Characterization of Population Genetic Structure of red swamp crayfish, Procambarus clarkii, in China

Genetic Mechanism Analysis Related to Cold Tolerance of Red Swamp Crayfish, Procambarus clarkii

In China, the red swamp crayfish (Procambarus clarkii), a notorious invasive species, has become an important economic freshwater species. In order to compare the genetic diversity and population structure of crayfish from northern and southern China, we collected 60 crayfish individuals from 4 crayfish populations in northern China and 2 populations in southern China for sequencing using the 2b-RAD technique. Additionally, the whole genome sequence information obtained by 2b-RAD of 90 individuals from 2 populations in northern China and 7 populations in southern China were downloaded from NCBI. After quality control, a total of 25,371 SNPs were detected from approximately 54.22 billion raw reads. Based on these SNPs, high genetic diversity was observed in the 15 crayfish populations in China. The pairwise FST values indicated that there was a large genetic differentiation of crayfish populations in northern and southern China. Despite common genetic backgrounds, due to geographical barriers, genetic divergence has been observed in northern and southern China crayfishes. The principal component analysis in combination with Admixture and Neighbor-Joining tree analysis showed that the crayfish fell into two clusters corresponding to geographical regions. The integrated analysis of whole genome and transcriptome data showed that two genes (CETN4 and CPEB2) might play important roles during crayfish resistance to a cold environment. This study reveals the genetic differentiation of crayfish populations in northern and southern China and provides clues to the genetic mechanism related to cold adaptation.

Transcriptomic analysis provides insights into the immune responsive genes in the Procambarus clarkii hepatopancreas challenged with Vibrio parahaemolyticus

Procambarus clarkii is an economically important species in China; however, its high mortality rate due to pathogenic bacteria, particularly Vibrio parahaemolyticus, results in significant economic loss. This study aimed to understand the immune response of crayfish to bacterial infection by comparing and analyzing transcriptome data of hepatopancreatic tissue from P. clarkii challenged with V. parahaemolyticus or treated with PBS. Physiological indices (TP, Alb, ACP, and AKP) were analyzed, and tissue sections were prepared. After assembling and annotating the data, 18,756 unigenes were identified. A comparison of the expression levels of these unigenes between the control and V. parahaemolyticus groups revealed 4037 DEGs, with 2278 unigenes upregulated and 1759 downregulated in the V. parahaemolyticus group. GO (Gene Ontology) enrichment analysis shows that the DGEs are mainly enriched in cellular anatomical activity, bindinga and cellular process, enrichment analysis of KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways showed that DGEs were mainly enriched in Base excision repair, Phagosome and Longevity regulating pathway. At the same time, lysosome was also enriched. The phagosome and lysosome pathways play a crucial role in the immune defense of crayfish against V. parahaemolyticus injection that will be highlighted. In addition, the expression levels of six selected immune-related DEGs were measured using qRT-PCR, which validated the results of RNA-seq analysis. This study provides a new perspective on the immune system and defense mechanisms of P. clarkii and a valuable foundation for further investigation of the molecular immune mechanisms of this species.

Effects of Dietary Melatonin on Antioxidant Capacity, Immune Defense, and Intestinal Microbiota in Red Swamp Crayfish (Procambarus clarkii)

The aim of this study was to investigate the effects of melatonin (MT) feed supplementation on the antioxidant capacity, immune defense, and intestinal flora in Procambarus clarkii (P. clarkii). Six groups of P. clarkii were fed test feeds containing different levels of MT: 0 mg/kg (control), 22.5, 41.2, 82.7, 165.1, and 329.2 mg/kg for a duration of 2 months. The specific growth rate, hepatosomatic index, and condition factor were recorded highest in the test group of shrimp fed an MT concentration of 165.1 mg/kg. Compared to the control group, the rate of apoptosis was lower in hepatopancreas cells of P. clarkii supplemented with high concentrations of MT. Analyses of antioxidant capacity and immune-response-related enzymes in the hepatopancreas indicated that dietary supplementation of MT significantly augmented both the antioxidant system and immune responses. Dietary MT supplementation significantly increased the expression levels of antioxidant-immunity-related genes and decreased the expression levels of genes linked to apoptosis. Dietary MT was associated with an elevation in the abundance of the Firmicutes and a reduction in the abundance of the Proteobacteria in the intestines; besides, resulting in an increase in the abundance of beneficial bacteria, such as Lactobacilli. The broken-line model indicated that the suitable MT concentration was 154.09-157.09 mg/kg. MT supplementation enhanced the growth performance of P. clarkii, exerting a positive influence on the intestinal microbiota, and bolstered both immune response and disease resistance. Thus, this study offered novel perspectives regarding the application of dietary MT supplementation within the aquaculture field.

Genomic insights into the conservation status of the Idle Crayfish Austropotamobius bihariensis Pârvulescu, 2019: low genetic diversity in the endemic crayfish species of the Apuseni Mountains

BACKGROUND

Biodiversity in freshwater ecosystems is declining due to an increased anthropogenic footprint. Freshwater crayfish are keystone species in freshwater ecosystems and play a crucial role in shaping the structure and function of their habitats. The Idle Crayfish Austropotamobius bihariensis is a native European species with a narrow distribution range, endemic to the Apuseni Mountains (Romania). Although its area is small, the populations are anthropogenically fragmented. In this context, the assessment of its conservation status is timely.

RESULTS

Using a reduced representation sequencing approach, we identified 4875 genomic SNPs from individuals belonging to 13 populations across the species distribution range. Subsequent population genomic analyses highlighted low heterozygosity levels, low number of private alleles and small effective population size. Our structuring analyses revealed that the genomic similarity of the populations is conserved within the river basins.

CONCLUSION

Genomic SNPs represented excellent tools to gain insights into intraspecific genomic diversity and population structure of the Idle Crayfish. Our study highlighted that the analysed populations are at risk due to their limited genetic diversity, which makes them extremely vulnerable to environmental alterations. Thus, our results emphasize the need for conservation measures and can be used as a baseline to establish species management programs.

Concentrations, sources and health risk of bisphenols in red swamp crayfish (Procambarus clarkii) from South-Eastern China

Bisphenol analogs (BPs) are extensively employed in commercial and industrial products and they have been found in a variety of environmental matrices and human samples. The red swamp crayfish (Procambarus clarkii) has been a trendy food in China in recent decades. However, the levels of BPs in Chinese crayfish and the associated hazards of human exposure remain unknown. Thus, in this study, the levels of eight BPs in crayfish gathered from five major provinces engaged in crayfish within the Yangtze River Basin were analyzed. Additionally, the health risks for humans by ingesting crayfish were calculated. BPs were frequently detected in crayfish tissues, indicating the wide occurrence of these chemicals. In comparison to other substitutions, BPA remains the dominant bisphenol analog. Most of the BPs were observed to accumulate in the hepatopancreas compared to the muscle, so consuming the hepatopancreas of crayfish is not recommended. With the exception of BPS, the Estimated Daily Intakes (EDIs) of the remaining BPs exceeded the Tolerable Daily Intake (TDI) specified by the European Food Safety Authority (EFSA) by a factor of 1.75-69.0. The mean hazard index (HI) values exceeded 1 for both hepatopancreas and muscle in all provinces, and the mean HI values for hepatopancreas were significantly higher than those for muscle, indicating potential health risks for local consumers.

Exposure and Health Risk Assessment of Heavy Metal in Crayfish from the Middle and Lower Reaches of the Yangtze River

Red swamp crayfish (Procambarus clarkia) is an exposed species to heavy metals due to their lifestyle of direct contact with sediments. Based on the complete crayfish industry, we focus on the presence of heavy metals in crayfish from different circulation links, which provides a new idea for the investigation of heavy metals in food. To analyze the exposure levels of heavy metals in crayfish during aquaculture and circulation, the five elements (Cd, Pb, Hg, Cr, Cu) in crayfish from 126 sampling sites were investigated. Cultured environmental samples were collected for Spearman correlation analysis. Monte Carlo simulation was used to analyze the uncertain health risks of heavy metals in crayfish. The results indicated that the average heavy metal concentrations in crayfish were all below the limit threshold values. The hepatopancreas was the main target organ for heavy metal accumulation (Cd: 0.3132 mg/kg; Pb: 0.0258 mg/kg; Hg: 0.0072 mg/kg; Cr: 0.1720 mg/kg; Cu: 10.6816 mg/kg). The positive correlation of heavy metal content between crayfish and sediments was not significant under the crayfish-rice coculture model. The 95th HI values for adults and children ranged from 0.022 to 0.042 and 0.071 to 0.137, well below 1, indicating that heavy metals do not pose a noncarcinogenic risk to humans. The potential carcinogenic risk of Cd and Cr in crayfish should be taken seriously, as the 95th CR values for children have reached 4.299 × 10-5 and 6.509 × 10-5, respectively.

Comparison of the gut microbiota and metabolism in different regions of Red Swamp Crayfish (Procambarus clarkii)

Background

The gut microbiota is very important for maintaining the homeostasis and health of crustaceans. Many factors affect the gut microbiota of crustaceans, one of which is temperature. However, it is currently unclear how temperature affects the gut microbiota and metabolites of Procambarus clarkii.

Methods

Using metagenomic sequencing and gas chromatography-mass spectrometry (GC-MS) techniques, the gut microbiota and metabolites of P. clarkii from Hubei (HB), Jiangsu (JS), Shandong (SD), and Zhejiang (ZJ) in China were investigated.

Results

Under the impact of temperature, the gut microbiota and metabolites of P. clarkii exhibit a specific trend of change. The primary pathogenic bacteria affecting P. clarkii are Citrobacter, Enterobacterium, and Aeromonas, which are affected by temperature. Two metabolites, namely, sugars and amino acids, are regulated by temperature.

Implication

This study demonstrated that the gut microbiota and gut metabolites of P. clarkii were considerably affected by temperature. It provides a theoretical basis for the systematic study of P. clarkii and provides a basis for a healthy culture of P. clarkii.

Identification of two galectin-4 proteins (PcGal4-L and PcGal4-L-CRD) and their function in AMP expression in Procambarus clarkii

Galectins, a family of lectins that bind to β-galactoside, possess conserved carbohydrate recognition domains (CRDs) and play a crucial role in recognizing and eliminating pathogens in invertebrates. Two galectin-4 genes (PcGal4) isoforms, named PcGal4-L and PcGal4-L-CRD, were cloned from the cDNA library of Procambarus clarkia in our study. PcGal4-L contains an open reading frame (ORF, 1089 bp), which encodes a protein consisting of 362 amino acids including a single CRD and six low complexity regions. The full-length cDNA of PcGal4-L-CRD contains a 483 bp ORF that encodes a protein of 160 amino acids, with a single CRD and a low-complexity region. The difference between the two PcGal4 isoforms is that PcGal4-L has 202 additional amino acids after the CRD compared to the PcGal4-L-CRD. These two isoforms are grouped together with other galectins from crustaceans through phylogenetic analysis. Further study revealed that total PcGal4 (including PcGal4-L and PcGal4-L-CRD) was primarily expressed in the muscle, gills and intestine. The mRNA levels of total PcGal4 in gills and hemocytes were significantly induced after challenge with Aeromonas hydrophila. Both recombinant PcGal4-L and its spliced isoform, PcGal4-L-CRD, could directly bind to lipopolysaccharides, peptidoglycan and five tested microorganisms, inducing a wide spectrum of microbial agglutination. The spliced isoform PcGal4-L-CRD showed a stronger binding ability than PcGal4-L. In addition, when the PcGal4 was knockdown, transcriptions of seven antimicrobial peptides (AMPs) genes (ALF5, ALF6, ALF8, CRU1, CRU2, CRU3 and CRU4) in gills and seven AMPs genes (ALF5, ALF6, ALF8, ALF9, CRU1, CRU3 and CRU4) in hemocytes were significantly decreased. Meanwhile, the survival rate of P. clarkii decreased in the PcGal4-dsRNA group. In summary, these results indicate that PcGal4 can mediate the innate immunity in P. clarkii by bacterial recognition and agglutination, as well as regulating AMP expression, thus recognition and understanding of the functions of galectin in crustaceans in immune resistance.

Antioxidation, immunity and hepatopancreatic histology of red swamp crayfish (Procambarus clarkii) subjected to low-temperature aerial exposure stress and re-immersion

Desiccation is a stressful situation that decapods often experience during live transportation. This study investigated the effects of low-temperature aerial exposures (LTAEs) (dry exposure (DL) and moist exposure (ML) at 6 °C) and re-immersion on the antioxidative and immune responses and hepatopancreatic histopathology in P. clarkii. Compared to the control group (normally feeding at 24.0 °C water temperature), the crayfish under LTAEs showed overall severe hepatopancreatic oxidative damage, with significantly increased malondialdehyde (MDA) contents and significantly reduced total antioxidant capacity (T-AOC), and oxidant damage was not fully recovered even after 12 h of re-immersion; the expression of hsp70 was significantly increased within 24-48 h of stress and re-immersion. The activity of hemolymphatic acid phosphatase (ACP) was significantly increased during 24-48 h of the stress and at 12 h of re-immersion; the activity of aspartic aminotransferase (AST) and alanine aminotransferase (ALT) was significantly increased throughout the experiment; and the gene expression of proPO or TLR was significantly increased during 12-48 h of the stress. Severe histopathological changes (lumen dilatation, vacuolation of epithelial cells and reduced cell numbers) were observed in hepatopancreas at 48 h of stress and 12 h of re-immersion. These results indicated that 48 h of low-temperature aerial exposure stress stimulated the non-specific immunity but adversely affected the antioxidation and hepatopancreatic histomorphology of P. clarkii, whereas 12 h of re-immersion was not sufficient to restore crayfish from stress to a normal state.

Sub-chronic ammonia exposure induces hepatopancreatic damage, oxidative stress, and immune dysfunction in red swamp crayfish (Procambarus clarkii)

Ammonia, as one of the primary water pollutants in aquaculture, has been shown to induce a wide range of ecotoxicological effects on aquatic animals. In order to investigate the antioxidant and innate immune responses in crustaceans disrupted by ammonia, red swamp crayfish (Procambarus clarkii) were exposed to 0, 15, 30, and 50 mg/L total ammonia nitrogen for 30 d, the alterations of antioxidant responses as well as innate immunity were studied. The results showed that the severity of hepatopancreatic injury were aggravated by the increasing ammonia levels, which were mainly characterized by tubule lumen dilatation and vacuolization. The swollen mitochondria and disappeared mitochondria ridges suggested that oxidative stress induced by ammonia targets the mitochondria. Concurrently, enhanced MDA levels, and decreased GSH levels as well as the decreased transcription and activity of antioxidant enzymes, including SOD, CAT, and GPx were noticed, which suggested that high concentrations of ammonia exposure induce oxidative stress in P. clarkii. Furthermore, a significant decrease of the hemolymph ACP, AKP, and PO along with the significant downregulation of immune-related genes (ppo, hsp70, hsp90, alf1, ctl) jointly indicated that ammonia stress inhibited the innate immune function. Our findings demonstrated that sub-chronic ammonia stress induced hepatopancreatic injury and exert suppressive effects on the antioxidant capacity as well as innate immunity of P. clarkii. Our results provide a fundamental basis for the deleterious effects of ammonia stress on aquatic crustaceans.

Exposure and Health Risk Assessment of Per- and Polyfluoroalkyl Substances in Crayfish from the Middle and Lower Reaches of the Yangtze River

Per- and polyfluoroalkyl substances (PFASs) are a novel class of emerging persistent organic pollutants (POPs) owing to their environmental persistence and bioaccumulation. Red swamp crayfish is a major source of exposure to PFASs, while the dietary intake of PFASs from crayfish is still unclear. We investigated the concentrations of PFASs in 130 batches of crayfish and 100 environmental samples from Middle and Lower Reaches of the Yangtze River Delta. Seven Perfluoroalkyl carboxylic acids (PFCAs), 3 Perfluoroalkyl sulfonates (PFSAs), and 6:2 Cl-PFESA were analyzed by ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Meanwhile, PFASs exposure levels were examined concretely in four tissues of crayfish and different circulation links. The average daily intake (ADI) risk model was used to evaluate the human health risk of consuming crayfish and suggested that the risk of PFASs exposure is at a low level.

MafG-like contribute to copper and cadmium induced antioxidant response by regulating antioxidant enzyme in Procambarus clarkii

Avian musculoaponeurotic fibrosarcoma (Maf) proteins play an important role in Nrf2/Keap1 signaling pathway, which mainly resist the oxidant stress. The members of sMaf have a high homology basic leucine zipper (bZIP) and lack trans activation domain, and could interact with other transcriptional regulatory factors as a molecular chaperone. In this study, a full-length MafG-like gene was cloned from Procambarus Clarkii, designated as PcMafG-like, which consisted of an ORF length of 246 bp encoding 82 amino acids, a 5' untranslated region (UTR) of 483 bp, and a 3' UTR of 111 bp. The domain of PcMafG-like had a bZIP-Maf domain that binds to DNA. The cDNA sequence of PcMafG-like was 99 % similar to that of Penaeus vannamei. The mRNA of PcMafG-like was expressed in all tested tissues, and the highest expression was in muscle tissue. Under stimulation of Cu²⁺ and Cd²⁺, PcMafG-like was significantly up-regulated in hepatopancreas and gill, and the same result was testified by situ hybridization. The representative antioxidant genes, CAT, GPx and CZ-SOD, were significantly induced by Cu²⁺; CAT and GPx was induced by Cd²⁺. PcMafG-dsRNA significantly inhibited the expression of these up-regulated genes, but also inhibited the expression of other detected genes CZ-SOD, GST-θ and GST-1like. The antioxidant effect of PcMafG-like was further verified by oxidative stress markers (T-SOD, CuZnSOD, GPx, CAT, GSH and MDA) kits. Cu²⁺ and Cd²⁺ could induce the contents of these oxidative stress markers (MDA, GSH, CZ-SOD, CAT in Cu²⁺/Cd²⁺ treated group, and GSH-Px in Cd²⁺ group), while interference of PcMafG-like significantly inhibited the up-regulation. Furthermore, hematoxylin-eosin staining experiments showed that the degree of pathological damage was dose-dependent and time-dependent, and the pathological damage was more serious after dsRNA interfered with PcMafG-like. In addition, subcellular localization showed that PcMafG-like gene existed in nucleus. The recombinant protein PcMafG-like was expressed and purified in prokaryotic expression. The affinity analysis of promoter by agarose gel electrophoresis suggested that PcMafG-like could bind with CAT promoter in vitro. This indicated that PcMafG-like could activate antioxidant genes.

Health risk assessment of perchlorate and chlorate in red swamp crayfish (Procambarus clarkii) in China

Perchlorate and chlorate are both strong oxidants and thyroid toxicants that are widely distributed in soil, water and human foods. The red swamp crayfish (Procambarus clarkii) is a common aquatic organism that is popular in Chinese culinary dishes. Dietary intake is the main route of human exposure to perchlorate and chlorate, though the health risks of crayfish consumption are unknown. Thus, this study investigated the quantities of perchlorate and chlorate in red swap crayfish from sampling sites in five provinces located near the Yangtze River in China, along with the associated health risks of consuming this species. Perchlorate was detected in 55.6-100 % of crayfish samples in each sampling location, and chlorate was found in 100 % of samples cross all sites. Concentrations of perchlorate in crayfish from upstream provinces (Hubei, Hunan and Jiangxi) were higher than those from downstream provinces (Anhui and Jiangsu). Perchlorate and chlorate concentrations were positively correlated in crayfish, suggesting that chlorate may be a degradation byproduct of perchlorate. The quantities of both pollutants in hepatopancreas tissue were higher than in muscle tissues (p < 0.05), such that we do not recommend ingesting crayfish hepatopancreas. Hazard quotient (HQ) values for chlorate in crayfish were <1 across all provinces, suggesting no potential health risk of chlorate exposure through crayfish consumption. However, perchlorate concentrations in crayfish from the Jiangxi province had an associated HQ value >1, suggesting potential risks for human health. These results will be useful in informing mitigation measures aimed at reducing perchlorate exposure associated with crayfish consumption.

Distinct vulnerability to oxidative stress determines the ammonia sensitivity of crayfish (Procambarus clarkii) at different developmental stages

Red swamp crayfish (Procambarus clarkii) has increasingly become a high-value freshwater product in China. During the intensive cultivation, excessive ammonia exposure is an important lethal factor of crayfish. We investigated the toxic effects and mechanisms of ammonia on crayfish at two different developmental stages. A preliminary ammonia stress test showed a 96-h LC₅₀ of 135.10 mg/L and 299.61 mg/L for Stage_1 crayfish (8.47 ± 1.68 g) and Stage_2 crayfish (18.33 ± 2.41 g), respectively. During a prolonged ammonia exposure (up to 96 h), serum acid phosphatase and alkaline phosphatase showed a time-dependent decrease. Histological assessment indicated the degree of hepatopancreatic injury, which was mainly characterized as tubule lumen dilatation, degenerated tubule, vacuolization and dissolved hepatic epithelial cell, increased with exposure time. Enhanced malondialdehyde level and reduced antioxidant capacity of hepatopancreas were also observed. The mRNA expression and activity of catalase and superoxide dismutase showed an initial up-regulation within 24 h, and then gradually down-regulated with the exposure time. In the post-treatment recovery period, the Stage_2 crayfish exerted a stronger antioxidant and detoxification capacity than that of the Stage_1 crayfish, and thus quickly recovered from the ammonia exposure. Our findings provide a further understanding of the adverse effects of ammonia stress and suggest guidelines for water quality management during crayfish farming.

Genetic Diversity Evaluation and Population Structure Analysis of Red Swamp Crayfish (Procambarus clarkii) from Lakes and Rice Fields by SSR Markers

The red swamp crayfish (Procambarus clarkii) is an important aquatic animal and has developed as a popular aquaculture species in China. In this study, a total of 72,839 SSR motifs were identified from transcriptional data, and 20 microsatellite markers of them were finally developed to assess the genetic diversities of seven wild populations from natural lakes and nine cultured populations from rice fields. Genetic diversity was slightly higher in the cultured populations than in the wild populations. The degree of genetic differentiation between cultured populations is slight, while a moderate to a large degree of genetic differentiation between wild populations and most of the variations occurred within individuals (79%). The analysis of cluster, principal coordinate analysis and STRUCTURE were similar, and they showed that isolation-by-distance pattern was not significant. The microsatellite markers developed in this study can not only be used for genetic monitoring of population but also provide important information for the management of breeding and cultured population in red swamp crayfish.

A Multi-Medium Analysis of Human Health Risk of Toxic Elements in Rice-Crayfish System: A Case Study from Middle Reach of Yangtze River, China

Rice-crayfish system has been extensively promoted in China in recent years. However, the presence of toxic elements in soil may threaten the quality of agricultural products. In this study, eight toxic elements were determined in multi-medium including soil, rice, and crayfish from the rice-crayfish system (RCS) and conventional rice culture (CRC) area. Crayfish obtained a low level of toxic element content, and mercury (Hg) in rice from RCS showed the highest bioavailability and mobility. Health risk assessment, coupled with Monte Carlo simulation, revealed that the dietary exposure to arsenic (As) and Hg from rice and crayfish consumption was the primary factor for non-carcinogenic risk, while Cd and As were the dominant contributors to the high carcinogenic risk of rice intake for adults and children, respectively. Based on the estimated probability distribution, the probabilities of the total cancer risk (TCR) of rice intake for children from RCS were lower than that from CRC.

Exploration of an XX/XY Sex Determination System and Development of PCR-Based Sex-specific Markers in Procambarus clarkii Based on Next-Generation Sequencing Data

Many economic crustacean species have sex dimorphisms during their growth. Exploring the sex determination system and developing sex-specific molecular marker(s) are very helpful for carrying out sex control breeding, and next-generation sequencing has been used as an efficient way to explore them in recent years. In this study, first, the genetic sex determination system of P. clarkii was explored as an XX/XY system by analyzing the 2b-RAD sequencing data. Furthermore, DNA samples of male and female individuals from a P. clarkii family were pooled separately for whole-genome resequencing. Based on the data of whole-genome resequencing, the 9,163 male- and female-specific bias sites with higher feasibility were obtained based on the assumption of the XX/XY sex determination system, and four sites were selected to design the sex-specific marker primers. One efficient sex-specific marker was identified with a sex discrimination rate of 99.49% (195/196) when applied to five different geographical groups with 196 individuals. The results of this study would provide a foundation for the realization of P. clarkii sex control and could provide some reference for investigating the sex determination system and sex molecular marker(s) of other crustacean species based on next-generation sequencing data.

A new insight into the SNP genotyping using high-resolution melting method after the correlation analysis of the SNPs with WSSV-resistant traits

Procambarus clarkii is an important freshwater cultured crayfish in China. With the gradual development of its aquaculture industry, research on white spot disease, which is harmful to healthy culture of P. clarkii, increases gradually. The prophenoloxidase (proPO) system is an important part of crayfish's innate immunity and plays a role in virus resistance. In this study, based on the early discovery of three SNP sites in the intron of proPO gene, the linkage disequilibrium and haplotype were analyzed for the SNPs, and it was found that there was a strong linkage disequilibrium relationship among them. Through the analysis on association between the haplotypes and genotype of each SNP site with the WSSV-resistant traits, the detection of the SNP_7081 genotype was considered as the most convenient and efficient way for WSSV-resistant group selection. Furtherly, the high-resolution melting curve (HRM), which is a rapid and economic genotyping method, was chosen to establish for SNP_7081 site genotyping. The 68 bp target fragment with 27.94% GC content was amplified and melting curve analysis were performed. However, the appearance of false negatives which led to unable automatically grouped although the melting curves of genotypes CC, C>T and T>C were obviously different, and could be treated as standard to manually genotype the samples with an accuracy rate of 97.61%. The low GC content which correlated with the Tm value, was confirmed as the reason for the false negatives by the assay about the recombinant plasmid PMD18-T-SNP_7081 constructed with 45.24% GC content. Eventually, the adaptor primers were used to increase the GC content of the target fragment, and a modified HRM method for genotyping SNP_7081 site that could group automatically was established, which could provide a new insight for the HRM method to genotype SNPs.

Health risk assessment and bioaccumulation of heavy metals in Procambarus clarkii from six provinces of China

Contamination with heavy metals in wild red swamp crayfish (Procambarus clarkii) from 7 different geographical areas in six provinces of China (Hubei, Hunan, Jiangxi, Anhui, Jiangsu, and Shandong) was evaluated. Concentrations of chromium (Cr), arsenic (As), lead (Pb), cadmium (Cd), and mercury (Hg) in the abdominal muscle, gonad, and hepatopancreas were determined by inductively coupled plasma mass spectrometry (ICP-MS) and atomic fluorescence spectrometer (AFS). Except for the Cd content in the hepatopancreas, the contents of selected heavy metals in three different tissues were significantly lower than the proposed limits provided by United States Environmental Protection Agency (USEPA). The maximum accumulations of Cd and Pb were in the hepatopancreas, while the maximum accumulation of As was in the gonad, and the maximum accumulations of Hg and Cr were in the abdominal muscle. The highest contents of Cr, Hg, and Pb were all detected in Dongting Lake, Hunan, which was consistent with the trend of the metal pollution index (MPI). Risk value of the target hazard quotient (THQ) was below 1.0, suggesting that the intake of selected heavy metals through crayfish consumption would not pose a significant health risk to consumers.

Population Ecology and Genetic Diversity of the Invasive Alien Species Procambarus clarkii in Lake Trasimeno (Italy)

Simple Summary

The population of Procambarus clarkii was surveyed twenty years after its introduction into Lake Trasimeno (Central Italy), investigating both ecological and genetic aspects. Our results confirmed that P. clarkii is well acclimatized with a stable population structure, mainly characterized by a unique mitochondrial lineage, suggesting that a single introduction event may have occurred in the lake, complemented by secondary events.

Abstract

The deliberate or accidental introduction of invasive alien species (IAS) causes negative ecological and economic impacts altering ecosystem processes, imperiling native species and causing damage to human endeavors. A monthly monitoring program was performed in Lake Trasimeno (Central Italy) from July 2018 to July 2019 in order to provide an upgrade of the population ecology of Procambarus clarkii and to assess the genetic diversity by analyzing the relationships among mitochondrial DNA diversity. Our results confirmed that P. clarkii is well acclimatized in the lake, revealing a stable population structure favored by the resources and conditions typical of this ecosystem, which seem to be optimal for the maintenance of the species. Four distinct mitochondrial haplotypes were detected, but one of them was clearly overrepresented (76%), suggesting that a single predominant introduction event may have occurred in this area, likely followed by secondary events. The identification of the typical genetic variants provides a better understanding of the evolutionary scenarios of P. clarkii in this biotope and it can be helpful in management plans concerning the expanding populations of this invasive alien species.

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Simple Summary

The distribution of Kashgarian loach (Triplophysa yarkandensis) is limited to the Tarim River basin, which is the largest inland river in China. However, the population size of T. yarkandensis has been diminishing, and it is critically endangered in the Tarim River basin due to the gradual depletion of water resources, together with alien invasion and agricultural cultivation in Tarim River. In this study, we adopted the RAD-seq method to investigate the population genetics of T. yarkandensis, and a high degree of genetic variations and significant genetic differentiation was detected among T. yarkandensis populations in the Tarim River basin. The obtained data contribute to understanding the genetic status of T. yarkandensis, and help to provide the scientific management strategies and direct future monitoring and utilization of the genetic resource in Xinjiang region.

Abstract

The distribution of Triplophysa yarkandensis is restricted to Xinjiang’s Tarim River basin. We collected 119 T. yarkandensis samples from nine geographic populations in the Tarim River basin and utilized the RAD-seq method for SNP genotyping. In this study, a total of 164.81 Gb bases were generated with the Illumina platform, and 129,873 candidate SNPs were obtained with the Stacks pipeline for population genetic analyses. High levels of genetic diversity were detected among nine populations. The AMOVA results showed that the majority of genetic variations originated from among populations (F_ST = 0.67), and the pairwise F_ST values ranged from 0.4579 to 0.8736, indicating high levels of genetic differentiation among these populations. The discriminate analysis of principal components (DAPCs) and neighbor joining (NJ) tree revealed that the nine populations could be separated into two clusters (i.e., south and north populations), and modest genetic differentiation between south and north populations was observed, while the individuals from several populations were not clustered together by geographical location. The evidence of two genetic boundaries between south and north populations (except TTM) was supported by barrier analysis. The Bayesian skyline plotting indicated that T. yarkandensis populations in the Tarim River basin had not experienced genetic bottlenecks, and the effective population size remained stable. This study first clarified the genetic diversity and differentiation of T. yarkandensis populations in the Tarim River basin, and it provided valuable molecular data for conservation and management of natural populations.

Molecular Characterization and Cross-Allergenicity of Tropomyosin from Freshwater Crustaceans

Tropomyosin is a major allergen responsible for cross-allergenicity in a number of shellfish species. Although extensively characterized in marine crustaceans, the information of tropomyosin is limited to a few freshwater crustacean species. As a result, more cross-reactivity evidence and information of tropomyosin at the molecular level are required for the detection of freshwater crustaceans in the food industry. In this study, we explored tropomyosin allergenicity in four freshwater crustacean species: prawn (Macrobrachium rosenbergii and Macrobrachium lanchesteri) and crayfish (Procambarus clarkii and Cherax quadricarinatus). Immunoblotting, liquid chromatography-tandem mass spectrometry, and immunoprecipitation studies indicated that tropomyosin was recognized by the sera's IgE of crustacean-allergic volunteers. Cloning and characterization of nucleotide sequences of tropomyosin cDNA from M. lanchesteri and C. quadricarinatus revealed highly conserved amino acid sequences with other crustaceans. This study emphasized the role of tropomyosin as a universal marker for the detection of both freshwater and marine crustaceans in the food industry.

Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii

Background

The red swamp crayfish Procambarus clarkii is a freshwater species that possesses high adaptability, environmental tolerance, and fecundity. P. clarkii is artificially farmed on a large scale in China. However, the molecular mechanisms of ovarian development in P. clarkii remain largely unknown. In this study, we identified four stages of P. clarkii ovary development, the previtellogenic stage (stage I), early vitellogenic stage (stage II), middle vitellogenic stage (stage III), and mature stage (stage IV) and compared the transcriptomics among these four stages through next-generation sequencing (NGS).

Results

The total numbers of clean reads of the four stages ranged from 42,013,648 to 62,220,956. A total of 216,444 unigenes were obtained, and the GC content of most unigenes was slightly less than the AT content. Principal Component Analysis (PCA) and Anosim analysis demonstrated that the grouping of these four stages was feasible, and each stage could be distinguished from the others. In the expression pattern analysis, 2301 genes were continuously increase from stage I to stage IV, and 2660 genes were sharply decrease at stage IV compared to stages I-III. By comparing each of the stages at the same time, four clusters of differentially expressed genes (DEGs) were found to be uniquely highly expressed in stage I (136 genes), stage II (43 genes), stage III-IV (49 genes), and stage IV (22 genes), thus exhibiting developmental stage specificity. Moreover, in comparisons between adjacent stages, the number of DEGs between stage III and IV was the highest. GO enrichment analysis demonstrated that nutrient reservoir activity was highest at stage II and that this played a foreshadowing role in ovarian development, and the GO terms of cell, intracellular and organelle participated in the ovary maturation during later stages. In addition, KEGG pathway analysis revealed that the early development of the ovary was mainly associated with the PI3K-Akt signaling pathway and focal adhesion; the middle developmental period was related to apoptosis, lysine biosynthesis, and the NF-kappa B signaling pathway; the late developmental period was involved with the cell cycle and the p53 signaling pathway.

Conclusion

These transcriptomic data provide insights into the molecular mechanisms of ovarian development in P. clarkii. The results will be helpful for improving the reproduction and development of this aquatic species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07537-x.

Developmental, Dietary, and Geographical Impacts on Gut Microbiota of Red Swamp Crayfish (Procambarus clarkii)

Red swamp crayfish (Procambarus clarkii) breeding is an important economic mainstay in Hubei province, China. However, information on the gut microbiota of the red swamp crayfish is limited. To address this issue, the effect of developmental stage, diet (fermented or non-fermented feed), and geographical location on the gut microbiota composition in the crayfish was studied via high-throughput 16S rRNA gene sequencing. The results revealed that the dominant phyla in the gut of the crayfish were Proteobacteria, Bacteroidetes,Firmicutes, Tenericutes, and RsaHF231. The alpha diversity showed a declining trend during development, and a highly comparable gut microbiota clustering was identified in a development-dependent manner. The results also revealed that development, followed by diet, is a better key driver for crayfish gut microbiota patterns than geographical location. Notably, the relative abundance of Bacteroidetes was significantly higher in the gut of the crayfish fed with fermented feed than those fed with non-fermented feed, suggesting the fermented feed can be important for the functions (e.g., polysaccharide degradation) of the gut microbiota. In summary, our results revealed the factors shaping gut microbiota of the crayfish and the importance of the fermented feed in crayfish breeding.

Two relish isoforms produced by alternative splicing participate in the regulation of antimicrobial peptides expression in Procambarus clarkii intestine

Nuclear factor κB (NF-κB) plays a key role in the innate immunity of invertebrates. Relish belongs to the NF-κB family. In insects, alternative splicing induces the sequence diversity of the Relish gene. However, information on the roles of various relish isoforms in crustacean innate immune response is limited. Here, two alternatively spliced Relish isoforms (designated as SPcRelish and LPcRelish) were identified from freshwater crayfish (Procambarus clarkii), and functional analysis was performed. The Relish gene has 25 exons and 24 introns. The long isoform LPcRelish is fully spliced, whereas the short isoform SPcRelish is alternatively spliced and contains exon 1-9 and a retention of intron 9. LPcRelish contains the Rel homology domain (RHD), the ig-like, plexins, transcription factors (IPT), and ankyrin-repeat (ANK) inhibitory domain. However, SPcRelish contains only the RHD and IPT domain, and does not have an ANK domain. The transcripts of SPcRelish and LPcRelish can be regulated by Vibrio parahaemolyticus. The intestinal immunological barrier and bacterial balance in the intestine play crucial roles in host health. In this study, we analyzed the connection between Relish isoforms and the transcripts of antimicrobial peptides (AMPs) in intestine. The transcripts of all the tested AMPs, except ALF-41125, were upregulated by V. parahaemolyticus. The knock down of the SPcRelish gene resulted in a significant decrease in the expression levels of ALF-7032, ALF-13162, and Crustin-42012 during V. parahaemolyticus invasion. The expression levels of four AMP genes (ALF-41125, ALF-42430, Crustin-41354, and Crustin-42993) were obviously increased in V. parahaemolyticus-challenged SPcRelish-silenced crayfish. ALF-7032, ALF-9228, ALF-13162, ALF-42430, Crustin-41354, Crustin-42012, and Crustin-42993 were evidently downregulated in V. parahaemolyticus-infected LPcRelish-silenced crayfish. Overall, generating the two Relish isoforms by alternative splicing may be an important mechanism of the host immune system to promote molecular diversity, which results in the functional diversity of the relish transcription factor.

Genetic diversity of Procambarus clarkii populations based on mitochondrial DNA and microsatellite markers in different areas of Guangxi, China

The red swamp crayfish (Procambarus clarkii) is a famous invasive species. However, it has become one of the most important freshwater aquaculture resources in China. Herein, we focus on five artificial cultured populations of P. clarkii in Guangxi, southern China to investigate the genetic diversity based on mitochondrial DNA and microsatellites. The results revealed that the genetic diversity of P. clarkii populations in southern Guangxi (NN and DT) was lower than in central (LZ and LB) and northern (RS) Guangxi. A total of 17 haplotypes were captured from 100 individuals and haplotype 2 mainly existed, and the number of haplotype in NN and DT was less than other populations. The AMOVA showed that genetic variation was determined by within populations. The observed mismatch distribution of overall populations fit the expected distributions, indicating that no obvious demographic expansion, but unimodal was observed in RS, LZ and LB. Fst among most of groups exhibited moderate differentiation. Nevertheless, the gene flow demonstrated there had extensive gene exchanges between different populations, particularly between LZ and LB. UPGMA tree revealed that NN and DT belonged to the same clade, whereas the remaining populations were in the other clade. According to the genetic diversity, there is a need to improve the germplasm resources of P. clarkii in southern Guangxi.

Minimum sample sizes for invasion genomics: Empirical investigation in an invasive whitefly

Analysis of population genetics provides insights into the evolutionary processes, among which the sample size choice is per se a crucial issue in the analysis. Genome-wide high-throughput techniques based on RADseq have been increasingly used in studies on the population genomics of invasive species. However, there is little information available regarding optimal sample sizes for analyzing population genomics of invasive species. In this study, we first use type IIB endonucleases restriction site-associated DNA (2b-RAD) to mine thousands of single nucleotide polymorphisms (SNPs) for native and introduced populations in Q1 clade (SPB and 17JN) and Q2 clade (ISQ and UAS0601) of the whitefly, Bemisia tabaci (Gennadius) MED (also known as B. tabaci biotype Q). Then, we used resampling techniques to create simulated populations with a random subset of individuals and 3,000 SNPs to determine how many individuals should be sampled for accurate estimates of intra- and interpopulation genetic diversity. We calculated the intrapopulation genetic diversity parameters (unbiased expected heterozygosity, observed heterozygosity, and the number of effect alleles) and pairwise genetic differentiation F ST; finally, an ad hoc statistic, ΔK, was used to determine the optimal value. Our results showed that a sample size greater than four individuals (n ≥ 4) has little impact on estimates of genetic diversity within whitefly populations; moreover, precise estimate of F ST can be easily achieved at a very small simple size (n = 3 or 4). Our results will provide in-depth understanding of the optimization of sampling schemes in population genomics of invasive species.

Genome survey sequencing of red swamp crayfish Procambarus clarkii

Red swamp crayfish, Procambarus clarkii, presently is an important aquatic commercial species in China. The crayfish is a hot area of research focus, and its genetic improvement is quite urgent for the crayfish aquaculture in China. However, the knowledge of its genomic landscape is limited. In this study, a survey of P. clarkii genome was investigated based on Illumina's Solexa sequencing platform. Meanwhile, its genome size was estimated using flow cytometry. Interestingly, the genome size estimated is about 8.50 Gb by flow cytometry and 1.86 Gb with genome survey sequencing. Based on the assembled genome sequences, total of 136,962 genes and 152,268 exons were predicted, and the predicted genes ranged from 150 to 12,807 bp in length. The survey sequences could help accelerate the progress of gene discovery involved in genetic diversity and evolutionary analysis, even though it could not successfully applied for estimation of P. clarkii genome size.