The Genome of Salmonid Herpesvirus 1

Salmonid herpesvirus 1 (SalHV-1) is a pathogen of the rainbow trout (Oncorhynchus mykiss). Restriction endonuclease mapping, cosmid cloning, DNA hybridization, and targeted DNA sequencing experiments showed that the genome is 174.4 kbp in size, consisting of a long unique region (U_L; 133.4 kbp) linked to a short unique region (U_S; 25.6 kbp) which is flanked by an inverted repeat (R_S; 7.7 kbp). U_S is present in virion DNA in either orientation, but U_L is present in a single orientation. This structure is characteristic of the Varicellovirus genus of the subfamily Alphaherpesvirinae but has evidently evolved independently, since an analysis of randomly sampled DNA sequence data showed that SalHV-1 shares at least 18 genes with channel catfish virus (CCV), a fish herpesvirus whose complete sequence is known and which is unrelated to mammalian herpesviruses. The use of oligonucleotide probes demonstrated that in comparison with CCV, the conserved SalHV-1 genes are located in U_L in at least five rearranged blocks. Large-scale gene rearrangements of this type are also characteristic of the three mammalian herpesvirus subfamilies. The junction between two SalHV-1 gene blocks was confirmed by sequencing a 4,245-bp region which contains the dUTPase gene, part of a putative spliced DNA polymerase gene, and one other complete gene. The implications of these findings in herpesvirus taxonomy are discussed.Herpesviruses are a large group of complex, double-stranded DNA viruses which infect vertebrates from teleost (bony) fish to humans. They exhibit narrow host specificites, most infecting only a single species in nature, and are thus considered likely to have evolved with their hosts. Comparisons of primary amino acid sequences predicted from complete genome sequences have shown that mammalian herpesviruses are genetically very divergent but nonetheless share a set of about 40 homologous genes, thus providing compelling evidence that these viruses evolved from a single ancestral herpesvirus (reviewed in reference 7). Moreover, genetic comparisons support the division of the family into three subfamilies, Alphaherpesvirinae, Betaherpesvirinae, and Gammaherpesvirinae, as proposed previously from biological criteria (15). The order of genes is largely conserved within each subfamily, whereas members of different subfamilies are more distantly related and exhibit several large-scale genomic rearrangements (4, 9). Viral phylogenies derived from rigorous sequence comparisons generally fit well with host phylogenies deduced from the fossil record, thus supporting the view that mammalian herpesviruses have cospeciated with their hosts, and this has allowed a time frame to be assigned (13, 14). Moreover, limited sequence data also indicate that avian herpesviruses fit readily into the subfamily Alphaherpesvirinae.Nearly all research on herpesviruses has involved mammalian (and, to a lesser extent, avian) herpesviruses, and little is known about the many herpesviruses which infect cold-blooded vertebrates. The most extensively studied member of the latter group, channel catfish virus (CCV; ictalurid herpesvirus 1), was initially classified as a herpesvirus on the basis of its virion morphology and as a member of the Alphaherpesvirinae on the basis of its biological properties (15). Analysis of the complete genome sequence (6) indicated, however, that CCV has no specific relationship with mammalian herpesviruses at the level of primary amino acid sequence, in that no counterpart of a protein which is encoded only by mammalian herpesviruses, such as a structural protein, was detected in CCV. Thus CCV cannot be accommodated by the current taxonomy. The virus does encode several enzymes which are also specified by mammalian herpesviruses, such as DNA polymerase, dUTPase, and thymidine kinase. The genes encoding these proteins, however, are ubiquitous and could quite possibly have been acquired independently by the mammalian and fish herpesvirus lineages. Moreover, the CCV enzymes are no more closely related to their counterparts in other herpesviruses than to those in other organisms.These findings may be interpreted in two ways. First, CCV and mammalian herpesviruses arose independently and have convergently acquired similar virion morphologies. Second, they evolved from an ancestral herpesvirus but have diverged so extensively over the 400 million years since their hosts separated that little sequence evidence remains. Several lines of evidence support the latter view, but it is fair to say that the case is not yet overwhelming. The best genetic indication for divergence rests in a single highly conserved protein which is encoded by two exons in the mammalian herpesviruses and three in CCV (open reading frames [ORFs] 62, 69, and 71). This protein apparently has a distant relative in bacteriophage T4 which functions as a subunit of the terminase involved in DNA packaging, but the fact that no cellular counterpart has yet been discovered highlights it as the best candidate for a gene which may have been inherited from a common ancestor rather than acquired via independent capture events. Moreover, despite the lack of conservation of the amino acid sequences of structural proteins, structural and functional congruences have been detected. Thus, the detailed three-dimensional structure of the CCV capsid is strikingly similar to that of herpes simplex virus type 1 (3). Also, local sequence features of the putative scaffold protein involved in CCV capsid formation suggest that it may be autoproteolytically processed via a pathway that is otherwise found only in mammalian herpesviruses (8).Evidence for a herpesvirus lineage that lies outside the current taxonomic scheme has prompted investigations of its extent. Comparisons of CCV with salmonid herpesviruses appear useful in this respect, since the fossil record indicates that the three main subgroups of euteleosts (salmoniforms, neoteleosts, and ostariophysans, the latter including catfish) diverged around 130 million years ago (1). Salmonid fish are host to several herpesviruses, the principal of which are salmonid herpesviruses 1 and 2 (SalHV-1 and SalHV-2) (reviewed in reference 19). SalHV-1 was isolated on several occasions from a rainbow trout (Oncorhynchus mykiss) hatchery in the state of Washington in association with excessive mortality in young fish (20). The virus causes disease when injected into young rainbow trout maintained at 6 to 9°C but not in other salmonid species. SalHV-2 was isolated from Oncorhynchus masou, a landlocked Japanese form of Pacific salmon (11). It is serologically distinct from and has a wider host range than SalHV-1, causing virulent disease in the young of several Oncorhynchus species, including the rainbow trout. It also exhibits a higher temperature optimum for growth in cell culture than SalHV-1.Partial sequence data for two genes have previously indicated that SalHV-2 is related to CCV (2). In this report, I describe the genome structure and gene arrangement of SalHV-1 and show that this virus is evolutionarily related to SalHV-2 and CCV. The data indicate that the processes which have resulted in the generation of certain genome structures and large-scale gene rearrangements during mammalian herpesvirus evolution have parallels in fish herpesvirus evolution. They also imply that fish herpesviruses occupy a distinct evolutionary space of an size equivalent to that occupied by mammalian herpesviruses and urge an accommodation in the herpesvirus taxonomy.     

Systemic herpes-like virus in catfish Ictalurus melas (Italy) differs from Ictalurid herpesvirus 1 (North America)

A herpesvirus was isolated during 2 occurrences of mass mortality among adult catfish Ictalurus melas raised in different farms in northern Italy. The agent replicated in the channel catfish ovary (CCO) cell line from channel catfish I. punctatus, inducing a cytopathic effect similar to that caused by Ictalurid herpesvirus 1 (also referred to as channel catfish herpesvirus, CCV). The new herpesvirus, designated I. melas herpesvirus (IcmHV) did not react with polyclonal rabbit or monoclonal antibodies directed to CCV in either neutralization or indirect immunofluorescence assays. The virions of IcmHV possessed a hexagonal nucleocapsid of 107 nm in diameter surrounded by an envelope with a diameter of 227 nm (n = 20) typical for members of the family Herpesviridae. Virions of IcmHV purified from infected CCO cells contained 17 polypeptides ranging in size from 17.5 to 175 kDa and most differed in molecular weight from those found for CCV. The IcmHV was also distinct from CCV when compared by restriction fragment length polymorphisms (RFLP) of genomic DNA following digestions with the endonucleases Kpn I and Sac I. Lastly, the virulence of IcmHV for channel catfish fry and juveniles, respectively, was demonstrated by experimental infections induced by bath exposure or intraperitoneal injection that resulted in 78 to 96% cumulative mortality in groups of exposed fish. Preventing the introduction of this agent into geographic regions where significant channel catfish production occurs should be a high priority.     

An overlapping bacterial artificial chromosome system that generates vectorless progeny for channel catfish herpesvirus

Herpesviruses are important pathogens of humans and other animals. Herpesvirus infectious clones that can reconstitute phenotypically wild-type (wt) virus are extremely valuable tools for elucidating the roles of specific genes in virus pathophysiology as well as for making vaccines. Ictalurid herpesvirus 1 (channel catfish herpesvirus [CCV]) is economically very important and is the best characterized of the herpesviruses that occur primarily in bony fish and amphibians. Here, we describe the cloning of the hitherto recalcitrant CCV genome as three overlapping subgenomic bacterial artificial chromosomes (BACs). These clones allowed us to regenerate vectorless wt CCVs with a phenotype that is indistinguishable from that of the wt CCV from which the BACs were derived. To test the recombinogenic systems, we next used the overlapping BACs to construct a full-length CCV BAC by replacing the CCV ORF5 with the BAC cassette and cotransfecting CCO cells. The viral progeny that we used to transform Escherichia coli and the resulting BAC had only one of the 18-kb terminal repeated regions. Both systems suggest that one of the terminal repeat regions is lost during the replicative stage of the CCV life cycle. We also demonstrated the feasibility of introducing a targeted mutation into the CCV BAC infectious clone by constructing a CCV ORF12 deletion mutant and showed that ORF12 encodes a nonessential protein for virus replication. This is the first report of the generation of an infectious BAC clone of a member of the fish and amphibian herpesviruses and its use to generate recombinants.     

Identification of envelope protein orf10 of channel catfish herpesvirus

Channel catfish virus (CCV) is a viral pathogen of fry and fingerling channel catfish and can cause significant commercial loss. Previous studies have shown that the CCV virion contains at least 25 predicted structural proteins, including viral protein 10, which is encoded by the orf10 gene of the CCV. In this paper, the orf10 gene was expressed in Escherichia coli and used to produce a specific antibody. Western blot analysis confirmed that open reading frame 10 is an envelope protein. A viral neutralization assay demonstrated that open reading frame 10 antiserum was able to inhibit CCV infection of channel catfish ovary cells, suggesting that viral protein 10 is likely to play an important role in the CCV infection of channel catfish ovary cells.     

Cloning and characterization of myogenic regulatory genes in three Ictalurid species

We report sequence, tissue expression and map-position data for myogenin, MYOD1, myostatin and follistatin in three Ictalurid catfish species: channel catfish (Ictalurus punctatus), blue catfish (I. furcatus) and white catfish (Ameiurus catus). These genes are involved in muscle growth and development in mammals and may play similar roles in catfish. Amino acid sequences were highly conserved among the three Ictalurid species (>95% identity), moderately conserved among catfish and zebrafish (approximately 80% identity), and less conserved among catfish and humans (approximately 40-60% identity) for all four genes. Gene structure (number of exons and introns and exon-intron boundaries) was conserved between catfish and other species for all genes. Myogenin and MYOD1 expression was limited to skeletal muscle in juvenile channel catfish, similar to expression patterns for these genes in other fish and mammalian species. Myostatin was expressed in a variety of tissues in juvenile channel catfish, a pattern common in other fish species but contrasting with data from mammals where myostatin is primarily expressed in skeletal muscle. Follistatin was expressed in juvenile catfish heart, testes and spleen. All four genes contained polymorphic microsatellite repeats in non-coding regions and linkage analysis based on inheritance of these microsatellite loci was used to place the genes on the channel catfish linkage map. Information provided in this study will be useful in further studies to determine the role these genes play in muscle growth and development in catfish.     

The interferon system of teleost fish

Interferons (IFNs) are secreted proteins, which induce vertebrate cells into an antiviral state. In mammals, three families of IFNs (type I IFN, type II IFN and IFN-lambda) can be distinguished on the basis of gene structure, protein structure and functional properties. Type I IFNs, which include IFN-alpha and IFN-beta, are encoded by intron lacking genes and have a major role in the first line of defense against viruses. The human IFN-lambdas have similar biological properties as type I IFNs, but are encoded by intron containing genes. Type II IFN is identical to IFN-gamma, which is produced by T helper 1 cells in response to mitogens and antigens and has a key role in adaptive cell mediated immunity. IFNs, which show structural and functional properties similar to mammalian type I IFNs, have recently been cloned from Atlantic salmon, channel catfish, pufferfish, and zebrafish. Teleost fish appear to have at least two type I IFN genes. Phylogenetic sequence analysis shows that the fish type I IFNs form a group separated from the avian type I IFNs and the mammalian IFN-alpha, -beta and -lambda groups. Interestingly, the fish IFNs possess the same exon/intron structure as the IFN-lambdas, but show most sequence similarity to IFN-alpha. Recently, IFN-gamma genes have also been cloned from several fish species and shown to have the same exon/intron structure as mammalian IFN-gamma genes. The antiviral effect of mammalian type I IFN is exerted through binding to the IFN-alpha/beta-receptor, which triggers signal transduction through the JAK-STAT signal transduction pathway resulting in expression of Mx and other antiviral proteins. Putative IFN receptor genes have been identified in pufferfish. Several interferon regulatory factors and members of the JAK-STAT pathway have also been identified in various fish species. Moreover, Mx and several other interferon stimulated genes have been cloned and studied in fish. Furthermore, antiviral activity of Mx protein from Atlantic salmon and Japanese flounder has recently been demonstrated.     

Antibody response of channel catfish after channel catfish virus infection and following dexamethasone treatment

Channel catfish virus (CCV, Ictalurid herpesvirus 1) and CCV disease have been extensively studied. Yet, little is known about CCV-host interaction after resolution of the primary infection. In order to determine potential recrudescence of CCV from latency, we established latency by exposing channel catfish juveniles with CCV or a thymidine kinase-negative recombinant (CCVlacZ) at a dose that caused less than 20% mortality. Then, we evaluated antibody response by serially sampling the same fish at 0 (pre-infection), 30, 60 and 90 d post challenge (DPC). We then attempted to induce viral recrudescence by intramuscular administration of dexamethasone and sampled the fish at 2, 4, 7, or 10 d post treatment. Recrudescence was evaluated by leukocyte co-cultivation and cell culture of tissue homogenates but no virus was detected. Western blot data demonstrated the highest number of seropositive fish by 30 DPC and a secondary antibody induction after dexamethasone treatment. The antigen specificity of the secondary response corresponded to viral proteins with molecular masses similar to those recognized by the same fish by 30 DPC. The recognized proteins were predominantly large, ranging from approximately 90 to >200 kDa. Expression analysis of selected virus genes at 90 DPC and following dexamethasone treatment demonstrated occasional immediate-early virus gene expression in peripheral blood leukocytes. Early and late gene expression was rarely detected. The combined data suggest restricted re-activation of CCV in our experimental system. Primary and secondary responses and virus gene expression were demonstrated in CCVlacZ-exposed fish but were less frequent than in CCV-exposed fish.     

Cloning and characterisation of a channel catfish (Ictalurus punctatus) Mx gene

A 2.5 kb full-length cDNA clone of a channel catfish (Ictalurus punctatus) Mx gene was obtained using RACE (rapid amplification of cDNA ends) polymerase chain reaction (PCR) from RNA extracted from the liver of poly I:C stimulated channel catfish. The gene consists of an open reading frame of 1905 nucleotides encoding a 635 amino acid protein. The predicted protein is 72.5 kDa and contains the dynamin family signature, a tripartite GTP binding motif and a leucine zipper, characteristic of all known Mx proteins. The catfish Mx protein exhibited 79% identity with perch Mx and between 71% and 74% identity with the three Atlantic salmon and the three rainbow trout Mx proteins. Mx mRNA was constitutively expressed in channel catfish ovary (CCO) cells, but in higher quantities in response to poly I:C treatment. Mx was induced in channel catfish following injection with channel catfish virus (CCV) and poly I:C.     

斑点叉尾鮰病毒实时荧光LAMP检测方法的建立

斑点叉尾鮰病毒(Channel catfish virus, CCV)属于大DNA病毒, 是一种能引起斑点叉尾鮰(Letalurus punetaus)病毒性疾病的重要病原。研究以编码产物为磷酸激酶的CCV ORF77基因为靶标, 设计了能识别靶基因上的8个独立区域的6条特异引物, 利用基于环介导等温扩增技术(Loop-mediated isothermal amplification, LAMP)建立了用于CCV的实时荧光LAMP快速检测方法。结果显示, 建立的实时荧光LAMP检测方法在63℃恒温反应45min条件下, 反应大约12min后出现明显的峰值, 最低检测限度为100个拷贝的病毒质粒DNA, 检出时间为35min; 并且具有良好的特异性, 与白斑综合症病毒(WSSV)、传染性皮下及造血组织坏死病毒(IHHNV)、锦鲤疱疹病毒(KHV)、真鲷虹彩病毒(RSIV)、传染性脾肾坏死病毒(ISKNV)和新加坡石斑鱼虹彩病毒(SGIV)等常见水生动物病原DNA均没有交叉反应; 同一样品于试验内及试验间重复性试验发现, 20个平行样品的扩增曲线基本重合, 表现出良好的重复性。通过对实际样品的检测结果显示, 实时荧光LAMP检测方法能够特异性的检出CCV。因此, 研究建立的CCV实时荧光LAMP检测方法操作简单、检测快速、特异性好、灵敏度高、结果可靠, 能为斑点叉尾鮰养殖现场和实验室的斑点叉尾鮰疱疹病毒病病原的快速诊断和实时监测方面提供技术支撑。     

Toll-like receptor 3 and TICAM genes in catfish: species-specific expression profiles following infection with Edwardsiella ictaluri

Toll-like receptors (TLRs) are a family of transmembrane proteins that recognize specific pathogen-associated molecular patterns and use conserved signaling pathways to activate proinflammatory cytokines and type-1 interferons to fight infection. TLR3 in mammals is best known for its recognition of dsRNA as ligand and its MyD88-independent signaling. TLR3, upon recognition of dsRNA, recruits and binds its adaptor protein TIR domain-containing adapter molecule (TICAM) 1. Here we report the genomic sequences and structures of TLR3 and a TICAM adaptor from channel catfish (Ictalurus punctatus). Whereas a partial TLR3 cDNA sequence has been reported from channel catfish, and complete TLR3 genes are known from other teleost fish species, a complete TICAM sequence has not been previously reported from a nonmammalian species. Analysis of catfish TLR3 and TICAM expression after infection with Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish (ESC), suggested a conserved TLR3-TICAM receptor–adaptor relation in catfish. Comparison of TLR3 and TICAM expression profiles in channel catfish with those from the closely related blue catfish species (Ictalurus furcatus), which exhibits strong resistance to ESC, revealed a striking pattern of species-specific expression. A dramatic downregulation of TLR3 and TICAM gene expression was observed in blue catfish head kidney and spleen, which we speculate may be the result of maturation and migration of different cell types to and from the lymphoid tissues following infection.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Puttharat Baoprasertkul and Eric Peatman contributed equally to this work.     

Structural characterisation and expression analysis of toll-like receptor 2 gene from catfish

Toll-like receptors (TLRs) are important components of innate immunity. They were found to recognise specific structures on pathogens termed pathogen-associated molecular patterns (PAMPs) and utilise conserved signaling pathways to activate pro-inflammatory cytokines and type-1 interferons. In spite of much understanding gained from the mammalian systems, many fish TLRs are unknown. Recent studies in Japanese flounder as well as in zebrafish suggested that the ligand binding and activation of inflammatory responses in fish may be different from and more complex than those found in mammals. In channel catfish, the major aquaculture species in the United States, only partial sequences of TLR3 and TLR5 were reported. As a part of efforts to characterise the innate immune components in channel catfish, here we cloned and sequenced both the cDNA and the gene for TLR2, a receptor believed mostly responsible for recognition of lipopeptides on the surface of most Gram-positive bacteria. However, expression analysis after infection with a Gram-negative bacterium, Edwardsiella ictaluri indicated that TLR2 was modestly down-regulated in the head kidney tissue of blue catfish, and with a similar pattern in the head kidney of channel catfish though the down-regulation in channel catfish was not statistically significant. In the spleen, an insignificant down-regulation was initially observed early after infection, with an increase of TLR expression later after infection. These results suggest the involvement of TLR2 in the responses after the bacterial infection. As LPS is believed to be the major PAMP for Gram-negative bacteria, additional research is warranted to determine the functions and mechanisms of TLR2 in infections of Gram-negative bacteria.     

Susceptibility of channel catfish fry to Channel Catfish Virus (CCV) challenge increases with age

Susceptibility of channel catfish to Channel Catfish Virus Disease (CCVD) has been generally considered to be inversely related to age. However, in experimental immersion challenges, we found that channel catfish fry, 3 to 8 d post hatch (dph), are most resistant to CCV and susceptibility increases with age. Initial studies involved 2 spawns that had high CCV carrier percentage. To determine if the resistance seen in the fry was related to the CCV carrier status of the parents, we selected 4 spawns from CCV negative parents and 2 spawns from CCV positive parents and immersion challenged them at 8, 23, 36 and 60 dph with 0, 2.5 x 10(4) or 2.5 x 10(6) plaque forming units (PFU) of CCV l(-1). Survivors of the low-dose exposed groups were rechallenged at 120 dph with 2.5 x 10(6) PFU CCV l(-1). Each brood demonstrated increasing susceptibility to CCVD with age and only the fish that were initially exposed at 60 dph developed protective immunity. Time course assays evaluating tissue levels of virus in channel catfish exposed to CCV at 7, 21 and 42 dph suggested that the resistance was an early event in the infection process. The resistance in fry was most pronounced in fish from CCV positive spawns and was correlated to neutralizing antibody titers in the maternal parent in the 8 dph challenge. However, other factors may be involved because all groups displayed the initial resistance and subsequent susceptibility to CCVD. The age effect may be an important influence on the progression of CCVD outbreaks and indicates the need to consider age for experimental challenges. Additionally, we documented the level of vertical transmission of CCV. Fry from the 4 positive spawns had a CCV prevalence of 40 to 75 %.     

Translational machinery of channel catfish: II. Complementary DNA and expression of the complete set of 47 60S ribosomal proteins

Ribosomal protein genes have become widely used as markers for phylogenetic studies and comparative genomics, but they have not been available in fish. We have cloned and sequenced a complete set of all 47 60S ribosomal protein cDNAs from channel catfish (Ictalurus punctatus), of which 43 included the complete protein encoding regions. Most ribosomal protein mRNAs in channel catfish are highly similar to their mammalian counterparts. However, L4, L14, and L29 are significantly shorter in channel catfish than in mammals due to deletions in the 3' end of the gene. Two distantly related L5 cDNAs, L5a and L5b, were found in channel catfish. L5a is more similar to L5 in other vertebrates, while L5b showed significant levels of divergence, suggesting independent evolution of the two L5-encoding genes. The 47 ribosomal protein genes are generally highly expressed and together account for 11-14% of overall gene expression, depending on the tissues. Expression levels were highly variable both within a single tissue among different ribosomal protein genes, and among tissues with regard to a single ribosomal protein gene. Strong tissue preference expression was also observed for some ribosomal proteins. This set of ribosomal protein gene sequences represents one of the most complete sets from any single organism and will aid in fish phylogenetic and comparative genomic studies.     

Isolation and Enrichment of Abundant Microsatellites from a Channel Catfish (Ictalurus punctatus) Brain cDNA Library

Efforts to construct a genetic linkage map of channel catfish have involved identification of random genomic microsatellite markers, as well as anchored Type I loci (expressed genes) from channel catfish. To identify Type I markers we constructed a directional cDNA library from brain tissue to obtain expressed catfish sequences that could be used for single nucleotide polymorphism (SNP) marker development. These cDNA sequences surprisingly contained a high proportion of microsatellites (about 14%) in noncoding regions of expressed sequence tags (ESTs), many of which were not associated with known sequences. To further identify cDNAs with microsatellites and reduce the number of sequencing reactions needed for marker development, we enriched this library for repeat sequences and sequenced clones from both directions. A total of 1644 clones from seven repeat-enriched captures (CA, GT, CT, GA, MTT, TAG, and TAC) were sequenced from both ends, and 795 nonredundant clones were assembled. Thirty-seven percent of the clones contained microsatellites in the trimmed sequence. After assembly in the TIGR Catfish Gene Index (CfGI), 154 contigs matched known vertebrate genes and 92 contigs contained microsatellites. When BLAST-matched orthologues were available for similarity alignments, 28% of these contigs contained repeats in the 5'-UTR, 72% contained repeats in the 3'-UTR, and 8% contained repeats at both ends. Using biotinylated repeat oligonucleotides coupled with streptavidin-coated magnetic beads, and rapid, single-pass hybridization, we were able to enrich our plasmid library greater than two-fold for repeat sequences and increase the ability to link these ESTs with known sequences greater than six-fold.     

Isolation and enrichment of abundant microsatellites from a channel catfish (Ictalurus punctatus) brain cDNA library

Efforts to construct a genetic linkage map of channel catfish have involved identification of random genomic microsatellite markers, as well as anchored Type I loci (expressed genes) from channel catfish. To identify Type I markers we constructed a directional cDNA library from brain tissue to obtain expressed catfish sequences that could be used for single nucleotide polymorphism (SNP) marker development. These cDNA sequences surprisingly contained a high proportion of microsatellites (about 14%) in noncoding regions of expressed sequence tags (ESTs), many of which were not associated with known sequences. To further identify cDNAs with microsatellites and reduce the number of sequencing reactions needed for marker development, we enriched this library for repeat sequences and sequenced clones from both directions. A total of 1644 clones from seven repeat-enriched captures (CA, GT, CT, GA, MTT, TAG, and TAC) were sequenced from both ends, and 795 nonredundant clones were assembled. Thirty-seven percent of the clones contained microsatellites in the trimmed sequence. After assembly in the TIGR Catfish Gene Index (CfGI), 154 contigs matched known vertebrate genes and 92 contigs contained microsatellites. When BLAST-matched orthologues were available for similarity alignments, 28% of these contigs contained repeats in the 5'-UTR, 72% contained repeats in the 3'-UTR, and 8% contained repeats at both ends. Using biotinylated repeat oligonucleotides coupled with streptavidin-coated magnetic beads, and rapid; single-pass hybridization, we were able to enrich our plasmid library greater than two-fold for repeat sequences and increase the ability to link these ESTs with known sequences greater than six-fold.     

Herpesviruses and the Type III Interferon System

Type III interferons (IFNs) represent the most recently discovered group of IFNs. Together with type I IFNs (e.g. IFN-α/β), type III IFNs (IFN-λ) are produced as part of the innate immune response to virus infection, and elicit an anti-viral state by inducing expression of interferon stimulated genes (ISGs). It was initially thought that type I IFNs and type III IFNs perform largely redundant functions. However, it has become evident that type III IFNs particularly play a major role in antiviral protection of mucosal epithelial barriers, thereby serving an important role in the first-line defense against virus infection and invasion at contact areas with the outside world, versus the generally more broad, potent and systemic antiviral effects of type I IFNs. Herpesviruseses are large DNA viruses, which enter their host via mucosal surfaces and establish lifelong, latent infections. Despite the importance of mucosal epithelial cells in the pathogenesis of herpesviruses, our current knowledge on the interaction of herpesviruses with type III IFN is limited and largely restricted to studies on the alphaherpesvirus herpes simplex virus (HSV). This review summarizes the current understanding about the role of IFN-λ in the immune response against herpesvirus infections.