Multiplex immune-related genes expression analysis response to bacterial challenge in mud crab, Scylla paramamosain

Toxic effects of cadmium exposure on intestinal histology, oxidative stress, microbial community, and transcriptome change in the mud crab (Scylla paramamosain)

Cadmium is one of hazardous pollutants that has a great threat to aquatic organisms and ecosystems. The intestine plays important roles in barrier function and immunity to defend against environmental stress. However, whether cadmium exposure caused the intestine injury is not well studied. Thus, the aim of this study was to explore the potential mechanisms of cadmium toxicity in the intestine of mud crab (Scylla paramamosain) via physiological, histological, microbial community, and transcriptional analyses. Mud crabs were exposed to 0, 0.01, and 0.125 mg/L cadmium. After a 21-day of cadmium exposure, 0.125 mg/L cadmium caused intestine damaged by decreasing superoxide dismutase and catalase activities, and increasing hydrogen peroxide and malondialdehyde levels. Integrated biological index analysis confirmed that the toxicity of cadmium exhibited a concentration-dependent manner. Comparative transcriptional analyses showed that the up-regulations of several genes associated with heat shock proteins, detoxification and anti-oxidant defense, and two key signaling pathways (PI3k-Akt and apoptosis) revealed an adaptive response mechanism against cadmium exposure. Transcriptomic analysis also suggested that cadmium exposure disturbed the expression of ion transport and immune-related genes, indicating that it has negative effects on the immune functions of the mud crab. Furthermore, the intestinal microbial diversity and composition were significantly influenced by cadmium exposure. The abundance of the dominant phyla Fusobacteria and Bacteroidetes significantly changed after cadmium exposure. KEGG pathway analysis demonstrated that cadmium exposure could change energy metabolism and environmental information processing. Overall, we concluded that excessive cadmium exposure could be potentially exerted adverse effects to the mud crab health by inducing oxidative damage, decreasing immune system, disrupting metabolic function, and altering intestinal microbial composition. These results provided a novel insight into the mechanism of cadmium toxicity on crustaceans.

The injection of one recombinant C-type lectin (LvLec) induced the immune response of hemocytes in Litopenaeus vannamei

To explore the immune function of C-type lectin in shrimp, one recombinant C-type lectin (LvLec) was injected into Litopenaeus vannamei. There were four treatments in the experiment: saline group (as control group), recombinant C-type lectin group (LvLec, 1 mg mL^-1), Vibrio harveyi group (V. harveyi, 10⁶ cfu mL^-1) and recombinant C-type lectin combined with Vibrio harveyi group (LvLec + V. harveyi, 1 mg mL^-1 + 10⁶ cfu mL^-1). The sampling time was set at 0, 3, 6, 9, 12, 24 h after the injection. The results showed that the total hemocyte count decreased significantly and the phagocytic activity improved notably after the injection of LvLec, V. harveyi or LvLec + V. harveyi. Prophenoloxidase (proPO) activity decreased, while phenoloxidase (PO) activity increased and the changing degree of each group exhibited a significant difference. The hemagglutinating activity and bacteriolytic activity improved significantly, while the antimicrobial activity did not show a remarkable change in all of the groups. There were also changes that occurred in the levels of second messengers (cAMP, cGMP) and protein kinase (PKA, PKG). After the injection of LvLec, V. harveyi or LvLec + V. harveyi, the concentration of cGMP and PKA increased significantly, while the concentration of cAMP and PKG did not change remarkably. The results above suggested that rLvLec could induce nonspecific immune response, including phagocytosis, release of PO, hemagglutination and bacteriolysis through cGMP-PKA pathway in vivo.

Transcriptome and metabolome integration analysis of mud crab Scylla paramamosain challenged to Vibrio parahaemolyticus infection

Vibrio parahaemolyticus (V. parahaemolyticus) is a common pathogen for marine crustacean, which causes severe illnesses in aquatic animals. Therefore, it is meaningful to explore the mechanism during V. parahaemolyticus infection. In this study, to investigate the immune responses of mud crab Scylla paramamosain (S. paramamosain) to V. parahaemolyticus, we established the metabolic and transcriptional profiles of mud crab hemocytes challenged with V. parahaemolyticus. The results indicated that V. parahaemolyticus infection could induce a series of metabolism alterations at both metabolome and transcriptome levels, including biosynthesis of amino acids and Aminoacyl-tRNA, Purine and pyrimidine metabolism, TCA cycle and glutamine metabolism. In this context, through the integration of metabolomics and transcriptomics, our study provided a more comprehensive understanding of the biological process in mud crab against pathogen infection.

Innate immune responses and metabolic alterations of mud crab (Scylla paramamosain) in response to Vibrio parahaemolyticus infection

Vibrio parahaemolyticus is one of the major pathogens caused diseases in cultured mud crab (Scylla paramamosain). Mud crabs lack an adaptive immune system, their defenses depend almost on innate immunity. Evaluation of the molecular responses of mud crabs to pathogens is essential for control of disease occurrence in farmed animals. In this study, the impacts of V. parahaemolyticus on immunity-related genes and metabolites in mud crabs of different groups (PG, SG and MG refer to controlled, survival and moribund groups, respectively) were investigated. Our results revealed that V. parahaemolyticus infection stimulated significant expressions of immune-related genes (prophenoloxidase, alpha 2-macroglobulin, lysosomal-associated membrane protein, Rab5, C-type lectin B and anti-lipopolysaccharide factor 5) in the MG within 72 h post-infection. The ATP content was significantly reduced in all tissues except muscle of moribund mud crabs. A total of 668 metabolites (including 190 down-regulated and 145 up-regulated) were identified and assigned to 77 pathways in both SG and MG. Metabolites involved in the saturated fatty acid are up-regulated, whereas unsaturated fatty acid and amino acid metabolisms are down-regulated in the immune system of mud crabs during the bacterial infection in MG. Furthermore, a reduction of hemocyte number and an increase of microbial abundance was found in MG. Our results demonstrated that V. parahaemolyticus induced death of mud crabs through reducing the metabolites associate with energy biosynthesis and innate immune system (i.e. proliferation of hemocyte and melanization), resulting in decrease of ATP in different tissues and failed to clearance of pathogens, respectively. The findings of this study provide a basic information of the responses of mud crab on bacterial infection, which is essential for prevention and control of diseases in mud crab aquaculture.

Identification of immune-related genes in gills of Chinese mitten crabs (Eriocheir sinensis) during adaptation to air exposure stress

The Chinese mitten crab, Eriocheir sinensis, is the most important crab in China. Air exposure is regarded as one of the crucial restriction factors in the crab cultivation and transportation process. Numerous studies have shown that air exposure stress can cause many negative effects on aquatic farming animals. However, the molecular mechanisms of drying on Chinese mitten crabs are still poorly studied. In this study, gill reference transcriptome was assembled and differentially expressed gene (DGE) analysis was conducted between air exposure 16 h and normal dissolved oxygen of Chinese mitten crab. A total of 76075 transcripts were generated and 50800 unigenes with a mean length of 1090 bp and N50 length of 1584 bp were observed. Transcriptomic comparison revealed 352 DEGs between air exposure 16 h group and control group, including 122 up-regulated genes and 230 down-regulated genes. Gene ontology (GO) analysis revealed that these DEGs involved in 16 biological process subcategories, 8 cellular component subcategories and 6 molecular function subcategories. Further Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis annotated 352 DEGs to 85 pathways, and some pathways were regarded as related with immune system and diseases, such as phagosome, systemic lupus erythematosus, and alcoholism. Eight genes involved in multiple KEGG signaling pathways were validated by qRT-PCR. This study demonstrates the first gill transcriptomic analysis challenged with air exposure stress in Chinese mitten crab and provides valuable gene resources for understanding the crab gill immunity, which can provides insight into the immune response of crab against air exposure stress.

Cloning and functional characterization of thioredoxin genes from large yellow croaker Larimichthys crocea

Thioredoxin(Trx)with a redox-active disulfide/dithiol in the active site, is an ubiquitous disulfide reductase majorly responsible for maintaining the balance of reactive oxygen species. In this study, the complete thioredoxin-like protein 1 (designated as LcTrx) was cloned from large yellow croaker Larimichthys crocea through rapid amplification of cDNA ends. The full-length cDNA of LcTrx was 1295 bp in length containing a 131 bp 5' untranslated region (UTR) ,a 3'UTR of 294bp with a poly (A) tail, and an 870 bp open reading frame (ORF) encoding a polypeptide of 289 amino acids. Protein sequence analysis revealed that LcTrx contains the evolutionarily conserved redox motif CRPC (Cys-Arg-Pro-Cys-). Multiple alignments revealed that LcTrx is highly identical to Trx from other organisms, especially in the CRPC motifs. The recombinant LcTrx showed obvious insulin reduction activity in vitro. The LcTrx transcripts were constitutively expressed in all examined tissues with the highest levels found in the muscles and the lowest in the head kidney. Results of Vibrio parahaemolyticus infection experiment showed that the expression levels of LcTrx were tissue and time dependent. In the liver and kidney, LcTrx was down-regulated both at 12 h and 48 h post-infection. In contrast, LcTrx showed induced expression in the spleen and head kidney at same post-infection time points. The different responses to pathogen stimulation indicated the diversified physiological function of LcTrx in the four examined tissues.

A laboratory exercise for detecting microbial contaminants

The development and evaluation of a 6-hours laboratory class, based on capillary electrophoresis (CE) and the detection of microbial contaminants, is described. It can be easily scaled up or down, to suit class sizes up to 188 and completed in a shorter time scale. CE uses narrow-bore fused-silica capillaries to separate a complex array of large and small molecules. A laboratory exercise has been devised to illustrate how CE-based genetic analysis system processes DNA fragment analysis to detect three microbial contaminants. The protocol is relatively inexpensive and uses standard molecular biology reagents and equipment. © 2018 by The International Union of Biochemistry and Molecular Biology, 46(3):279-284, 2018.

Hybridization improved bacteria resistance in abalone: Evidence from physiological and molecular responses

Hybridization is an effective way of improving germplasm in abalone, as it often generates benign traits in the hybrids. The hybrids of Haliotis discus hannai and H. gigantea have shown heterosis in terms of disease resistance than one or both parental species. In the present study, to elucidate the physiological and molecular mechanism of this heterosis, we analyzed the dynamic changes of several immune indexes including survival rate, total circulating haemocyte count (THC), phagocytic activity, reactive oxygen species level (ROS) and phenoloxidase activity (PO) in two parental species, H. discus hannai (DD) and H. gigantea (GG), and their reciprocal hybrids H. discus hannai ♀ × H. gigantea ♂ (DG), H. gigantea ♀ × H. discus hannai ♂ (GD) challenged with a mixture of Vibrio harveyi, V. alginolyticus and V. parahaemolyticus (which have been demonstrated to be pathogenic to abalone). Besides, we cloned and analyzed three important immune genes: heat shock protein 70 (hsp70), ferritin and cold shock domain protein (csdp) in H. discus hannai and H. gigantea, then further investigated their mRNA level changes in the four abalone genotypes after bacterial challenge. Results showed that these physiological and molecular parameters were significantly induced by bacterial exposure, and their changing patterns were obviously different between the four genotypes: (1) Survival rates of the two hybrids were higher than both parental species after bacterial exposure; (2) DG had higher THC than the other three genotypes; (3) Phagocytosis responded slower in the hybrids than in the parental species; (4) DD's ROS level was lower than the other three genotypes at 48 h post infection; (5) Phenoloxidase activity was lower in DD during the infection compared to the other genotypes; (6) mRNA levels of hsp70 and csdp, were always lower in at least one parental species (DD) than in the hybrids after the bacterial exposure. Results from this study indicate that the hybrids are more active or efficient in immune system function, hence they could effectively defense against a bacterial invasion, leading to higher survival rates after challenge. This study provides physiological and molecular evidences for interpreting the disease resistant heterosis in this abalone hybrid system, which could help us in a better understanding and utilization of heterosis in abalone aquaculture.

Cloning, tissue distribution and nutritional regulation of a fatty acyl Elovl4-like elongase in mud crab, Scylla paramamosain (Estampador, 1949)

In this report, the full-length cDNA of fatty acyl Elovl4-like elongase was cloned from the hepatopancreas of Scylla paramamosain by rapid-amplification of cDNA ends (RACE). To the best of our knowledge, this is the first report of Elovl4-like elongase in crustaceans. The full-length cDNA of Elovl4-like was 1119bp, which included a 5'-terminal untranslated region (UTR) of 58bp, a 3'-terminal UTR of 44bp and an open reading frame (ORF) of 1017bp encoding a polypeptide of 338 amino acids. Tissue distribution analysis revealed that Elovl4-like transcripts are widely distributed in various organs, with high mRNA levels in the hepatopancreas and cranial ganglia. Further, Elovl4-like transcriptional levels in hepatopancreas were up-regulated in proportion to the replacement of dietary fish oil (FO) with soybean oil (SO). The result showed that Elovl4-like transcripts increased about 0.83 and 1.12-fold respectively when SO constituted 80% and 100% of total oil (P<0.05). These results may contribute to better understanding of the long-chain polyunsaturated fatty acids (LC-PUFA) biosynthetic pathway and regulation mechanism in this species.

A mannose-specific C-type lectin from Fenneropenaeus merguiensis exhibited antimicrobial activity to mediate shrimp innate immunity

Being one type of pattern recognition receptors (PRRs), lectins exhibit a crucial role in the defense mechanism of invertebrates which are deficient in an adaptive immune system. A new C-type lectin called FmLC3 was isolated from hepatopancreas of Fenneropenaeus merguiensis by cloning approaches, RT-PCR and 5' and 3' RACE (rapid amplification of cDNA ends). A full-length cDNA of FmLC3 contains 607 bp with one open reading frame of 480bp, encoding a 159-amino acids peptide. The predicted primary structure of FmLC3 is composed of a signal peptide, a carbohydrate recognition domain with an EPN motif and one Ca²⁺ binding site-2, including a double-loop region assisted by two conserved disulfide linkages. FmLC3 had a molecular mass of 17.96kDa and pI of 4.92. In normal or unchallenged shrimp, the mRNA expression of FmLC3 was detected only in hepatopancreas whilst its native proteins were found in hemolymph, heart, stomach and intestine but not in the expressed tissue, indicating that after being synthesized in hepatopancreas, FmLC3 would be secreted to other tissues. The significant up-regulation of FmLC3 was manifested in shrimp challenged with Vibrio harveyi or white spot syndrome virus. After knockdown with gene-specific double-stranded RNA and following by co-pathogenic inoculation, the FmLC3 expression was severely suppressed with coherence of increasing in cumulative mortality and reduction of the median lethal time. Recombinant FmLC3 (rFmLC3) had agglutinating activity towards diverse bacterial strains in a Ca²⁺-dependent manner. Its activity was inhibited by lipopolysaccharide and mannose, implying that FmLC3 was mannose-binding C-type lectin. Moreover, rFmLC3 could bind directly to various microbial strains with Ca²⁺-requirement. Otherwise, rFmLC3 exhibited the antimicrobial activity by inhibiting effectively the microbial growth in vitro. All these results signified that FmLC3 might act as PRR to recognize with a broad specificity for diverse pathogens, and contribute in shrimp immune response via the agglutination, binding and antimicrobial activity.

Lipopolysaccharide-specific binding C-type lectin with one CRD domain from Fenneropenaeus merguiensis (FmLC4) functions as a pattern recognition receptor in shrimp innate immunity

In crustaceans, an innate immune system is solely required because they lack an adaptive immunity. One kind of pattern recognition receptors (PRRs) that plays a particular role in the innate immunity of aquatic shrimp is lectin. A new diverse C-type lectin (FmLC4) was cloned from the hepatopancreas of Fenneropenaeus merguiensis by using RT-PCR and 5' and 3' rapid amplification of cDNA ends approaches. A full-length FmLC4 cDNA comprises 706 bp with an open reading frame of 552 bp, encoding a peptide of 184 amino acids. The predicted primary sequence of FmLC4 consists of a signal peptide of 19 amino acids, a molecular mass of 20.4 kDa, an isoelectric point of 5.13, one carbohydrate recognition domain with a QPD motif and a Ca²⁺ binding site as well as a double-loop characteristic supported by two conserved disulfide bonds. The FmLC4 mRNA expression was found only in the hepatopancreas of normal shrimp and significantly up-regulated upon challenge the shrimp with Vibrio harveyi or white spot syndrome virus (WSSV). Recombinant FmLC4 (rFmLC4) could agglutinate various bacterial strains with Ca²⁺-dependence. Lipopolysaccharide (LPS) could specifically inhibit the agglutinating activity and potently bind to rFmLC4, indicating that FmLC4 was LPS-specific binding C-type lectin. Moreover, rFmLC4 itself displayed the in vivo effective clearance of the pathogenic bacterium V. harveyi. Altogether, FmLC4 may serve as LPS-specific PRR to recognize opportunistic bacterial and viral pathogens, and thus to play a role in the immune defense of aquatic shrimp via the binding and agglutination.

ArHsp40, a type 1 J-domain protein, is developmentally regulated and stress inducible in post-diapause Artemia franciscana

Upon diapause termination and exposure to favorable environmental conditions, cysts of the crustacean Artemia franciscana reinitiate development, a process dependent on the resumption of metabolic activity and the maintenance of protein homeostasis. The objective of the work described herein was to characterize molecular chaperones during post-diapause growth of A. franciscana. An Hsp40 complementary DNA (cDNA) termed ArHsp40 was cloned and shown to encode a protein with an amino-terminal J-domain containing a conserved histidine, proline, and aspartic acid (HPD) motif. Following the J-domain was a Gly/Phe (G/F) rich domain, a zinc-binding domain which contained a modified CXXCXGXG motif, and the carboxyl-terminal substrate binding region, all characteristics of type I Hsp40. Multiple alignment and protein modeling showed that ArHsp40 is comparable to Hsp40s from other eukaryotes and likely to be functionally similar. qRT-PCR revealed that during post-diapause development, ArHsp40 messenger RNA (mRNA) varied slightly until the E2/E3 stage and decreased significantly upon hatching. The immunoprobing of Western blots demonstrated that ArHsp40 was also relatively constant until E2/E3 and then declined dramatically. The drop in ArHsp40 when metabolism and protein synthesis were increasing was unexpected and demonstrated developmental regulation. The reduction in ArHsp40 at such an active life history stage indicates, as one possibility, that A. franciscana possesses additional Hsp40s, one or more of which replaces ArHsp40 as development progresses. Increased synthesis upon heat shock established that in addition to being developmentally regulated, ArHsp40 is stress inducible and, because it is found in mature cysts, ArHsp40 has the potential to contribute to stress tolerance during diapause.

Diversity of cytosolic HSP70 Heat Shock Protein from decapods and their phylogenetic placement within Arthropoda

The 70kDa heat shock proteins (HSP70) are considered the most conserved members of the HSP family. These proteins are primordial to the cell, because of their implications in many cellular pathways (e. g., development, immunity) and also because they minimize the effects of multiple stresses (e. g., temperature, pollutants, salinity, radiations). In the cytosol, two ubiquitous HSP70s with either a constitutive (HSC70) or an inducible (HSP70) expression pattern are found in all metazoan species, encoded by 5 or 6 genes (Drosophila melanogaster or yeast and human respectively). The cytosolic HSP70 protein family is considered a major actor in environmental adaptation, and widely used in ecology as an important biomarker of environmental stress. Nevertheless, the diversity of cytosolic HSP70 remains unclear amongst the Athropoda phylum, especially within decapods. Using 122 new and 311 available sequences, we carried out analyses of the overall cytosolic HSP70 diversity in arthropods (with a focus on decapods) and inferred molecular phylogenies. Overall structural and phylogenetic analyses showed a surprisingly high diversity in cytosolic HSP70 and revealed the existence of several unrecognised groups. All crustacean HSP70 sequences present signature motifs and molecular weights characteristic of non-organellar HSP70, with multiple specific substitutions in the protein sequence. The cytosolic HSP70 family in arthropods appears to be constituted of at least three distinct groups (annotated as A, B and C), which comprise several subdivisions, including both constitutive and inducible forms. Group A is constituted by several classes of Arthropods, while group B and C seem to be specific to Malacostraca and Hexapoda/Chelicerata, respectively. The HSP70 organization appeared much more complex than previously suggested, and far beyond a simple differentiation according to their expression pattern (HSC70 versus HSP70). This study proposes a new classification of cytosolic HSP70 and an evolutionary model of the distinct forms amongst the Arthropoda phylum. The observed differences between HSP70 groups will probably have to be linked to distinct interactions with co-chaperones or other co-factors.

Simultaneous typing of seven porcine pathogens by multiplex PCR with a GeXP analyser

A novel high-throughput method was developed for simultaneous detection and differentiation of seven porcine pathogens by multiplex PCR based on a GenomeLab Gene Expression Profiler (GeXP) analyser. The pathogens included in this study were pseudorabies virus (PRV), classical swine fever virus (CSFV), African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine parvovirus (PPV), porcine circovirus type 2 (PCV-2) and Japanese encephalitis virus (JEV). Seven pairs of chimeric primers, consisting of a pathogen-specific sequence fused to a universal sequence at the 5' end, were used to initiate the PCR, after which a set of universal primers was used for the subsequent cycles of the PCR. Amplification products were separated by capillary electrophoresis and identified using fluorescence spectrophotometry. The specificity of the GeXP assay was examined with single and mixed pathogen cDNA/DNA templates. The specific DNA product amplification peaks of seven pathogens were observed on the GeXP analyser. Negative controls did not produce DNA products. The sensitivity was evaluated by performing the assay on serial 10-fold dilutions of the plasmids containing the target sequence. Under optimised conditions this assay achieved a sensitivity of 100-1000 copies/μL for a single virus and 1000 copies/μL when all of the seven pre-mixed viral targets were present. Furthermore, the GeXP-PCR assay was 100% specific when 58 clinical samples were tested in comparison with the conventional PCR method. In conclusion, the GeXP assay is a rapid, cost-effective, sensitive, specific and high throughput method for simultaneously detecting seven pathogens that infect swine.

Molecular characterization of heat-shock protein 90 gene and its expression in Gobiocypris rarus juveniles exposed to pentachlorophenol

Heat-shock protein 90 (HSP90) is an abundant and highly conserved molecular chaperone, and it fulfills a housekeeping function in contributing to the folding, maintenance of structural integrity, and proper regulation of a subset of cytosolic proteins. In this study, the full-length 2693-bp cDNA of HSP90 was cloned by rapid amplification of cDNA ends (RACE) technique from the liver of rare minnow (Gobiocypris rarus) for the first time, designated as GrHSP90. The complete coding sequence of GrHSP90 is 2181 bp in length, which encodes a polypeptide of 726 amino acids with a predicted molecular mass of 83.4 kDa and a theoretical isoelectric point of 4.90. Phylogenetic tree analysis indicated that deduced protein GrHSP90 had extensive sequence similarities to other fish HSP90s. Tissue distribution showed that GrHSP90 was constitutively expressed in a wide range of tissues including gill, blood, brain, fin, gonad, heart, intestine, kidney, liver, muscle, spleen, skin, and swim bladder. The highest expression was found in the gonad. Furthermore, significant increase in GrHSP90 mRNA in the liver was observed after exposure to pentachlorophenol ≥8 µg/L (p < 0.05). Our results suggest that GrHSP90 is indeed an ortholog of the HSP90 family and may be act as a biomarker to assess the effect of environmental contaminant.

Transcriptome analysis of the mud crab (Scylla paramamosain) by 454 deep sequencing: assembly, annotation, and marker discovery

In this study, we reported the characterization of the first transcriptome of the mud crab (Scylla paramamosain). Pooled cDNAs of four tissue types from twelve wild individuals were sequenced using the Roche 454 FLX platform. Analysis performed included de novo assembly of transcriptome sequences, functional annotation, and molecular marker discovery. A total of 1,314,101 high quality reads with an average length of 411 bp were generated by 454 sequencing on a mixed cDNA library. De novo assembly of these 1,314,101 reads produced 76,778 contigs (consisting of 818,154 reads) with 5.4-fold average sequencing coverage. The remaining 495,947 reads were singletons. A total of 78,268 unigenes were identified based on sequence similarity with known proteins (E≤0.00001) in UniProt and non-redundant protein databases. Meanwhile, 44,433 sequences were identified (E≤0.00001) using a BLASTN search against the NCBI nucleotide database. Gene Ontology (GO) analysis indicated that biosynthetic process, cell part, and ion binding were the most abundant terms in biological process, cellular component, and molecular function categories, respectively. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis revealed that 4,878 unigenes distributed in 281 different pathways. In addition, 19,011 microsatellites and 37,063 potential single nucleotide polymorphisms were detected from the transcriptome of S. paramamosain. Finally, thirty polymorphic microsatellite markers were developed and used to assess genetic diversity of a wild population of S. paramamosain. So far, existing sequence resources for S. paramamosain are extremely limited. The present study provides a characterization of transcriptome from multiple tissues and individuals, as well as an assessment of genetic diversity of a wild population. These sequence resources will facilitate the investigation of population genetic diversity, the development of genetic maps, and the conduct of molecular marker-assisted breeding in S. paramamosain and related crab species.

Transcriptome-wide identification and characterization of the Procambarus clarkii microRNAs potentially related to immunity against Spiroplasma eriocheiris infection

We used the Illumina/Solexa deep sequencing technology to sequence two small RNA libraries prepared from hemocytes of Procambarus clarkii under normal and infection conditions. The high-throughput sequencing approach resulted in approximately 12,801,827 and 8,410,455 raw reads corresponding to 10,949,754 and 6,648,161 high-quality mappable reads for the normal and infected hemocyte samples, respectively. Bioinformatic analyses identified 195 unique miRNAs, including 30 that are conserved in crustaceans, 48 that are novel to crayfish but are present in other arthropods (PN-type), and 117 that are completely new (PC-type). Thirty-three miRNAs displayed significant differential expressions between the two hemocyte samples (p < 0.0001). Of these, 15 (45.5%) were significantly up-regulated and 18 (54.5%) were significantly down-regulated upon challenge with Spiroplasma eriocheiris. Integrating comparative genomic and bibliomic analysis, of the 33 significant miRNAs identified, 19 were conserved and immune-related in P. clarkii and Eriocheir sinensis infected with S. eriocheiris infection; 24 were conserved and immune-related in P. clarkii and Marsupenaeus japonicus immune response to S. eriocheiris or white spot syndrome virus (WSSV) infection. Function annotation of target genes revealed a broad range of biological processes and signal transduction pathways that regulated by crayfish miRNAs. Thereinto, pcl-miR-34, pcl-miR-7, PN-pcl-let-7, pcl-miR-1, and pcl-miR-2b are highly conserved in vertebrates and invertebrates and function in the similar pathways. To our knowledge, this is the first report of comprehensive identification of P. clarkii miRNAs and of expression analysis of P. clarkii miRNAs after exposure to S. eriocheiris in crayfish, and many miRNAs were differentially regulated under normal and infection conditions. Our results should help develop new control strategies for efficient immune protection against S. eriocheiris infections in crustaceans.