.
Topics: Animals; Hemocytes; Immunity, Innate; Astacoidea; White spot syndrome virus 1; Penaeidae
PubMed: 36761772
DOI: 10.3389/fimmu.2023.1121528