Polymorphism of the superoxide dismutase gene family in the bay scallop (Argopecten irradians) and its association with resistance/susceptibility to Vibrio anguillarum

Cell death and antioxidant responses in Mytilus galloprovincialis under heat stress: Evidence of genetic loci potentially associated with thermal resilience

The global seawater temperature is expected to further rise in the following years. While species have historically adapted to climatic variations, the current pace of climate change may exceed their ability to adapt. The abnormally increased seawater temperatures occasionally lead to high mortalities of marine bivalve mollusks, threatening the productivity of aquaculture and the sustainability of wild populations. This study investigates the antioxidant and cell death mechanisms of the Mediterranean mussel Mytilus galloprovincialis during a 25-day exposure to temperatures of 24°C, 26°C, and 28°C, by analyzing the transcription of key genes and assessing the oxidative damage on days 1, 3, 12, and 25. In addition, individuals resilient (survived at 28°C until day 30) and susceptible (died early at 26°C and 28°C) to thermal stress were collected to investigate potential polymorphisms in associated genes. The results showed increased transcription of antioxidant genes at higher temperatures. Elevated pro-apoptotic indices were initially observed at 26°C and a higher mortality than at 28°C. However, final mortality was much higher at 28°C. At 26°C, mussels exhibited the highest oxidative damage and pro-apoptotic indices after 25 days. At 28°C, although oxidative damage occurred after 24 hours, survivors maintained a prolonged activated antioxidant defense and increased lc3b transcription, which likely contributed to the observed reduction of pro-apoptotic and oxidative damage metrics on day 25, compared to 26°C. Further, the coding sequences of catalase, intracellular Cu-Zn superoxide dismutase (Cu-Zn sod), and fas-associated protein with death domain (fadd) from heat-resilient and heat-susceptible mussels were analyzed. Based on statistical correlation of nucleotide and genotype frequencies with resilience phenotypes, two novel single nucleotide polymorphisms (SNPs) in Cu-Zn sod and one in fadd were detected, potentially correlating with thermal stress resilience. These findings offer valuable insights into the physiological and genetic adaptations of M. galloprovincialis to rising temperatures and highlight loci potentially linking to thermal resilience.

An SNP at the target site of cid-miR-nov-1043 in the TOLLIP 3' UTR decreases mortality rate in grass carp subjected to ENU-induced mutagenesis following grass carp reovirus infection

N-ethyl-N-nitrosourea (ENU) selection is a useful technique to generate new mutations that may cause some functional changes in the gene. Through our previous genomic bulked segregant analysis (BSA), one single nucleotide polymorphism (SNP) at the 3' UTR of Toll interacting protein gene (TOLLIP^982T>C) was identified in grass carp (Ctenopharyngodon idella) subjected to ENU-induced mutagenesis. We found that the overexpression of cid-miR-nov-1043 mimics significantly suppressed the luciferase activity of the TOLLIP 3' UTR, but TOLLIP^982T>C mutation at the target site can decrease the binding affinity between the miRNA cid-miR-nov-1043 and TOLLIP 3' UTR, reducing the inhibition of TOLLIP mRNA transcription in grass carp subjected to ENU-induced mutagenesis. More importantly, we demonstrated that TOLLIP mRNA transcription levels in the gills, liver, kidney and the isolate white cells of the mutant grass carp were significantly (p < 0.01) higher than those in the corresponding tissues from the wild-type grass carp following infection with Grass Carp Reovirus (GCRV) for seven days, while the downstream gene of TOLLIP transforming growth factor β-activated kinase 1 (TAK1) and TAK1-binding protein 1 (TAB1), were higher expressed in wild-type grass carp. As a negative regulator in the pro-inflammatory pathway of NF-κB, TOLLIP inhibits the excessive inflammation in ENU grass carp after GCRV infection. Consistent with the TOLLIP expression, histopathological results demonstrated more severe inflammation in wild-type grass carp, compared to the TOLLIP^982T>C mutant grass carp on the seventh day. Severe inflammation will lead to thoroughly infiltration of chloride and inflammatory cells in the gill filaments. This seriously hindered the exchange of oxygen, which ultimately disrupted blood circulation. Meanwhile, the survival rate of the mutant grass carp was significantly (p < 0.01) higher than that of the wild-type grass carp, indicating that the TOLLIP^982T>C mutants showed strong anti-viral abilities. Our results revealed that an SNP in the TOLLIP 3' UTR may contribute to the suppression of serve inflammation subjected to ENU-induced mutagenesis following GCRV infection, which may be helpful for future resistant breeding development of grass carp.

Characterization and Expression of Genes Encoding Superoxide Dismutase in the Oriental Armyworm, Mythimna separata (Lepidoptera: Noctuidae)

Superoxide dismutase (SOD) is an antioxidant metalloenzyme that catalyzes the dismutation of the superoxide anion O2- to O2 and H2O2. Many studies have focused on the role of SOD in response to abiotic stress, but its role during biotic stress, such as changes in organismal population density, has rarely been investigated. The oriental armyworm, Mythimna separata, is an economically important pest that exhibits phenotypic changes in response to population density. Solitary and gregarious phases occur at low and high population density, respectively. To examine the role of SODs in response to population density stress, we cloned two genes encoding SOD, MsCuZnSOD and MsMnSOD, and compared their expression in solitary and gregarious phases of M. separata. The MsCuZnSOD and MsMnSOD ORFs were 480 and 651 bp and encoded predicted protein products of 159 and 216 amino acids, respectively. The two SODs contained motifs that are typical of orthologous proteins. Real-time PCR indicated that the two SOD genes were expressed throughout developmental stages and were significantly upregulated in more mature stages of gregarious M. separata. Expression of the two SOD genes in various tissues of sixth-instar larvae was higher in gregarious versus solitary insects. Furthermore, expression of the SOD genes was significantly upregulated in response to crowding in solitary individuals, but suppressed in gregarious insects subjected to isolation. Collectively, these results suggest that population density may be key factor in the induction of SOD genes in M. separata.

Identification of SNP markers associated with tolerance to ammonia toxicity by selective genotyping from de novo assembled transcriptome in Litopenaeus vannamei

The high concentration of ammonia from deteriorated aquaculture environments and the intensive culture system could increase the susceptibility to pathogens and even cause high mortality in Litopenaeus vannamei. In addition, we have revealed that the ammonia-tolerant shrimp also have high disease resistance in L. vannamei. In the present study, in order to identify SNP markers associated with tolerance to ammonia toxicity, we developed and characterized SNPs from our previous transcriptome sequencing data of ammonia-stressed and control groups, and a marker-trait association analysis was performed for marker-assisted selection (MAS) to increase production in L. vannamei. A total of 318,919 SNPs were identified from the transcriptome sequences, and 25,772 SNPs were found from the 1826 ammonia-responsive genes with functional annotation. We selected 49 SNPs from 26 ammonia-responsive genes that had strong homologies to known genes in the shrimp and probably involved in immune function as candidate markers for genotyping, among which 39 SNPs were polymorphic for further marker-trait association analysis with the ammonia-tolerant (AT) and ammonia-sensitive (AS) groups. Finally, 12 out of the 49 SNP markers were identified to be associated with ammonia tolerance, containing 10 loci with significantly different allele frequencies and 10 loci with significantly different genotyping frequencies between the AT and AS groups. Among the associated markers, the G allele of TSP-1 (the first locus from the thrombospondin gene), the A allele of TSP-3, and the C allele of XBP1-5 (the fifth locus from X-box binding protein 1) only presented in the AT groups, but they were absent from the AS groups, which would be the preference of the MAS for the ammonia-tolerant shrimp. In addition, when the 12 associated SNP markers were used for analysis, the genetic diversity of the AT groups were significantly higher than that of the AS groups, but when the 39 loci were used there was no difference. This is the first report for the markers associated with ammonia tolerance in this species, indirectly with disease resistance, which provided important potential for genetic selection to increase survival rate and production in shrimp farming.

A mitochondrial manganese superoxide dismutase involved in innate immunity is essential for the survival of Chlamys farreri

Superoxide dismutase (SOD) ubiquitously found in both prokaryotes and eukaryotes functions as the first and essential enzyme in the antioxidant system. In the present study, a manganese SOD (designated as CfmtMnSOD) was cloned from Zhikong scallop Chlamys farreri. The complete cDNA sequence of CfmtMnSOD contained a 681 bp open reading frame (ORF), encoding a peptide of 226 amino acids. A SOD_Fe_N domain and a SOD_Fe_C domain were found in the deduced amino acid sequence of CfmtMnSOD. The mRNA transcripts of CfmtMnSOD were constitutively expressed in all the tested tissues, including gill, gonad, hepatopancreas, hemocytes, mantle and muscle, with the highest expression level in hemocytes. After the stimulation of Vibrio splendidus, Staphylococcus aureus and Yarrowia lipolytica, the mRNA transcripts of CfmtMnSOD in hemocytes all significantly increased. The purified rCfmtMnSOD protein exhibited Mn²⁺ dependent specific and low stable enzymatic activities. After Vibrio challenge, the cumulative mortality of CfmtMnSOD-suppressed scallops was significantly higher than those of control groups and the semi-lethal time for CfmtMnSOD-suppressed scallops was rather shorter than those of control groups either. Moreover, the final mortality rate of CfmtMnSOD-suppressed group was significant higher than those of control groups, even without Vibrio challenge. All these results indicated that CfmtMnSOD was efficient antioxidant enzyme involved in the innate immunity, and also essential for the survival of C. farreri.

Infectious diseases of marine molluscs and host responses as revealed by genomic tools

More and more infectious diseases affect marine molluscs. Some diseases have impacted commercial species including MSX and Dermo of the eastern oyster, QPX of hard clams, withering syndrome of abalone and ostreid herpesvirus 1 (OsHV-1) infections of many molluscs. Although the exact transmission mechanisms are not well understood, human activities and associated environmental changes often correlate with increased disease prevalence. For instance, hatcheries and large-scale aquaculture create high host densities, which, along with increasing ocean temperature, might have contributed to OsHV-1 epizootics in scallops and oysters. A key to understanding linkages between the environment and disease is to understand how the environment affects the host immune system. Although we might be tempted to downplay the role of immunity in invertebrates, recent advances in genomics have provided insights into host and parasite genomes and revealed surprisingly sophisticated innate immune systems in molluscs. All major innate immune pathways are found in molluscs with many immune receptors, regulators and effectors expanded. The expanded gene families provide great diversity and complexity in innate immune response, which may be key to mollusc's defence against diverse pathogens in the absence of adaptive immunity. Further advances in host and parasite genomics should improve our understanding of genetic variation in parasite virulence and host disease resistance.

Polymorphism in a serine protease inhibitor gene and its association with the resistance of bay scallop (Argopecten irradians) to Listonella anguillarum challenge

Serine protease inhibitors (SPIs) play a crucial role in regulation of both host and bacterial serine protease. They are classified into several protein families, where Kazal-type inhibitors are one of families with multi-domain. In the present study, the polymorphism of AiSPI from Bay scallop Argopecten irradians was found to be associated with disease resistance of bay scallop against Listonella anguillarum. Nine single nucleotide polymorphisms (SNPs) were identified in the exon region of AiSPI, where five SNPs were non-synonymous mutation. Three of these mutations were located in "kazal-like 3"domain, two SNP loci positioned at +536, +1312 were selected for further association studies. For the locus +536, the genotype frequency of A/G in the resistant stock (12.8%) was significantly lower (p < 0.05) than that in the susceptible stock (35.1%), while, the genotype A/A in the resistant stock (87.2%) was significantly higher in comparison with susceptible stock (64.9%) (p < 0.05). The G allele frequencies were 6.4% and 17.6% in resistant stock and susceptible stock, respectively, and χ²-test revealed a significant difference in the frequency distribution between the two stocks (p < 0.05). But there was no significant association between the mutation C-T at locus +1312 with either resistant or susceptible group (p > 0.05). The genotype frequencies of T/T, T/C, C/C at locus +1312 were 94.6%, 2.7% and 2.7% respectively in the susceptible stock, while 100%, 0% and 0% respectively in the resistant stock. The amino acid change for the mutation at locus +536 A-G was from asparagine to serine, and the predicted homology model of this amino acid variation could affect its function as well as the structural integrity of the domain. In vitro elastase inhibition assay of the protein variants at locus +536 was conducted to explicate the effect of SNP. The increasing concentration of protein (0 mmol/L- 2.93 mmol/L) was incubated with 80 nmol/L elastase where the residual enzyme activity values for rAiSPI (N) with A variant and rAiSPI (S) with G variant were started to reduce from 0.40 to 0.215 and 0.435 to 0.356, respectively. The elastase inhibition ability of rAiSPI (N) variant was significantly higher than that of rAiSPI (S) (p < 0.01). The results suggested that the mutation at locus +536A/A significantly associated with disease resistance of bay scallop would shed light for selective breeding program.

The immune system and its modulation mechanism in scallop

Scallops are a cosmopolitan family of bivalves, and some of them are highly prized as dominant aquaculture species. In the past decades, there have been increasing studies on the basic biology and immunology of scallops, and this review summarizes the research progresses of immune system and its modulation mechanism in scallop. As invertebrate, scallops lack adaptive immunity and they have evolved an array of sophisticated strategies to recognize and eliminate various invaders by employing a set of molecules and cells. It is evident that basic immune reactions such as immune recognition, signal transduction, and effector synthesis involved in immune response are accomplished in a variety of ways. They rely upon an extensive repertoire of phagocytosis, apoptosis and encapsulation of the circulating hemocytes for eliminating invasive pathogens, as well as the production of immune effectors that are active against a large range of pathogens or sensitive for the environmental stress. Furthermore, the molecular constitutions, metabolic pathways and immunomodulation mechanisms of the primitive catecholaminergic, cholinergic, enkephalinergic system and NO system in scallop are also discussed, which can be taken as an entrance to better understand the origin and evolution of the neuroendocrine-immune regulatory network in lower invertebrates.

Development of Vibrio spp. infection resistance related SNP markers using multiplex SNaPshot genotyping method in the clam Meretrix meretrix

The clam Meretrix meretrix is a commercially important mollusc species in the coastal areas of South and Southeast Asia. In the present study, large-scale SNPs were genotyped by the Multiplex SNaPshot genotyping method among the stocks of M. meretrix with different Vibrio spp. infection resistance profile. Firstly, the AUTOSNP software was applied to mine SNPs from M. meretrix transcriptome, and 323 SNP loci (including 120 indels) located on 64 contigs were selected based on Uniprot-GO associations. Then, 38 polymorphic SNP loci located on 15 contigs were genotyped successfully in the clam stocks with different resistance to Vibrio parahaemolyticus infection (11-R and 11-S groups). Pearson's Chi-square test was applied to compare the allele and genotype frequency distributions of the SNPs between the different stocks, and seven SNP markers located on three contigs were found to be associated with V. parahaemolyticus infection resistance trait. Haplotype-association analysis showed that six haplotypes had significantly different frequency distributions in 11-S and 11-R (P < 0.05). With selective genotyping between 09-R and 09-C populations, which had different resistance to Vibrio harveyi infection, four out of the seven selected SNPs had significantly different distributions (P < 0.05) and therefore they were considered to be associated with Vibrio spp. infection resistance. Sequence alignments and annotations indicated that the contigs containing the associated SNPs had high similarity to the immune related genes. All these results would be useful for the future marker-assisted selection of M. meretrix strains with high Vibrio spp. infection resistance.

SNP detection of TLR8 gene, association study with susceptibility/resistance to GCRV and regulation on mRNA expression in grass carp, Ctenopharyngodon idella

Toll-like receptor 8 (TLR8), a prototypical intracellular member of TLR family, is generally linked closely to antiviral innate immune through recognizing viral nucleic acid. In this study, 5'-flanking region of Ctenopharyngodon idella TLR8 (CiTLR8), 671bp in length, was amplified and eight SNPs containing one SNP in the intron, three SNPs in the coding region (CDS) and four SNPs in the 3'-untranslated region (UTR) were identified and characterized. Of which 4062 A/T was significantly associated with the susceptibility/resistance to GCRV both in genotype and allele (P < 0.05), while 4168 C/T was extremely significantly associated with that (P < 0.01) according to the case (susceptibility)-control (resistance) analysis. Following the verification experiment, further analyses of mRNA expression, linkage disequilibrium (LD), haplotype and microRNA (miRNA) target site indicated that 4062 A/T and 4168 C/T in 3'-UTR might affect the miRNA regulation, while the exertion of antiviral effects of 4062 A/T might rely on its interaction with other SNPs. Additionally, the high-density of SNPs in 3'-UTR might reflect the specific biological functions of 3'-UTR. And also, the mutation of 747 A/G in intron changing the potential transcriptional factor-binding sites (TFBS) nearby might affect the expression of CiTLR8 transcriptionally or post-transcriptionally. Moreover, as predicted, the A/G transition of the only non-synonymous SNP (3846 A/G) in CDS causing threonine/alanine variation, could shorten the length of the α-helix and ultimately affect the integrity of the Toll-IL-1 receptor (TIR) domain. The functional mechanism of 3846 A/G might also involve a threonine phosphorylation signaling. This study may broaden the knowledge of TLR polymorphisms, lay the foundation for further functional research of CiTLR8 and provide potential markers as well as theoretical basis for resistance molecular breeding of grass carp against GCRV.

Gene discovery in the tropical scallop Nodipecten nodosus: construction and sequencing of a normalized cDNA library

We report the construction and characterization of a normalized cDNA library from the digestive gland of the marine bivalve Nodipecten nodosus, a commercially valuable tropical scallop. A total of 288 clones were sequenced, and 250 unique sequences were obtained. The cDNA library showed a small sequence redundancy (2.3%) and high numbers of recombinant (99.9%) and independent clones (2.0 × 10(6) cfu), indicating that the cDNA library generated in this study is a profitable resource for efficient gene discovery for N. nodosus. EST functional annotation by Gene Ontology term assignment revealed the identification of sequences potentially involved in aquaculture and ecotoxicology relevant processes such as apoptosis, growth, lipid metabolism, reproduction, development, response to stress and immunity.

Concholepas concholepas Ferritin H-like subunit (CcFer): Molecular characterization and single nucleotide polymorphism associated to innate immune response

Ferritin has been identified as the principal protein of iron storage and iron detoxification, playing a pivotal role for the cellular homeostasis in living organisms. However, recent studies in marine invertebrates have suggested its association with innate immune system. In the present study, one Ferritin subunit was identified from the gastropod Concholepas concholepas (CcFer), which was fully characterized by Rapid Amplification of cDNA Ends technique. Simultaneously, a challenge test was performed to evaluate the immune response against Vibrio anguillarum. The full length of cDNA Ccfer was 1030 bp, containing 513 bp of open reading frame that encodes to 170 amino acid peptide, which was similar to the Ferritin H subunit described in vertebrates. Untranslated Regions (UTRs) were identified with a 5'UTR of 244 bp that contains iron responsive element (IRE), and a 3'UTR of 273 bp. The predicted molecular mass of deduced amino acid of CcFer was 19.66 kDa and isoelectric point of 4.92. Gene transcription analysis revealed that CcFer increases against infections with V. anguillarum, showing a peak expression at 6 h post-infection. Moreover, a single nucleotide polymorphism was detected at -64 downstream 5'UTR sequence (SNP-64). Quantitative real time analysis showed that homozygous mutant allele (TT) was significantly associated with higher expression levels of the challenged group compared to wild (CC) and heterozygous (CT) variants. Our findings suggest that CcFer is associated to innate immune response in C. concholepas and that the presence of SNPs may involve differential transcriptional expression of CcFer.

Polymorphisms of anti-lipopolysaccharide factors in the swimming crab Portunus trituberculatus and their association with resistance/susceptibility to Vibrio alginolyticus

Anti-lipopolysaccharide factor (ALF) is an important antimicrobial peptide (AMP) that can bind and neutralize major component of Gram-negative bacteria cell wall, lipopolysaccharide (LPS). Seven isoforms of anti-lipopolysaccharide factors (PtALF1-7) were previously identified from the swimming crab Portunus trituberculatus in our laboratory. Here, polymorphisms of PtALF1-7 were detected and their association with resistance/susceptibility to Vibrio alginolyticus (a main Gram-negative bacteria causing high mortality in P. trituberculatus) were investigated. We identified 127, 96, 103, 53 and 158 single nucleotide polymorphisms (SNPs) in genomic fragments of PtALF1-3, PtALF4, PtALF5, PtALF6 and PtALF7, respectively. Among them, totally sixteen SNPs were significantly associated with resistance/susceptibility to V. alginolyticus (P < 0.05). Of these sixteen SNPs, most were located in introns and noncoding exons, while two synonymous SNPs and one nonsynonymous SNP were in coding exons. Additionally, simple sequence repeats (SSRs) were only identified in introns and noncoding exons of PtALF4, PtALF5 and PtALF7. Although no significant difference of allele frequencies was found, these SSRs had different polymorphic alleles according to the repeat number between susceptible and resistant stocks. After further confirmation, polymorphisms investigated here might be applied as potential molecular markers for future selection of resistant strains to diseases caused by Gram-negative bacteria.

Genomic sequence comparison, promoter activity, SNP detection of RIG-I gene and association with resistance/susceptibility to grass carp reovirus in grass carp (Ctenopharyngodon idella)

As an intracellular pattern recognition receptor (PRR), retinoic acid-inducible gene-I (RIG-I) is responsible for detection of nucleic acids from pathogens in infected cells and activation of type I interferon (IFN). In the present study, the 5'-flanking region, introns and single nucleotide polymorphisms (SNPs) of CiRIG-I (Ctenopharyngodon idella RIG-I) were identified and characterized. The genomic CiRIG-I was 12810 bp in length, consisted of an 1864 bp 5'-flank region whose promoter activity was confirmed, 15 exons and 14 introns. By pooled DNA sequencing, two SNPs were detected in the 5'-flanking region; 10 SNPs were discovered in introns; and one SNP was found in exons. After a challenge experiment, these SNPs were selected to analyze their association with the resistance/susceptibility of C. idella to grass carp reovirus (GCRV), using case-control study. Chi-square test was employed to assess the association. The result showed that -780 C/T, 4731 C/T, 4945 A/G, 8461 C/T, and haplotype 3428A-3432G were significantly associated with the phenotype (P<0.05). To confirm the correlation, another independent challenge experiment was performed, in which the cumulative mortality of -780 genotype CC, 4731 genotype CC and 4945 genotype AA were significantly lower than that of -780 genotype TT, 4731 genotype TT and 4945 genotype GG, respectively (P<0.05). In addition, the SNP-SNP interaction analysis revealed that there was no significant interaction among those SNPs (P>0.05). These significant SNPs and the haplotype might be potential genetic markers for the molecular selection of C. idella strains that are resistant to GCRV.

Association between the polymorphism of CfPGRP-S1 gene and disease susceptibility/resistance of zhikong scallop (Chlamys farreri) to Listonella anguillarum challenge

Peptidoglycan recognition protein (PGRP) is a pattern recognition receptor, playing important roles in the innate immune response against invasive pathogens. The single nucleotide polymorphism (SNP) loci in scallop PGRP gene (CfPGRP) were screened from Chlamys farreri to investigate their association with disease resistance of scallop against Listonella anguillarum. Thirteen SNP sites were identified in PGRP domain of CfPGRP, and two of them at positions 4407 and 4408 which are located in the same codon resulted in a nonsynonymous substitution. The genotype frequency of CG/CG in the resistant stock was significantly lower than that in susceptible stock (0% vs 32.4%), while that of CG/TA in the resistant stock was significantly higher than that in susceptible stock (P < 0.01). The pathogen-associated molecular patterns (PAMP) binding activity of two recombinant proteins, rCfPGRP-S1 (R) with CG variant in 4407-4408 site, rCfPGRP-S1 (Y) with TA variant in 4407-4408 site, were elucidated by examining their P/N value at 405 nm with ELISA assay. The in vitro binding activities of the two rCfPGRP-S1 variants to both lipopolysaccharide (LPS) and peptidoglycan (PGN) varied (P < 0.05) in a dose-dependent manner, and rCfPRPP-S1(Y) exhibited significantly higher affinity to PGN and LPS than that of rCfPGRP-S1(R) (P < 0.05). The growth inhibition assay was conducted to find the antibacterial activities of the two variants. Both rCfPGRP-S1(R) and rCfPGRP-S1 (Y) displayed obvious activity to suppress the growth of Escherichia coli, but there was no significant difference in suppression activity of two variants (P > 0.05). The results suggested that the polymorphism at locus 4407-4408 of CfPGRP-S1 considerably affected its PAMP binding activity, and the SNP locus 4407-4408 CG/TA was associated with disease resistance of scallop against L. anguillarum infection, which could be used as a candidate marker for future selection in zhikong scallop breeding program.

Single nucleotide polymorphisms in i-type lysozyme gene and their correlation with vibrio-resistance and growth of clam Meretrix meretrix based on the selected resistance stocks

I-type lysozyme is considered to play crucial roles in both anti-bacteria and digestion function of the bivalve, which signifies that it is related to both immunity and growth. In this study, based on the principle of case-control association analysis, using the stock materials with different vibrio-resistance profile obtained by selective breeding, single nucleotide polymorphisms (SNPs) in the DNA partial sequence of an i-type lysozyme of Meretrix meretrix (MmeLys) were discovered and examined for their association with vibrio-resistance and growth. Twenty-seven SNPs were detected and fifteen of them were genotyped in clam stocks with different resistance to Vibrio harveyi (09-C and 09-R) and to Vibrio parahaemolyticus (11-S and 11-R). Allele frequency distribution among different stocks was compared. And wet weight of clams with different genotype at each SNP locus was compared. The results indicated that SNP locus 9 was associated with V. harveyi and V. parahaemolyticus resistance and growth of M. meretrix. Loci 12 and 14 were associated with both V. parahaemolyticus-resistance and growth, and also have the potential to be related with V. harveyi-resistance of M. meretrix. Therefore these three SNPs especially locus 9 were the potential markers which may be involved in assisting resistance selective breeding. In addition, this study showed evidence that improvements in clam resistance to vibriosis could be achieved through selective breeding. All results provided encouragement for the continuation of the selective breeding program for vibrio-resistance gain in clam M. meretrix and the application of polymorphisms in MmeLys to the future marker assisted selection.

Intracellular Copper Zinc Superoxide dismutase (icCuZnSOD) from Asian seabass (Lates calcarifer): molecular cloning, characterization and gene expression with reference to Vibrio anguillarum infection

Copper Zinc Superoxide dismutase (CuZnSOD) is the family of most important antioxidant metalloenzymes that protects tissues from damage by reactive oxygen species (ROS). In the present study, the intracellular copper zinc SOD from the Asian seabass Lates calcarifer (Lc-icCuZnSOD) was identified by RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE) technique. The full-length cDNA of Lc-icCuZnSOD consisted of 809 nucleotides with an open-reading frame of 465 bp encoding 154 amino acids and N-Glycosylation site (NVTA) within. The predicted molecular mass of the protein is 15.84 kDa with an estimated pI of 5.52. The deduced amino acid sequence of Lc-icCuZnSOD shared high degree of homology with known CuZnSODs from other species. CuZn binding sites (H47, H49, H64, and H121 for Cu(2+) and H72, H81, and ASP84 for Zn(2+)), two cysteine residues (aa 58 and 147) that form a disulfide bond, and CuZnSOD family signature sequences (GFHVHAFGDNT, aa 45-55 and GNAGGRLACGVI, aa 139-150) were highly conserved among fish species. Temporal and tissue specific expression of Lc-icCuZnSOD was significantly differentially altered in Asian seabass challenged with Vibrio anguillarum indicating possible role in antioxidant activities involved in the innate immune defense mechanisms.

Transcriptome analysis in Concholepas concholepas (Gastropoda, Muricidae): mining and characterization of new genomic and molecular markers

The marine gastropod Concholepas concholepas, locally known as the "loco", is the main target species of the benthonic Chilean fisheries. Genetic and genomic tools are necessary to study the genome of this species in order to understand the molecular basis of its development, growth, and other key traits to improve the management strategies and to identify local adaptation to prevent loss of biodiversity. Here, we use pyrosequencing technologies to generate the first transcriptomic database from adult specimens of the loco. After trimming, a total of 140,756 Expressed Sequence Tag sequences were achieved. Clustering and assembly analysis identified 19,219 contigs and 105,435 singleton sequences. BlastN analysis showed a significant identity with Expressed Sequence Tags of different gastropod species available in public databases. Similarly, BlastX results showed that only 895 out of the total 124,654 had significant hits and may represent novel genes for marine gastropods. From this database, simple sequence repeat motifs were also identified and a total of 38 primer pairs were designed and tested to assess their potential as informative markers and to investigate their cross-species amplification in different related gastropod species. This dataset represents the first publicly available 454 data for a marine gastropod endemic to the southeastern Pacific coast, providing a valuable transcriptomic resource for future efforts of gene discovery and development of functional markers in other marine gastropods.

A primitive Toll-like receptor signaling pathway in mollusk Zhikong scallop Chlamys farreri

As a member of pattern-recognition receptors (PRRs), the Toll-like receptor (TLR) and its signaling pathway play pivotal roles in recognizing various pathogen-associated molecular patterns (PAMPs), and buildup the front-line against invading pathogens. In the present study, the sequence features and mRNA expression profiles of five key genes involved in TLR signal pathway were characterized, and their functions in the immune responses were also investigated in order to validate the TLR signaling pathway and its potential roles in the immune defense of Zhikong scallop Chlamys farreri. These five genes, including CfTLR, CfMyD88, CfTRAF6, CfIκB and CfNFκB, exhibited significant similarity with their homologues from other model organisms, and contained the typical motifs. A strong interaction between the TIR domain from CfTLR and CfMyD88 protein was revealed via ELISA assays. The mRNA transcripts of these five genes were all up-regulated after LPS stimulation, indicating that they were involved in the immune response against LPS. When CfTLR expression was inhibited by RNAi technology, the mRNA expression level of CfMyD88, CfTRAF6, CfIκB, CfNFκB and G-type lysozyme were all decreased, while those of superoxide dismutase and catalase were increased. After Listonella anguillara challenge, the apoptosis level of those CfTLR-suppressed scallops was significantly lower than that in control groups (p<0.05) at the beginning of bacteria challenge, while the cumulative mortality was significantly higher than that of control groups (p<0.05). These results collectively favored that a rather canonical MyD88-dependent TLR pathway existed in scallop and this pathway was involved in immune signaling to active the diverse downstream reaction including anti-oxidant, anti-bacteria and apoptosis.

Three isoforms of anti-lipopolysaccharide factor identified from eyestalk cDNA library of swimming crab Portunus trituberculatus

Anti-lipopolysaccharide factors (ALFs), as the potent antimicrobial peptides, can bind and neutralize lipopolysaccharide (LPS) and exhibit broad spectrum antimicrobial activities. In this study, three isoforms of the ALF homologues (PtesALF1-3) were identified from eyestalk cDNA library of swimming crab Portunus trituberculatus. The full-length cDNA sequences of PtesALF1, 2 and 3 were 1138, 1052 and 1057 bp encoding 92, 108 and 123 amino acids, respectively. PtesALF1-3 contained two conserved cysteine residues and shared high similarity with other reported ALFs. Predicted tertiary structures of PtesALF2 and 3 containing four β-strands and three α-helix were similar to that described in Limulus polyphemus, while PtesALF1 had only one α-helix in its spatial structure. Sequence analysis revealed PtesALF1-3 were encoded by the same genomic locus and generated by alternative splicing of the pre-mRNA. Totally 89 SNPs including 18 in coding region and 71 in noncoding region were detected by direct sequencing of 30 genomic samples. The mRNA expression of PtesALF1 and PtesALF1-3 transcripts was mainly detected in haemocytes but showed different expression pattern in other tissues including hepatopancreas, gill, eyestalk and muscle. After challenge with Vibrio alginolyticus, the temporal expression level of PtesALF1-3 transcripts in haemocytes showed a clear time-dependent response expression pattern with two peaks within the experimental period of 32 h, while PtesALF1 was up-regulated only once with obvious decrease at 6 h and significant increase at 24 h. These results suggest that the PtesALF isoforms have different tissue specificity and might provide multiple protective functions against invading bacteria in P. trituberculatus.

A selenium-dependent glutathione peroxidase in the Japanese scallop, Mizuhopecten yessoensis: cDNA cloning, promoter sequence analysis and mRNA expression

Glutathione peroxidase (GPx) is an antioxidant enzyme that protects cells from oxidative damage in the innate immune responses against bacterial infections. GPx is also involved in immune defenses. In this study, we report cloning and characterization of a GPx (designated as MyGPx) coding sequences and promoter from Japanese scallop, Mizuhopecten yessoensis. The full-length 1081 nt MyGPx mRNA contained a 28 nt 5' untranslated region (UTR), a 603 nt open reading frame and a 450 nt 3' UTR containing a polyadenylation signal (AATAAA). Multiple sequence alignment revealed that amino acids essential to enzymatic function of MyGPx proteins were highly conserved. A 1628 nt 5'-flanking sequence of MyGPx was identified by genome walking. Here, several potential transcription factor binding sites were detected in the putative promoter region, and nine single nucleotide polymorphisms (SNPs) were found in the 5' sequence flanking the promoter region. Quantitative Real time PCR (qRT-PCR) was employed to measure GPx mRNA expression in adult tissues and monitor mRNA expression patterns during embryonic development and following stimulation by the bacteria Vibrillo anguillarum. Collectively, the results suggest that MyGPx fulfills an important function during M. yessoensis development and may be an important immune effector in adult molluscs.