Comprehensive EST analysis of Atlantic halibut (Hippoglossus hippoglossus), a commercially relevant aquaculture species

Characteristics and functional analysis of a novel mannose receptor in Penaeus vannamei

The mannose receptor (MR) plays a key role in the innate immune system as a pattern recognition receptor. Here, a novel type of mannose receptor, named PvMR2, was identified from Penaeus vannamei (P. vannamei). The PvMR2 coding sequence (CDS) obtained was 988 base pairs in length, encoding a protein consisting of 328 amino acids. This protein includes a signal peptide and two classical C-type lectin domains (CTLD). Quantitative real-time PCR showed that PvMR2 was distributed in all detected tissues, with the highest levels in the intestines and stomach. Following a bacterial challenge with Vibrio anguillarum (V. anguillarum), PvMR2 showed significant up-regulation in both the intestines and stomach of shrimp. To validate the function of PvMR2, recombinant proteins were extracted and purified using a His-tag. The resulting rPvMR2 demonstrated binding capability with lipopolysaccharides (LPS) and peptidoglycan (PGN) in a dose-dependent manner, affirming its binding affinity. The purified rPvMR2 demonstrated calcium-independent binding activity towards both Gram-positive bacteria (V. anguilliarum and Vibrio parahaemolyticus) and Gram-negative bacteria (Escherichia coli and Aeromonas Veronii). Antibacterial assays confirmed that rPvMR2 inhibits bacterial growth. Intestinal adhesion and adhesion inhibition experiments confirmed that the rPvMR2 can be used to reduce the adhesion capacity of harmful bacteria in the gut. Phagocytosis experiments have shown that rPvMR2 promotes phagocytosis in hemocytes and protects the host from external infection. Treatment with recombinant PvMR2 significantly bolstered bacterial clearance within the hemolymph and markedly augmented shrimp survival post-infection with V. anguillarum. These results suggest that PvMR2 has agglutination, growth inhibition, adhesion inhibition, clearance promotion, and phagocytosis effects on harmful bacteria, and plays a crucial role in the antimicrobial immune response of P. vannamei.

Gene Expression and Phenotypic Assessment of Egg Quality across Developmental Stages of Atlantic Cod throughout the Spawning Season

Egg quality in fishes is commonly determined by fertilisation success and cleavage patterns as a phenotypic outcome of underlying regulatory mechanisms. Although these phenotypic estimators of egg quality are useful in farming conditions, these "good quality" egg batches do not always translate to good larval growth and survival. The identification of genes involved in embryonic development may help find links between genetic factors of maternal origin and egg quality. Herein, the relative expression of seven stage-specific developmental genes of Atlantic cod was analysed using quantitative PCR to understand the function during embryogenesis and its relationship with egg quality. Genes ccnb2 and pvalb1 showed significant differential expression between developmental stages and significant upregulation from blastula and somite stages, respectively. The comparison of spawning batches showed that the relative gene expression of genes ccnb2, acta, tnnt3 and pvalb1 was significantly higher from the middle of the spawning season where phenotypic quality estimators establish the best egg quality. Moreover, a positive significant correlation was observed between quality estimators based on egg morphology and the genetic expression of genes acta and acta1 during somitogenesis. This study suggests that the combination of quality estimators, genetics and batch timing could help optimise reproductive protocols for commercial stocks of Atlantic cod.

A C-type lectin with a single CRD from Onychostoma macrolepis mediates immune recognition against bacterial challenge

C-type lectins (CTL) are a large group of pattern-recognition proteins and to play important roles in glycoprotein metabolism, multicellular integration, and immunity. Based on their overall domain structure, they can be classified as different groups that possess different physiological functions. A typical C-type lectin (named as OmLec1) was identified from the fish, Onychostoma macrolepis, an important cultured fish in China. Open reading frame of OmLec1 contains a 570 bp, encoding a protein of 189 amino acids that includes a signal peptide and a single carbohydrate-recognition domain. The phylogenetic analysis showed that OmLec1 could be grouped with C-type lectin from other fish. OmLec1 was expressed in all the tissues in our study, and the expression level was highest in liver. And its relative expression levels were significantly upregulated following infection with Aeromonas hydrophila. The recombinant OmLec1 protein (rOmLec1) could agglutinate some Gram-negative bacteria and Gram-positive bacteria in vitro in the presence of Ca²⁺, showing a typical Ca²⁺-dependent carbohydrate-binding protein. Furthermore, rOmLec1 purified from E. coli BL21 (DE3), strongly bound to LPS and PGN, as well as all tested bacteria in a Ca²⁺-dependent manner. These results indicate that OmLec1 plays a central role in the innate immune response and as a pattern recognition receptor that recognizes diverse pathogens among O. macrolepis.

A C-type lectin (OmCTL) in Onychostoma macrolepis: Binding ability to LPS, PGN and agglutinating activity against bacteria

C-type lectins (CTLs) are calcium-dependent carbohydrate-binding proteins that mainly bind to carbohydrate-based or other ligands to mediate cell adhesion, recognize pathogens, and play important roles in the immune system. In the present study, a novel C-type lectin (OmCTL) isolated from Onychostoma macrolepis was investigated. The open reading frame of OmCTL comprises 468 bp, encoding a 155 amino acid polypeptide with an 18 amino acid putative signaling peptide. The predicted primary OmCTL structure contains a signal peptide, a single carbohydrate recognition domain (CRD) and an EPN/WND motif required for carbohydrate-binding specificity. Using tissue expression pattern analysis, OmCTL has been shownto be highly expressed in the liver, and is also detected in other tissues. OmCTL was significantly upregulated in the liver and spleen following infection with Aeromonas hydrophila, suggesting its involvement in immune response. The recombinant OmCTL protein (rOmCTL) agglutinated two gram-negative bacteria, Escherichia coli and A. hydrophila, in vitro in the presence of Ca²⁺, showing that it is a typical Ca²⁺-dependent carbohydrate-binding protein.Furthermore, rOmCTL purified from E. coli BL21 (DE3) strongly bound to LPS and PGN, as well as all tested bacteria in a Ca²⁺-independent manner. These results indicate that OmCTL plays a central role in the innate immune response and as a pattern recognition receptor that recognizes diverse pathogens among O. macrolepis.

A C-type lectin, Nattectin-like protein (CaNTC) in Qihe crucian carp Carassius auratus: Binding ability with LPS, PGN and various bacteria, and agglutinating activity against bacteria

C-type lectins (CTLs), as the members of pattern-recognition receptors (PRRs), play the significant roles in innate immunity through binding with pathogen-associated molecular patterns (PAMPs) on the surface of microbe. In the present study, a novel CTL, Nattectin-like protein (named as CaNTC), was investigated in Qihe crucian carp Carassius auratus. The full-length cDNA of CaNTC was composed of 776 bp, with a 152 bp 5'-untranslated region (UTR), a 492 bp ORF encoding a 163-aa protein, and a 132 bp 3'-UTR with a polyadenylation signal sequence AATAAA and a poly(A) tail. The deduced amino acid sequence of CaNTC contained a signal peptide, a single carbohydrate recognition domain (CRD) which had four conserved disulfide-bonded cysteine residues (Cys⁵⁷-Cys¹⁵⁰, Cys¹²⁶-Cys¹⁴²), and an EPN/WND motif required for carbohydrate-binding specificity. With regard to the mRNA transcript of CaNTC, it was predominately expressed in liver. The temporal expressions of CaNTC were obviously up-regulated in liver, spleen and head-kidney after challenged by Aeromonas hydrophila and poly I: C, respectively, and the change pattern was in the time-depended manner. The recombinant CaNTC (rCaNTC) purified from Escherichia coli BL21 (DE3), exhibited strong binding ability with LPS and PGN, as well as all tested bacteria in a Ca²⁺-independent manner. With regard to the agglutinating activity of rCaNTC, rCaNTC was able to agglutinate rabbit erythrocytes and three kinds of bacteria (Gram-negative bacteria, Escherichia coli and A. hydrophila, and Gram-positive bacteria Staphylococcus aureus) in a Ca²⁺-dependent manner. These findings collectively demonstrated that CaNTC, as a PRR, could be involved in the innate immunity and play an important role in immune defense of C. auratus.

Subtle genetic population structure in Pacific halibut Hippoglossus stenolepis

Pacific halibut Hippoglossus stenolepis from 10 sampling locations throughout their range were investigated for signs of population structure. Two genetic data sets were created: (1) all individuals (n = 828) at few anonymous microsatellite markers (number of loci = 16); (2) fewer individuals (n = 435) genotyped at anonymous as well as expressed sequence-tag linked microsatellites (number of loci = 61). A combination of multidimensional scaling plots, discriminant analysis of principal components and pairwise differentiation estimates suggested that samples from the Aleutian Islands, particularly the western Aleutian Islands, were genetically distinct from samples collected in other regions. In addition, outlier analyses found that two markers linked to expressed sequence tags may be under directional selection and could explain the differentiation among samples. These results confirm findings from previous research and suggest that population structure may exist within a current management unit (i.e. International Pacific Halibut Commission Regulatory Area 4B).

The transcriptome of metamorphosing flatfish

BACKGROUND

Flatfish metamorphosis denotes the extraordinary transformation of a symmetric pelagic larva into an asymmetric benthic juvenile. Metamorphosis in vertebrates is driven by thyroid hormones (THs), but how they orchestrate the cellular, morphological and functional modifications associated with maturation to juvenile/adult states in flatfish is an enigma. Since THs act via thyroid receptors that are ligand activated transcription factors, we hypothesized that the maturation of tissues during metamorphosis should be preceded by significant modifications in the transcriptome. Targeting the unique metamorphosis of flatfish and taking advantage of the large size of Atlantic halibut (Hippoglossus hippoglossus) larvae, we determined the molecular basis of TH action using RNA sequencing.

RESULTS

De novo assembly of sequences for larval head, skin and gastrointestinal tract (GI-tract) yielded 90,676, 65,530 and 38,426 contigs, respectively. More than 57 % of the assembled sequences were successfully annotated using a multi-step Blast approach. A unique set of biological processes and candidate genes were identified specifically associated with changes in morphology and function of the head, skin and GI-tract. Transcriptome dynamics during metamorphosis were mapped with SOLiD sequencing of whole larvae and revealed greater than 8,000 differentially expressed (DE) genes significantly (p < 0.05) up- or down-regulated in comparison with the juvenile stage. Candidate transcripts quantified by SOLiD and qPCR analysis were significantly (r = 0.843; p < 0.05) correlated. The majority (98 %) of DE genes during metamorphosis were not TH-responsive. TH-responsive transcripts clustered into 6 groups based on their expression pattern during metamorphosis and the majority of the 145 DE TH-responsive genes were down-regulated.

CONCLUSIONS

A transcriptome resource has been generated for metamorphosing Atlantic halibut and over 8,000 DE transcripts per stage were identified. Unique sets of biological processes and candidate genes were associated with changes in the head, skin and GI-tract during metamorphosis. A small proportion of DE transcripts were TH-responsive, suggesting that they trigger gene networks, signalling cascades and transcription factors, leading to the overt changes in tissue occurring during metamorphosis.

An Enriched European Eel Transcriptome Sheds Light upon Host-Pathogen Interactions with Vibrio vulnificus

Infectious diseases are one of the principal bottlenecks for the European eel recovery. The aim of this study was to develop a new molecular tool to be used in host-pathogen interaction experiments in the eel. To this end, we first stimulated adult eels with different pathogen-associated molecular patterns (PAMPs), extracted RNA from the immune-related tissues and sequenced the transcriptome. We obtained more than 2x10⁶ reads that were assembled and annotated into 45,067 new descriptions with a notable representation of novel transcripts related with pathogen recognition, signal transduction and the immune response. Then, we designed a DNA-microarray that was used to analyze the early immune response against Vibrio vulnificus, a septicemic pathogen that uses the gills as the portal of entry into the blood, as well as the role of the main toxin of this species (RtxA1₃) on this early interaction. The gill transcriptomic profiles obtained after bath infecting eels with the wild type strain or with a mutant deficient in rtxA1₃ were analyzed and compared. Results demonstrate that eels react rapidly and locally against the pathogen and that this immune-response is rtxA1₃-dependent as transcripts related with cell destruction were highly up-regulated only in the gills from eels infected with the wild-type strain. Furthermore, significant differences in the immune response against the wild type and the mutant strain also suggest that host survival after V. vulnificus infection could depend on an efficient local phagocytic activity. Finally, we also found evidence of the presence of an interbranchial lymphoid tissue in European eel gills although further experiments will be necessary to identify such tissue.

First haploid genetic map based on microsatellite markers in Senegalese sole (Solea senegalensis, Kaup 1858)

The Senegalese sole (Solea senegalensis, Kaup 1858) is a flatfish species of great value for aquaculture. In this study, we develop the first linkage map in this species based on microsatellite markers characterized from genomic DNA libraries and EST databases of Senegalese sole and from other flatfish species. Three reference gynogenetic families were obtained by chromosome-manipulation techniques: two haploid gynogenetics, used to assign and order microsatellites to linkage groups and another diploid gynogenetic family, used for estimating marker-centromere distances. The consensus map consists of 129 microsatellites distributed in 27 linkage groups (LG), with an average density of 4.7 markers per LG and comprising 1,004 centimorgans (cM). Additionally, 15 markers remained unlinked. Through half-tetrad analysis, we were able to estimate the centromere distance for 81 markers belonging to 24 LG, representing an average of 3 markers per LG. Comparative mapping was performed between flatfish species LG and model fish species chromosomes (stickleback, Tetraodon, medaka, fugu and zebrafish). The usefulness of microsatellite markers and the genetic map as tools for comparative mapping and evolution studies is discussed.

Whole genome data for omics-based research on the self-fertilizing fish Kryptolebias marmoratus

Genome resources have advantages for understanding diverse areas such as biological patterns and functioning of organisms. Omics platforms are useful approaches for the study of organs and organisms. These approaches can be powerful screening tools for whole genome, proteome, and metabolome profiling, and can be used to understand molecular changes in response to internal and external stimuli. This methodology has been applied successfully in freshwater model fish such as the zebrafish Danio rerio and the Japanese medaka Oryzias latipes in research areas such as basic physiology, developmental biology, genetics, and environmental biology. However, information is still scarce about model fish that inhabit brackish water or seawater. To develop the self-fertilizing killifish Kryptolebias marmoratus as a potential model species with unique characteristics and research merits, we obtained genomic information about K. marmoratus. We address ways to use these data for genome-based molecular mechanistic studies. We review the current state of genome information on K. marmoratus to initiate omics approaches. We evaluate the potential applications of integrated omics platforms for future studies in environmental science, developmental biology, and biomedical research. We conclude that information about the K. marmoratus genome will provide a better understanding of the molecular functions of genes, proteins, and metabolites that are involved in the biological functions of this species. Omics platforms, particularly combined technologies that make effective use of bioinformatics, will provide powerful tools for hypothesis-driven investigations and discovery-driven discussions on diverse aspects of this species and on fish and vertebrates in general.

Transcriptome of the Atlantic halibut (Hippoglossus hippoglossus)

Although the Atlantic halibut (Hippoglossus hippoglossus) is an important commercial species, there is still a deficit with regard to the number of transcripts in the databases, which can be accessed and exploited for targeted candidate gene and pathway studies. In this study, the RNAs from head, skin and GI tract from different developmental stages were sequenced to generate 22,272 contigs of 500 base pairs or greater as a molecular resource for this species.

Exploring the larval transcriptome of the common sole (Solea solea L.)

BACKGROUND

The common sole (Solea solea) is a promising candidate for European aquaculture; however, the limited knowledge of the physiological mechanisms underlying larval development in this species has hampered the establishment of successful flatfish aquaculture. Although the fact that genomic tools and resources are available for some flatfish species, common sole genomics remains a mostly unexplored field. Here, we report, for the first time, the sequencing and characterisation of the transcriptome of S. solea and its application for the study of molecular mechanisms underlying physiological and morphological changes during larval-to-juvenile transition.

RESULTS

The S. solea transcriptome was generated from whole larvae and adult tissues using the Roche 454 platform. The assembly process produced a set of 22,223 Isotigs with an average size of 726 nt, 29 contigs and a total of 203,692 singletons. Of the assembled sequences, 75.2% were annotated with at least one known transcript/protein; these transcripts were then used to develop a custom oligo-DNA microarray. A total of 14,674 oligonucleotide probes (60 nt), representing 12,836 transcripts, were in situ synthesised onto the array using Agilent non-contact ink-jet technology. The microarray platform was used to investigate the gene expression profiles of sole larvae from hatching to the juvenile form. Genes involved in the ontogenesis of the visual system are up-regulated during the early stages of larval development, while muscle development and anaerobic energy pathways increase in expression over time. The gene expression profiles of key transcripts of the thyroid hormones (TH) cascade and the temporal regulation of the GH/IGF1 (growth hormone/insulin-like growth factor I) system suggest a pivotal role of these pathways in fish growth and initiation of metamorphosis. Pre-metamorphic larvae display a distinctive transcriptomic landscape compared to previous and later stages. Our findings highlighted the up-regulation of gene pathways involved in the development of the gastrointestinal system as well as biological processes related to folic acid and retinol metabolism. Additional evidence led to the formation of the hypothesis that molecular mechanisms of cell motility and ECM adhesion may play a role in tissue rearrangement during common sole metamorphosis.

CONCLUSIONS

Next-generation sequencing provided a good representation of the sole transcriptome, and the combination of different approaches led to the annotation of a high number of transcripts. The construction of a microarray platform for the characterisation of the larval sole transcriptome permitted the definition of the main processes involved in organogenesis and larval growth.

A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus)

Background

Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry.

Results

Expressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immune-related tissues after several parasitic challenges. The resulting database (“Turbot 2 database”) was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences (“Turbot 3 database”), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot (AR, AMH, SRY-related genes, CYP19A, ZPGs, STAR FSHR, etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified (BCL, TRAF, NCK, CD28 and TOLLIP, among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50–90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single nucleotide polymorphisms (SNPs) were also compiled. Further, 2,976 putative natural antisense transcripts (NATs) including microRNAs were also identified.

Conclusions

The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs.

Molecular cloning and characterization of a C-type lectin in roughskin sculpin (Trachidermus fasciatus)

C-type lectins, as the members of pattern-recognition receptors (PRRs), play significant roles in innate immunity responses through binding to the pathogen-associated molecular patterns (PAMPs) presented on surfaces of microorganisms. In our study, a C-type lectin gene (TfCTL1) was cloned from the roughskin sculpin using expression sequence tag (EST) and rapid amplification of cDNA ends (RACE) techniques. The full-length of TfCTL1 was 696 bp, consisting of a 95 bp 5' untranslated region (UTR), a 498 bp open reading frame (ORF) encoding a 165 amino acid protein, and a 103 bp 3' UTR with a polyadenylation signal sequence AATAAA and a poly(A) tail. The deduced amino acid sequence of TfCTL1 contained a signal peptide and a single carbohydrate recognition domain (CRD) which had four conserved disulfide-bonded cysteine residues (Cys(61)-Cys(158), Cys(134)-Cys(150)) and a Ca(2+)/carbohydrate-binding site (QPD motif). Results from the qRT-PCR indicated that TfCTL1 mRNA was predominately expressed in the liver. The temporal expression of TfCTL1 was obviously up-regulated in the skin, blood, spleen and heart in time dependent manners by lipopolysaccharide (LPS) challenge, whereas in the liver, TfCTL1 was initially down-regulated from 2 h to 48 h followed by an abrupt up-regulation at 72 h. Recombinant TfCTL1 CRD purified from Escherichia coli BL21 was able to agglutinate some Gram-positive bacteria, Gram-negative bacteria and a yeast in a Ca(2+)-dependent manner. Further analysis showed that TfCTL1 can bind to several kinds of microorganisms selectively in a Ca(2+)-independent manner. These results suggested that TfCTL1 might be involved in the innate response as a PRR.

Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates

Transferrin is a protein super-family involved in iron transport, a central process in cellular homeostasis. Throughout the evolution of vertebrates, transferrin members have diversified into distinct subfamilies including serotransferrin, ovotransferrin, lactoferrin, melanotransferrin, the inhibitor of carbonic anhydrase, pacifastin, and the major yolk protein in sea urchin. Previous phylogenetic analyses have established the branching order of the diverse transferrin subfamilies but were mostly focused on the transferrin repertoire present in mammals. Here, we conduct a comprehensive phylogenetic analysis of transferrin protein sequences in sequenced vertebrates, placing a special focus on the less-studied nonmammalian vertebrates. Our analyses uncover a novel transferrin clade present across fish, sauropsid, and amphibian genomes but strikingly absent from mammals. Our reconstructed scenario implies that this novel class emerged through a duplication event at the vertebrate ancestor, and that it was subsequently lost in the lineage leading to mammals. We detect footprints of accelerated evolution following the duplication event, which suggest positive selection and early functional divergence of this novel clade. Interestingly, the loss of this novel class of transferrin in mammals coincided with the divergence by duplication of lactoferrin and serotransferrin in this lineage. Altogether, our results provide novel insights on the evolution of iron-binding proteins in the various vertebrate groups.

Microarray-based identification of differentially expressed genes in families of turbot (Scophthalmus maximus) after infection with viral haemorrhagic septicaemia virus (VHSV)

Viral haemorrhagic septicaemia virus (VHSV) is one of the major threats to the development of the aquaculture industry worldwide. The present study was aimed to identify genes differentially expressed in several turbot (Scophthalmus maximus) families showing different mortality rates after VHSV. The expression analysis was conducted through genome-wide expression profiling with an oligo-microarray in the head kidney. A significant proportion of the variation in the gene expression profiles seemed to be explained by the genetic background, indicating that the mechanisms by which particular species and/or populations can resist a pathogen(s) are complex and multifactorial. Before the experimental infections, fish from resistant families (low mortality rates after VHSV infection) showed high expression of different antimicrobial peptides, suggesting that their pre-immune state may be stronger than fish of susceptible families (high mortality rates after VHSV infection). After infection, fish from both high- and low-mortality families showed an up-modulation of the interferon-induced Mx2 gene, the IL-8 gene and the VHSV-induced protein 5 gene compared with control groups. Low levels of several molecules secreted in the mucus were observed in high-mortality families, but different genes involved in viral entrance into target cells were down-regulated in low-mortality families. Moreover, these families also showed a strong down-modulation of marker genes related to VHSV target organs, including biochemical markers of renal dysfunction and myocardial injury. In general, the expression of different genes involved in the metabolism of sugars, lipids and proteins were decreased in both low- and high-mortality families after infection. The present study serves as an initial screen for genes of interest and provides an extensive overview of the genetic basis underlying the differences between families that are resistant or susceptible to VHSV infection.

Transcriptomic characterization of the larval stage in gilthead seabream (Sparus aurata) by 454 pyrosequencing

Gilthead seabream (Sparus aurata) is a teleost belonging to the family Sparidae with a high economical relevance in the Mediterranean countries. Although genomic tools have been developed in this species in order to investigate its physiology at the molecular level and consequently its culture, genomic information on post-embryonic development is still scarce. In this study, we have investigated the transcriptome of a marine teleost during the larval stage (from hatching to 60 days after hatching) by the use of 454 pyrosequencing technology. We obtained a total of 68,289 assembled contigs, representing putative transcripts, belonging to 54,606 different clusters. Comparison against all S. aurata expressed sequenced tags (ESTs) from the NCBI database revealed that up to 34,722 contigs, belonging to about 61% of gene clusters, are sequences previously not described. Contigs were annotated through an iterative Blast pipeline by comparison against databases such as NCBI RefSeq from Danio rerio, SwissProt or NCBI teleost ESTs. Our results indicate that we have enriched the number of annotated sequences for this species by more than 50% compared with previously existing databases for the gilthead seabream. Gene Ontology analysis of these novel sequences revealed that there is a statistically significant number of transcripts with key roles in larval development, differentiation, morphology, and growth. Finally, all information has been made available online through user-friendly interfaces such as GBrowse and a Blast server with a graphical frontend.

Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes

BACKGROUND

Grass carp (Ctenopharyngodon idella) is one of the most economically important freshwater fish, but its production is often affected by diseases that cause serious economic losses. To date, no good breeding varieties have been obtained using the oriented cultivation technique. The ability to identify disease resistance genes in grass carp is important to cultivate disease-resistant varieties of grass carp.

RESULTS

In this study, we constructed a non-normalized cDNA library of head kidney in grass carp, and, after clustering and assembly, we obtained 3,027 high-quality unigenes. Solexa sequencing was used to generate sequence tags from the transcriptomes of the head kidney in grass carp before and after grass carp reovirus (GCRV) infection. After processing, we obtained 22,144 tags that were differentially expressed by more than 2-fold between the uninfected and infected groups. 679 of the differentially expressed tags (3.1%) mapped to 483 of the unigenes (16.0%). The up-regulated and down-regulated unigenes were annotated using gene ontology terms; 16 were annotated as immune-related and 42 were of unknown function having no matches to any of the sequences in the databases that were used in the similarity searches. Semi-quantitative RT-PCR revealed four unknown unigenes that showed significant responses to the viral infection. Based on domain structure predictions, one of these sequences was found to encode a protein that contained two transmembrane domains and, therefore, may be a transmembrane protein. Here, we proposed that this novel unigene may encode a virus receptor or a protein that mediates the immune signalling pathway at the cell surface.

CONCLUSION

This study enriches the molecular basis data of grass carp and further confirms that, based on fish tissue-specific EST databases, transcriptome analysis is an effective route to discover novel functional genes.

Exploitation of a turbot (Scophthalmus maximus L.) immune-related expressed sequence tag (EST) database for microsatellite screening and validation

In this study, we identified and characterized 160 microsatellite loci from an expressed sequence tag (EST) database generated from immune-related organs of turbot (Scophthalmus maximus). A final set of 83 new polymorphic microsatellites were validated after the analysis of 40 individuals of Atlantic origin including both wild and farmed individuals. The allele number and the expected heterozygosity ranged from 2 to 18 and from 0.021 to 0.951, respectively. Evidences of null alleles at moderate-high frequencies were detected at six loci using population data. None of the analysed loci showed deviations from Mendelian segregation after the analysis of five full-sib families including approximately 92 individuals/family. The markers are used to consolidate the turbot genetic map, and because they are mostly EST-derived, they will be very useful for comparative genomic studies within flatfishes and with model fish species. Using an in silico approach, we detected significant homologies of microsatellite sequences with the EST databases of the flatfish species with highest genomic resources (Senegalese sole, Atlantic halibut, bastard halibut) in 31% of these turbot markers. The conservation of these microsatellites within Pleuronectiformes will pave the way for anchoring genetic maps of different species and identifying genomic regions related to productive traits.

Molecular profiling of marine fauna: integration of omics with environmental assessment of the world's oceans

Many species that contribute to the commercial and ecological richness of our marine ecosystems are harbingers of environmental change. The ability of organisms to rapidly detect and respond to changes in the surrounding environment represents the foundation for application of molecular profiling technologies towards marine sentinel species in an attempt to identify signature profiles that may reside within the transcriptome, proteome, or metabolome and that are indicative of a particular environmental exposure event. The current review highlights recent examples of the biological information obtained for marine sentinel teleosts, mammals, and invertebrates. While in its infancy, such basal information can provide a systems biology framework in the detection and evaluation of environmental chemical contaminant effects on marine fauna. Repeated evaluation across different seasons and local marine environs will lead to discrimination between signature profiles representing normal variation within the complex milieu of environmental factors that trigger biological response in a given sentinel species and permit a greater understanding of normal versus anthropogenic-associated modulation of biological pathways, which prove detrimental to marine fauna. It is anticipated that incorporation of contaminant-specific molecular signatures into current risk assessment paradigms will lead to enhanced wildlife management strategies that minimize the impacts of our industrialized society on marine ecosystems.

Construction and characterization of a normalized cDNA library from the river snail Bellamya aeruginosa after exposure to copper

The construction of a normalized cDNA library is a popular tool for identifying novel biomarkers for monitoring environmental pollution. In the present study, a normalized cDNA library was constructed from the river snail Bellamya aeruginosa after exposure to Cu(2+) by using the SMART technique. The titer of the cDNA library was 1.78 × 10(6) pfu/ml, with a recombinant efficiency of 95.8%. In addition, from 6,000 randomly selected and sequenced clones, 5,473 high-quality ESTs were identified. After processing the sequences, 3,961 unigenes representing 897 contigs and 3,064 singlets were obtained with 27.6% redundancy. Analysis of expressed sequenced tags using COG and GO annotation and KEGG pathway data showed that a large group of genes related to growth and development, signal transduction, and defense mechanisms were present in the cDNA library. Based on our findings, this normalized cDNA library will provide a valuable resource for further research on functional genes and ecotoxicology in B. aeruginosa.

Development of EST derived SSRs and SNPs as a genomic resource in Indian catfish, Clarias batrachus

Clarias batrachus, an Indian catfish species, is endemic to the Indian subcontinent and potential cultivable species. The genomic resources in C. batrachus in the form of ESTs containing microsatellite repeats (EST-SSR) and single nucleotide polymorphisms (SNPs) that are associated with the expressed genes from spleen were mined. From a total of 1,937 ESTs generated, 1,698 unique sequences were obtained, out of which 221 EST-SSRs were identified and 54% could be functionally annotated by similarity searches. A total of 23 contigs containing 3 or more ESTs were found to contain 31 SNP loci, out of which 8 ESTs showed similarity to genes of known function and 1 for hypothetical protein. Nine ESTs with SSRs and/or SNPs identified in this study were reported to be associated with diseases in human and animals. These identified loci can be developed into markers in C. batrachus, which can be useful in linkage mapping, comparative genomics studies and for its genetic improvement programmes.

Analysis of the Asian seabass transcriptome based on expressed sequence tags

Analysis of transcriptomes is of great importance in genomic studies. Asian seabass is an important fish species. A number of genomic tools in it were developed, while large expressed sequence tag (EST) data are lacking. We sequenced ESTs from nine normalized cDNA libraries and obtained 11 431 high-quality ESTs. We retrieved 8524 ESTs from dbEST database and analyzed all 19 975 ESTs using bioinformatics tools. After clustering, we obtained 8837 unique sequences (2838 contigs and 5999 singletons). The average contig length was 574 bp. Annotation of these unique sequences revealed that 48.9% of them showed significant homology to RNA sequences in GenBank. Functional classification of the unique ESTs identified a broad range of genes involved in different functions. We identified 6114 putative single-nucleotide polymorphisms and 634 microsatellites in ESTs. We discovered different temporal and spatial expression patterns of some immune-related genes in the Asian seabass after challenging with a pathogen Vibrio harveyi. The unique EST sequences are being used in developing a cDNA microarray to examine global gene expression and will also facilitate future whole-genome sequence assembly and annotation of Asian seabass and comparative genomics.

Transcriptomics for understanding marine fish larval development1This review is part of a virtual symposium on current topics in aquaculture of marine fish and shellfish

The larval phase is a crucial period in the life of marine fish. During this phase, the organism will acquire the phenotype of an adult fish through the development of tissues and organs and the maturation of some of the principal physiological functions. Many biological processes (differentiation, cellular proliferation, growth, etc.) are regulated during this period. These regulations take place at different biological levels and particularly concern the expression of genes involved in larval ontogenesis processes. The development of bioinformatic resources (DNA or cDNA sequences) and molecular tools enabling high throughput gene expression analysis (microarrays) have allowed the transcriptome of marine fish species to be studied. In the present review, we summarize the main findings from transcriptomic investigations of development of marine fish larvae. Special attention is paid to investigations of transcriptomic patterns during postembryonic development and to the impact of environmental or nutritional factors on the transcriptome of marine fish larvae. Transcriptomic approaches will be especially useful in the future for investigating the effect of temperature and water acidification (or pH) on the development of different fish species in the context of global climate change.

Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: new insights into anti-mineralogenic effect of vanadate

BACKGROUND

Fish has been deemed suitable to study the complex mechanisms of vertebrate skeletogenesis and gilthead seabream (Sparus aurata), a marine teleost with acellular bone, has been successfully used in recent years to study the function and regulation of bone and cartilage related genes during development and in adult animals. Tools recently developed for gilthead seabream, e.g. mineralogenic cell lines and a 4 × 44K Agilent oligo-array, were used to identify molecular determinants of in vitro mineralization and genes involved in anti-mineralogenic action of vanadate.

RESULTS

Global analysis of gene expression identified 4,223 and 4,147 genes differentially expressed (fold change - FC > 1.5) during in vitro mineralization of VSa13 (pre-chondrocyte) and VSa16 (pre-osteoblast) cells, respectively. Comparative analysis indicated that nearly 45% of these genes are common to both cell lines and gene ontology (GO) classification is also similar for both cell types. Up-regulated genes (FC > 10) were mainly associated with transport, matrix/membrane, metabolism and signaling, while down-regulated genes were mainly associated with metabolism, calcium binding, transport and signaling. Analysis of gene expression in proliferative and mineralizing cells exposed to vanadate revealed 1,779 and 1,136 differentially expressed genes, respectively. Of these genes, 67 exhibited reverse patterns of expression upon vanadate treatment during proliferation or mineralization.

CONCLUSIONS

Comparative analysis of expression data from fish and data available in the literature for mammalian cell systems (bone-derived cells undergoing differentiation) indicate that the same type of genes, and in some cases the same orthologs, are involved in mechanisms of in vitro mineralization, suggesting their conservation throughout vertebrate evolution and across cell types. Array technology also allowed identification of genes differentially expressed upon exposure of fish cell lines to vanadate and likely involved in its anti-mineralogenic activity. Many were found to be unknown or they were never associated to bone homeostasis previously, thus providing a set of potential candidates whose study will likely bring insights into the complex mechanisms of tissue mineralization and bone formation.

Molecular and comparative analyses of type IV antifreeze proteins (AFPIVs) from two Antarctic fishes, Pleuragramma antarcticum and Notothenia coriiceps

Antifreeze protein type IV (AFPIV) cDNAs and genomic DNAs from the Antarctic fishes Pleuragramma antarcticum (Pa) and Notothenia coriiceps (Nc) were cloned and sequenced, respectively. Each cDNA encoded 128 amino acids, with 94% similarity between the two and 83% similarity with AFPIV of the longhorn sculpin, Myoxocephalus octodecemspinosus. The genome structures of both genes consisted of four exons and three introns, and were highly conserved in terms of sequences and positions. In contrast, the third intron of PaAFPIV had additional nucleotides with inverted repeats at each end, which appeared to be a MITE-like transposable element. Comparative analysis revealed that fish AFPIVs were widely distributed across teleost fishes, well conserved in their intron positions, but more variable in intron sequences and sizes. However, the intron sequences of two Antarctic fishes were highly conserved, indicating recent radiation of notothenioids in the evolutionary lineage. The recombinant PaAFPIV and NcAFPIV were expressed in E. coli, and examined antifreeze activity. PaAFPIV and NcAFPIV gave ice crystals with star-shaped morphology, and thermal hysteresis (TH) values were 0.08°C at the concentration of 0.5mg/ml.

Development of polymorphic microsatellite markers in barfin flounder (Verasper moseri) and spotted halibut (Verasper variegatus) by the cross-species amplification

Barfin flounder (Verasper moseri) and spotted halibut (Verasper variegatus) are two commercially important flatfish species in the Northeast Asia. In the present study, we reported polymorphic microsatellite markers in V. moseri and V. variegatus by the cross-species amplification of microsatellite primers developed previously in two other related marine fish species. A total of 244 polymorphic microsatellite markers were selected for cross-species amplification in V. moseri and V. variegatus, of which 182 markers deriving from Atlantic halibut (Hippoglossus hippoglossus) and 62 markers deriving from Japanese flounder (Paralichthys olivaceus). A sample of 10 individuals were detected. As a result, a total of 67 loci showed polymorphisms in V. moseri, and 62 loci showed polymorphisms in V. variegatus, with the observed number of alleles per locus ranging from two to five in V. moseri, and from two to seven in V. variegatus, respectively. This paper provided more candidate microsatellite markers which could be useful for construction of genetic linkage maps, evaluation of population genetic structure and stock management of V. moseri and V. variegatus.

Genomic resources for flatfish research and their applications

Flatfishes are a group of teleosts of high commercial and environmental interest, whose biology is still poorly understood. The recent rapid development of different 'omic' technologies is, however, enhancing the knowledge of the complex genetic control underlying different physiological processes of flatfishes. This review describes the different functional genomic approaches and resources currently available for flatfish research and summarizes different areas where microarray-based gene expression analysis has been applied. The increase in genome sequencing data has also allowed the construction of genetic linkage maps in different flatfish species; these maps are invaluable for investigating genome organization and identifying genetic traits of commercial interest. Despite the significant progress in this field, the genomic resources currently available for flatfish are still scarce. Further intensive research should be carried out to develop larger genomic sequence databases, high-density microarrays and, more detailed, complete linkage maps, using second-generation sequencing platforms. These tools will be crucial for further expanding the knowledge of flatfish physiology, and it is predicted that they will have important implications for wild fish population management, improved fish welfare and increased productivity in aquaculture.

Design and performance of a turbot (Scophthalmus maximus) oligo-microarray based on ESTs from immune tissues

An expressed sequence tag database from immune tissues was used to design the first high-density turbot (Scophthalmus maximus) oligo-microarray with the aim of identifying candidate genes for tolerance to pathogens. Specific oligonucleotides (60 mers) were successfully designed for 2,716 out of 3,482 unique sequences of the database. An Agilent custom oligo-microarray 8 x 15 k (five replicates/gene; eight microarrays/slide) was constructed. The performance of the microarray and the sources of variation along microarray analysis were examined on spleen pools of controls and Aeromonas salmonicida-challenged fish at 3 days postinfection. Only 48 out of 2,716 probes did not show signal of hybridization on the 32 microarrays employed, thus demonstrating the consistency of the bioinformatic applications of our database. An asymmetric hierarchical design was employed to ascertain the noise associated with biological and technical (RNA extraction, labeling, hybridization, slide, and dye bias) factors using 1C and 2C labeling approaches. The high correlation coefficient between replicates at most factors tested demonstrated the high reproducibility of the signal. An analysis of random-effects variance revealed that technical variation was mostly negligible, and biological variation represented the main factor, even using pooled samples. One-color approach performed at least as well as 2C, suggesting their usefulness due to its higher design flexibility and lower cost. A relevant proportion of genes turn out to be differentially labeled depending on fluorophore, which alerts for the likely need of swapping replication in 2C experiments. A set of differentially expressed genes and enriched functions related to immune/defense response were detected at 3 days postchallenging.

EST resources and establishment and validation of a 16k cDNA microarray from Atlantic cod (Gadus morhua)

The Atlantic cod, Gadus morhua, is an important species both for traditional fishery and increasingly also in fish farming. The Atlantic cod is also under potential threat from various environmental changes such as pollution and climate change, but the biological impact of such changes are not well known, in particular when it comes to sublethal effects that can be difficult to assert. Modern molecular and genomic approaches have revolutionized biological research during the last decade, and offer new avenues to study biological functions and e.g. the impact of anthropogenic activities at different life-stages for a given organism. In order to develop genomic data and genomic tools for Atlantic cod we conducted a program were we constructed 20 cDNA libraries, and produced and analyzed 44006 expressed sequence tags (ESTs) from these. Several tissues are represented in the multiple cDNA libraries, that differ in either sexual maturation or immulogical stimulation. This approach allowed us to identify genes that are expressed in particular tissues, life-stages or in response to specific stimuli, and also gives us information about potential functions of the transcripts. The ESTs were used to construct a 16k cDNA microarray to further investigate the cod transcriptome. Microarray analyses were preformed on pylorus, pituitary gland, spleen and testis of sexually maturing male cod. The four different tissues displayed tissue specific transcriptomes demonstrating that the cDNA array is working as expected and will prove to be a powerful tool in further experiments.

Identification and analysis of immune-related transcriptome in Asian seabass Lates calcarifer

Background

Fish diseases caused by pathogens are limiting their production and trade, affecting the economy generated by aquaculture. Innate immunity system is the first line of host defense in opposing pathogenic organisms or any other foreign material. For identification of immune-related genes in Asian seabass Lates calcarifer, an important marine foodfish species, we injected bacterial lipopolysaccharide (LPS), a commonly used elicitor of innate immune responses to eight individuals at the age of 35 days post-hatch and applied the suppression subtractive hybridization (SSH) technique to selectively amplify spleen cDNA of differentially expressed genes.

Results

Sequencing and bioinformatic analysis of 3351 ESTs from two SSH libraries yielded 1692 unique transcripts. Of which, 618 transcripts were unknown/novel genes and the remaining 1074 were similar to 743 known genes and 105 unannotated mRNA sequences available in public databases. A total of 161 transcripts were classified to the category "response to stimulus" and 115 to "immune system process". We identified 25 significantly up-regulated genes (including 2 unknown transcripts) and 4 down-regulated genes associated with immune-related processes upon challenge with LPS. Quantitative real-time PCR confirmed the differential expression of these genes after LPS challenge.

Conclusions

The present study identified 1692 unique transcripts upon LPS challenge for the first time in Asian seabass by using SSH, sequencing and bioinformatic analysis. Some of the identified transcripts are vertebrate homologues and others are hitherto unreported putative defence proteins. The obtained immune-related genes may allow for a better understanding of immunity in Asian seabass, carrying out detailed functional analysis of these genes and developing strategies for efficient immune protection against infections in Asian seabass.

Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity

Background

The European sea bass (Dicentrarchus labrax) is a marine fish of great importance for fisheries and aquaculture. Functional genomics offers the possibility to discover the molecular mechanisms underlying productive traits in farmed fish, and a step towards the application of marker assisted selection methods in this species. To this end, we report here on the development of an oligo DNA microarray for D. labrax.

Results

A database consisting of 19,048 unique transcripts was constructed, of which 12,008 (63%) could be annotated by similarity and 4,692 received a GO functional annotation. Two non-overlapping 60mer probes were designed for each unique transcript and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Probe design was positively completed for 19,035 target clusters; the oligo microarray was then applied to profile gene expression in mandibles and whole-heads of fish affected by prognathism, a skeletal malformation that strongly affects sea bass production. Statistical analysis identified 242 transcripts that are significantly down-regulated in deformed individuals compared to normal fish, with a significant enrichment in genes related to nervous system development and functioning. A set of genes spanning a wide dynamic range in gene expression level were selected for quantitative RT-PCR validation. Fold change correlation between microarray and qPCR data was always significant.

Conclusions

The microarray platform developed for the European sea bass has a high level of flexibility, reliability, and reproducibility. Despite the well known limitations in achieving a proper functional annotation in non-model species, sufficient information was obtained to identify biological processes that are significantly enriched among differentially expressed genes. New insights were obtained on putative mechanisms involved on mandibular prognathism, suggesting that bone/nervous system development might play a role in this phenomenon.

Maternal gene expression in Atlantic halibut (Hippoglossus hippoglossus L.) and its relation to egg quality

BACKGROUND

The commercial production of Atlantic halibut (Hippoglossus hippoglossus L.) suffers from a major bottleneck due to the low success of producing juveniles for on-growing. Atlantic halibut females are routinely hand-stripped and incorrect timing of stripping can result in low quality eggs due to post-ovulatory aging. Post-ovulatory aging leads to compositional changes in eggs that include maternally provided proteins and RNAs. There have been few studies of the maternally provided mRNA transcripts that control early development in commercially important fish species. The present study aimed to study maternal gene expression in Atlantic halibut and its relation to egg quality parameters including blastomere symmetry and hatching success.

RESULTS

A maternal EST library containing 2341 sequences was constructed by suppressive subtractive hybridisation. Thirty genes were selected for expression studies; 23 novel genes and 7 genes with documented roles in early development. The expressions of twenty-one selected genes were measured by qPCR from fertilization to the 10-somite stage. Three genes were identified as strictly maternal genes that were expressed until the start of gastrulation; askopos (kop), si:dkey-30j22.9 (Tudor family member), and Tudor 5 protein (Tdrd5). The expressions of 18 genes at the 8-cell stage were correlated with egg quality parameters. The majority of genes showed either no or very minor correlations with egg quality parameter. However, two genes correlated positively with hatching success (r> 0.50, HHC00353: r = 0.58, p < 0.01; HHC01517: r = 0.56, p < 0.01) and one gene (HHC00255) was negatively correlated with the percentage of normal blastomeres (r = -0.62, p < 0.05).

CONCLUSIONS

During this study we have related maternal levels of gene expression to hatching success in fish. Poor hatching success was not correlated with a general decrease in transcript abundance but with low transcript levels of some specific genes. Thus, the molecular mechanisms leading to low Atlantic halibut egg quality cannot be entirely explained by post-ovulatory aging.

Evaluation of potential reference genes for real time RT-PCR studies in Atlantic halibut (Hippoglossus Hippoglossus L.); during development, in tissues of healthy and NNV-injected fish, and in anterior kidney leucocytes

Background

Real time RT-PCR has become an important tool for analyzing gene expression in fish. Although several housekeeping genes have been evaluated in Atlantic halibut (Hippoglossus Hippoglossus L.), appropriate reference genes for low copy mRNA transcripts at the earliest developmental stages have not been identified. No attempts have been reported to identify suitable reference genes in halibut infected with NNV or in stimulated halibut leucocytes. In this study, β-actin1 (ACTB1), elongation factor 1 alpha (EF1A1), hypoxanthine-guanine phosphoribosyltransferase 1 (HPRT1), ribosomal protein L7 (RPL7), tubulin beta 2C (Tubb2C), and ubiquitin-conjugating enzyme (UbcE) were evaluated as reference genes for normalization of real time RT-PCR data during Atlantic halibut development, in tissue of healthy and NNV-infected fish, and in in vivo and in vitro stimulated anterior kidney leucocytes.

Results

The expression of all six genes was relatively stable from the unfertilized egg until 12 day degrees post fertilization (ddpf). However, none of the selected genes were found to be stably expressed throughout halibut development. The mRNA levels of the six genes increased from 18 ddpf, when zygotic transcription is likely to be activated, and stabilized at different time points. The Excel-based software programs BestKeeper, geNorm, and NormFinder ranked EF1A1 and UbcE as the best candidate reference genes before activation of zygotic transcription, and RPL7 and EF1A1 as the best candidates after hatching. EF1A1 and RPL7 were also listed as the best reference genes when exploring the expression levels of the six genes in various halibut organs, both in non-injected fish and in mock- and NNV-injected fish. None of the reference genes were found optimal for normalization of real time RT-PCR data from in vitro stimulated anterior kidney leucocytes.

Conclusion

Generally, it was found that EF1A1 and RPL7 were the genes that showed least variation, with HPRT1 and UbcE as intermediate genes, and ACTB1 and Tubb2C as the least stable ones. None of the six reference genes can be recommended as reference gene candidates in ConA-PMA stimulated leucocytes. However, UbcE can be a good candidate in other experimental setups. This study emphasizes the need for reference gene evaluation, as universal reference genes have not been identified.

Generation and analysis of 10 000 ESTs from the half-smooth tongue sole Cynoglossus semilaevis and identification of microsatellite and SNP markers

Three normalized cDNA libraries were constructed, two of which were constructed from reproductive tissues ovary and testis, and the other one from pooled immune tissues including head kidney, intestine, liver and spleen. A total of 10 542 clones were sequenced generating 10 128 expressed sequence tags (ESTs). Cluster analysis indicated a total of 5808 unique sequences including 1712 contigs and 4096 singletons. A total of 4249 (73%) of the unique ESTs had significant hits to the non-redundant protein database, 2253 of which were annotated using Gene Ontology (GO) terms. A total of 311 microsatellites (with 246 having sufficient flanking sequences for primer design) and 6294 putative SNPs were identified. These genome resources provide the material basis for future microarray development, marker validation and genetic linkage and QTL analysis.

EST analysis and identification of gonad-related genes from the normalized cDNA library of large yellow croaker, Larimichthys crocea

On grounds of the especially limited numbers of identified gonad-specific or gonad-related genes of large yellow croaker Larimichthys crocea which may represent a major obstacle for the study of gonad development and sex differentiation, we initiated a sequencing program of Expressed Sequence Tags (ESTs) in large yellow croaker. In this study, we firstly constructed a normalized gonad cDNA library using the combination of SMART technique and DSN treatment. The titer of amplified cDNA library was 4.8x10(11) and the percentage of unique cDNA sequences of the library was 82.49%. 2916 unique cDNAs were clustered from the 3535 high quality ESTs. Among the 1785 ESTs which had significant homology with known genes in the NCBI database, about 64 significant gonad-related genes were found, accounting for 3.59% of the total unique cDNAs. Specifically, the testis-specific LRR gene and testis-specific chromodomain Y-like protein gene were identified from fish for the first time. Six gonad-related microsatellite-containing ESTs were identified from the 129 ESTs containing 149 microsatellites. Expression patterns of 10 of these gonad-related gene homologues in ovaries and testes were examined by qRT-PCR. The results will be powerful resources for our further investigation to establish the molecular mechanisms of gonad development and sex differentiation in large yellow croaker.

Identification of immune related genes in Atlantic halibut (Hippoglossus hippoglossus L.) following in vivo antigenic and in vitro mitogenic stimulation

To identify and characterize genes and proteins of the Atlantic halibut (Hippoglossus hippoglossus) immune system, six cDNA libraries were constructed from liver, kidney, spleen, peripheral blood, and thymus. Halibut were injected with nodavirus, infectious pancreatic necrosis virus (IPNV), or vibriosis vaccine and tissue samples were collected at various time points. Leukocytes from peripheral blood and spleen from stimulated and mock-injected fish were isolated and further in vitro activated with the mitogens, concanavalin A (Con A) and phorbol myristate acetate (PMA) to facilitate activation and proliferation. A total of 5117 high quality expressed sequence tags (ESTs) were identified and assembled into 781 contigs and 2796 singletons. Amongst these ESTs, 147 different putative immune related genes were identified. Several genes involved in innate and adaptive immune responses such as complement proteins, immunoglobulins, cell surface receptors, and cytokines and chemokines were identified. Of the immune related genes identified in this study, 44% had no match against any of the publicly available sequence data for halibut and thus can be considered as novel identification in halibut species. The approach of combining in vivo antigenic with in vitro mitogen stimulation, in addition to preparation of cDNA libraries from thymus enabled identification of many of the interesting genes including those involved in T-cell receptor complex.

Identification of two distinct types of beta-2 microglobulin in marine fish, Pagrus major and Seriola quinqueradiata

Two types of beta-2 microglobulin (beta2m) were identified in red seabream and yellowtail from expressed sequence tag (EST) analyses of kidney and spleen cells. A cluster of 21 ESTs from red seabream showed high homology to beta2m from other teleosts, while another cluster containing 7 ESTs was also homologous to beta2m. Similarly, two clusters containing 21 and 2 ESTs were identified to be homologous to beta2m in yellowtail. The genes in the large and small clusters of each fish were designated beta2m-1 and beta2m-2, respectively. Although the amino acid sequences of beta2m-1s were highly homologous to those identified in the other teleosts, those of beta2m-2s were less homologous to fish beta2m. beta2m-1 of red seabream lacks the first intron of two introns observed in vertebrates, and beta2m-2 lacks both introns. Phylogenetic analysis of vertebrate beta2m proteins suggested that the beta2m-2 in marine fish are distinct from beta2ms in the other teleosts.

Expressed sequence tags from the zhikong scallop (Chlamys farreri): discovery and annotation of host-defense genes

A high-quality cDNA library was constructed from whole body tissues of the zhikong scallop, Chlamys farreri, challenged by Listonella anguillarum. A total of 5720 clones were sequenced, yielding 5123 expressed sequence tags (ESTs). Among the 3326 unique genes identified, 2289 (69%) genes had no significant (E-value < 1e-5) matches to known sequences in public databases and 194 (6%) matched proteins of unknown functions. The remaining 843 (25%) genes that exhibited homology with genes of known functions, showed broad involvement in metabolic processes (31%), cell structure and motility (20%), gene and protein expression (12%), cell signaling and cell communication (8%), cell division (4%), and notably, 25% of those genes were related to immune function. They included stress response genes, complement-like genes, proteinase and proteinase inhibitors, immune recognition receptors and immune effectors. The EST collection obtained in this study provides a useful resource for gene discovery and especially for the identification of host-defense genes and systems in scallops and other molluscs.

Functional annotation and analysis of expressed sequence tags from the hepatopancreas of mitten crab (Eriocheir sinensis)

Due to its popularity as a traditional food, intensive harvesting of the mitten crab (Eriocheir sinensis) is common and has lead to an increase in disease incidence, resulting in catastrophic losses to crab aquaculture. The hepatopancreas of E. sinensis is not only an important digestive organ but also an indispensable immune organ. We constructed a nonnormalized cDNA library from the hepatopancreas of E. sinensis and acquired 3,297 high-quality expressed sequence tags representing 1,178 unigenes. More than half of these unigenes were novel genes for this species; the remaining had homologs in public databases, which is of great importance for future functional research. We also investigated the association of these genes with immune processes for insight into one of the main functions of the hepatopancreas besides metabolism. Despite the relatively low sampling scalar of our cDNA library, we were able to demonstrate several important properties of the hepatopancreatic transcriptome and identified numerous genes that were closely associated with immune responses. These results might serve as the basis for an in-depth genomics study of E. sinensis, including transcriptome analysis, physical mapping, and whole genome sequencing.

Profiling of infection specific mRNA transcripts of the European seabass Dicentrarchus labrax

Background

The European seabass (Dicentrarchus labrax), one of the most extensively cultured species in European aquaculture productions, is, along with the gilthead sea bream (Sparus aurata), a prospective model species for the Perciformes which includes several other commercially important species. Massive mortalities may be caused by bacterial or viral infections in intensive aquaculture production. Revealing transcripts involved in immune response and studying their relative expression enhances the understanding of the immune response mechanism and consequently also the creation of vaccines. The analysis of expressed sequence tags (EST) is an efficient and easy approach for gene discovery, comparative genomics and for examining gene expression in specific tissues in a qualitative and quantitative way.

Results

Here we describe the construction, analysis and comparison of a total of ten cDNA libraries, six from different tissues infected with V. anguillarum (liver, spleen, head kidney, gill, peritoneal exudates and intestine) and four cDNA libraries from different tissues infected with Nodavirus (liver, spleen, head kidney and brain). In total 9605 sequences representing 3075 (32%) unique sequences (set of sequences obtained after clustering) were obtained and analysed. Among the sequences several immune-related proteins were identified for the first time in the order of Perciformes as well as in Teleostei.

Conclusion

The present study provides new information to the Gene Index of seabass. It gives a unigene set that will make a significant contribution to functional genomic studies and to studies of differential gene expression in relation to the immune system. In addition some of the potentially interesting genes identified by in silico analysis and confirmed by real-time PCR are putative biomarkers for bacterial and viral infections in fish.

Allatostatin C and its paralog allatostatin double C: the arthropod somatostatins

Arthropods do not have one, but two genes encoding an allatostatin C-like peptide. The newly discovered paralog gene was called Ast-CC, and the peptide which it is predicted to make was called allatostatin double C (ASTCC). Genes for both allatostatin C (ASTC) and its paralog were found in the tick Ixodes scapularis as well as dipteran, lepidopteran, coleopteran, aphidoidean and phthirapteran insect species. In addition partial or complete cDNAs derived from Ast-CCs were found in a number of species, including Drosophila melanogaster, Bombyx mori and Rhodnius prolixus. The ASTCC precursors have a second conserved peptide sequence suggesting that they may produce two biologically active peptides. The predicted precursors encoded by the Ast-CCs have some unusual features, particularly in Drosophila, where they lack a signal peptide, and have instead a peptide anchor. These unusual structural features suggest that they are perhaps expressed by cells that are not specialized in neuropeptide synthesis and that in Drosophila ASTCC may be a juxtacrine. Data from the Fly Atlas project show that in Drosophila Ast-CC is little expressed. Nevertheless a P-element insertion in this gene is embryonic lethal, suggesting that it is an essential gene. Similarity between the precursors and receptors of ASTC/ASTCC and somatostatin suggests that ASTC/ASTCC and somatostatin have a common ancestor.