Evolution of CC chemokines in teleost fish: a case study in gene duplication and implications for immune diversity

Microfibrillar-associated protein 4 (MFAP4) genes in catfish play a novel role in innate immune responses

The lectin pathway of the complement system is characterized by two groups of soluble pattern recognition molecules, mannose-binding lectins (MBLs) and ficolins. These molecules recognize and bind carbohydrates in pathogens and activate complement leading to opsonization, leukocyte activation, and direct pathogen killing. While MBLs have been reported in many fish species, ficolins do not appear to be present in the teleost lineage, despite their importance in invertebrate and higher vertebrate innate immunity. A protein with a similar fibrinogen-like domain, microfibrillar-associated protein 4, MFAP4, is present in fish, albeit with no described immune function. We examined whether MFAP4 genes in fish may potentially act as pathogen receptors in the absence of ficolin. We isolated and characterized five MFAP4 genes from channel catfish. Linkage mapping and phylogenetic analysis indicated that at least three of the catfish MFAP4 genes are tightly clustered on a single chromosome, suggesting that they may have arisen through tandem duplication. Divergent, duplicated families of MFAP4 genes are also present in other teleost species. Expression analysis of the catfish MFAP4 transcripts revealed unique patterns of homeostatic expression among the genes in gill, spleen, skin, liver, and muscle. Expression of the five MFAP4 transcripts showed significant changes in expression as soon as 4h after infection with either Edwardsiella ictaluri or Flavobacterium columnare with modulation of expression continuing up to 7 d following pathogen exposure. Several different tissues and gene-specific patterns were captured and transcript expression changes of >30-fold were observed over the course of the bacterial challenges. Our results suggest a novel role for MFAP4 in teleost immune responses.

Specific regulation of the chemokine response to viral hemorrhagic septicemia virus at the entry site

The fin bases constitute the main portal of rhabdovirus entry into rainbow trout (Oncorhynchus mykiss), and replication in this first site strongly conditions the outcome of the infection. In this context, we studied the chemokine response elicited in this area in response to viral hemorrhagic septicemia virus (VHSV), a rhabdovirus. Among all the rainbow trout chemokine genes studied, only the transcription levels of CK10 and CK12 were significantly upregulated in response to VHSV. As the virus had previously been shown to elicit a much stronger chemokine response in internal organs, we compared the effect of VHSV on the gills, another mucosal site which does not constitute the main site of viral entry or rhabdoviral replication. In this case, a significantly stronger chemokine response was triggered, with CK1, CK3, CK9, and CK11 being upregulated in response to VHSV and CK10 and CK12 being down-modulated by the virus. We then conducted further experiments to understand how these different chemokine responses of mucosal tissues could correlate with their capacity to support VHSV replication. No viral replication was detected in the gills, while at the fin bases, only the skin and the muscle were actively supporting viral replication. Within the skin, viral replication took place in the dermis, while viral replication was blocked within epidermal cells at some point before protein translation. The different susceptibilities of the different skin layers to VHSV correlated with the effect that VHSV has on their capacity to secrete chemotactic factors. Altogether, these results suggest a VHSV interference mechanism on the early chemokine response at its active replication sites within mucosal tissues, a possible key process that may facilitate viral entry.

Characterization of mononuclear phagocytic cells in medaka fish transgenic for a cxcr3a:gfp reporter

Chemokines and chemokine receptors are key evolutionary innovations of vertebrates. They are involved in morphogenetic processes and play an important role in the immune system. Based on an analysis of the chemokine receptor gene family in teleost genomes, and the expression patterns of chemokine receptor genes during embryogenesis and the wounding response in young larvae of Oryzias latipes, we identified the chemokine receptor cxcr3a as a marker of innate immune cells. Cells expressing cxcr3a were characterized in fish transgenic for a cxcr3a:gfp reporter. In embryos and larvae, cxcr3a-expressing cells are motile in healthy and damaged tissues, and phagocytic; the majority of these cells has the morphology of tissue macrophages, whereas a small fraction has a dendritic phenotype. In adults, cxcr3a-positive cells continue to specifically express myeloid-associate markers and genes related to antigen uptake and presentation. By light microscopy and ultrastructural analysis, the majority of cxcr3a-expressing cells has a dendritic phenotype, whereas the remainder resembles macrophage-like cells. After challenge of adult fish with bacteria or CpG oligonucleotides, phagocytosing cxcr3a-positive cells in the blood up-regulated il12p40 genes, compatible with their function as part of the mononuclear phagocytic system. Our results identify a marker of teleost mononuclear phagocytic cells and suggest a surprising degree of morphological and functional similarity between the innate immune systems of lower and higher vertebrates.

Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish

Background

Systematic research on fish immunogenetics is indispensable in understanding the origin and evolution of immune systems. This has long been a challenging task because of the limited number of deep sequencing technologies and genome backgrounds of non-model fish available. The newly developed Solexa/Illumina RNA-seq and Digital gene expression (DGE) are high-throughput sequencing approaches and are powerful tools for genomic studies at the transcriptome level. This study reports the transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus using RNA-seq and DGE in an attempt to gain insights into the immunogenetics of marine fish.

Results

RNA-seq analysis generated 169,950 non-redundant consensus sequences, among which 48,987 functional transcripts with complete or various length encoding regions were identified. More than 52% of these transcripts are possibly involved in approximately 219 known metabolic or signalling pathways, while 2,673 transcripts were associated with immune-relevant genes. In addition, approximately 8% of the transcripts appeared to be fish-specific genes that have never been described before. DGE analysis revealed that the host transcriptome profile of Vibrio harveyi-challenged L. japonicus is considerably altered, as indicated by the significant up- or down-regulation of 1,224 strong infection-responsive transcripts. Results indicated an overall conservation of the components and transcriptome alterations underlying innate and adaptive immunity in fish and other vertebrate models. Analysis suggested the acquisition of numerous fish-specific immune system components during early vertebrate evolution.

Conclusion

This study provided a global survey of host defence gene activities against bacterial challenge in a non-model marine fish. Results can contribute to the in-depth study of candidate genes in marine fish immunity, and help improve current understanding of host-pathogen interactions and evolutionary history of immunogenetics from fish to mammals.

Viral hemorrhagic septicemia and infectious pancreatic necrosis viruses replicate differently in rainbow trout gonad and induce different chemokine transcription profiles

Viral hemorrhagic septicemia virus (VHSV) and infectious pancreatic necrosis virus (IPNV) are two rainbow trout (Oncorhynchus mykiss) pathogens. While IPNV is known to be vertically transmitted to the next generation through the oocyte, VHSV is known to replicate in the ovary and be transmitted horizontally through the ovarian fluid. In this work, we wanted to study whether these differences had an effect on the immune response triggered in the ovary, with a focus on the chemokine response. We have studied the kinetics of viral gene expression and the sites of replication, confirming that great differences exist between the replication of the two viruses in the gonad. Next, we studied the levels of expression of several CXC and CC chemokines in the ovary and found that while VHSV strongly triggered chemokine transcription, IPNV had almost no effect. This lack of immune response might be an advantage that permits its vertical transmission.

Cloning, characterization, and expression analysis of a CC chemokine gene from turbot (Scophthalmus maximus)

The chemokines are a superfamily of chemotactic cytokines playing an important role in leukocyte chemotaxis. Here, a turbot head kidney cDNA library was constructed in which KC70 was identified as a CC chemokine. Unknown 5' and 3' parts of the cDNA were amplified by 5' and 3' rapid amplification of cDNA ends (RACE). The complete cDNA of KC70 contains a 59-bp 5' UTR, a 336-bp ORF, and a 152-bp 3' UTR. Four exons and three introns were identified in KC70. Phylogenetic analysis showed that KC70 was similar to CCL19. In normal turbot KC70 was expressed in all tissues except brain and skin. Infection of turbot with pathogenic bacteria significantly increased expression of KC70 in the liver. Expression of KC70 in head kidney first increased and then decreased after bacterial challenge. No significant change was observed in the spleen after bacterial challenge. During embryonic development, KC70 was highly expressed after the gastrula stage. These results indicated KC70 plays important and multiple roles in turbot immune response.

Development of genomic resources in support of sequencing, assembly, and annotation of the catfish genome

Major progress has been made in catfish genomics including construction of high-density genetic linkage maps, BAC-based physical maps, and integration of genetic linkage and physical maps. Large numbers of ESTs have been generated from both channel catfish and blue catfish. Microarray platforms have been developed for the analysis of genome expression. Genome repeat structures are studied, laying grounds for whole genome sequencing. USDA recently approved funding of the whole genome sequencing project of catfish using the next generation sequencing technologies. Generation of the whole genome sequence is a historical landmark of catfish research as it opens the real first step of the long march toward genetic enhancement. The research community needs to be focused on aquaculture performance and production traits, take advantage of the unprecedented genome information and technology, and make real progress toward genetic improvements of aquaculture brood stocks.

Fibroblasts express immune relevant genes and are important sentinel cells during tissue damage in rainbow trout (Oncorhynchus mykiss)

Fibroblasts have shown to be an immune competent cell type in mammals. However, little is known about the immunological functions of this cell-type in lower vertebrates. A rainbow trout hypodermal fibroblast cell-line (RTHDF) was shown to be responsive to PAMPs and DAMPs after stimulation with LPS from E. coli, supernatant and debris from sonicated RTHDF cells. LPS was overall the strongest inducer of IL-1β, IL-8, IL-10, TLR-3 and TLR-9. IL-1β and IL-8 were already highly up regulated after 1 hour of LPS stimulation. Supernatant stimuli significantly increased the expression of IL-1β, TLR-3 and TLR-9, whereas the debris stimuli only increased expression of IL-1β. Consequently, an in vivo experiment was further set up. By mechanically damaging the muscle tissue of rainbow trout, it was shown that fibroblasts in the muscle tissue of rainbow trout contribute to electing a highly local inflammatory response following tissue injury. The damaged muscle tissue showed a strong increase in the expression of the immune genes IL-1β, IL-8 and TGF-β already 4 hours post injury at the site of injury while the expression in non-damaged muscle tissue was not influenced. A weaker, but significant response was also seen for TLR-9 and TLR-22. Rainbow trout fibroblasts were found to be highly immune competent with a significant ability to express cytokines and immune receptors. Thus fish fibroblasts are believed to contribute significantly to local inflammatory reactions in concert with the traditional immune cells.

Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

Twelve cDNA libraries from two species of catfish have been sequenced, resulting in the generation of nearly 500,000 ESTs.

Background

Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification.

Results

A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35% of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis.

Conclusions

This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.

Chemokine transcription in rainbow trout (Oncorhynchus mykiss) is differently modulated in response to viral hemorrhagic septicaemia virus (VHSV) or infectious pancreatic necrosis virus (IPNV)

Chemokines not only act as chemoattractants for immune cells, but also exert immunomodulatory actions, thus modulating the immune functions of their target cells. In rainbow trout (Oncorhynchus mykiss), twenty-four chemokines have been identified to date. Even though their sequences have been reported, their biological role has been scarcely elucidated and the role that these chemokines have on the antiviral response in fish has been poorly studied. In this sense, in the current work, we have determined the levels of expression of several of these rainbow trout chemokines (CXCd, gammaIP, CK1, CK3, CK5B, CK6, CK7A, CK9 and CK12) in head kidney and spleen during the course of a viral infection using two different viruses, viral hemorrhagic septicaemia virus (VHSV) and infectious pancreatic necrosis virus (IPNV), comparing them to the levels induced by poly I:C. We also determined the effects that the two viruses and poly I:C provoked on the levels of expression of these chemokines in vitro in head kidney leucocytes. Overall, VHSV was capable of modulating gammaIP, CXCd, CK1, CK3, CK5B, CK6 and CK12, while IPNV induced a very different chemokine profile and affected CK1, CK5B, CK6, CK7A, CK9 and CK12. On the other hand, a viral mimic such as poly I:C was capable of up-regulating gammaIP, CXCd, CK1, CK3, CK5B, CK7A and CK12. As more information becomes available concerning the immune role and target cells that these chemokines have on rainbow trout, we would be able to better interpret the importance of these differences in the pathogenicity of these two viruses.

Sequence analysis, characterization and mRNA distribution of channel catfish (Ictalurus punctatus Rafinesque, 1818) chemokine (C-X-C motif) receptor 4 (CXCR4) cDNA

Chemokine receptor CXCR4, a member of the G protein-coupled receptor superfamily, binds selectively CXCL12. This protein plays many important roles in immunological as well as pathophysiological functions. In this study, we identified and characterized the channel catfish CXCR4 transcript. The full-length nucleic acid sequence of channel catfish CXCR4 cDNA comprised of 1994 nucleotides, including an open reading frame, which appears to encode a putative peptide of 357 amino acid residues with a calculated molecular mass of 40.1kDa. By comparison with the human counterpart, the channel catfish CXCR4 peptide can be divided into domains, including seven transmembrane domains, four cytoplasmic domains, and four extracellular domains. The CXCR4 transcript was detected in spleen, anterior kidney, liver, intestine, skin and gill of all catfish examined in this study. Because four CXCL of channel catfish have been identified, the result provides valuable information for further exploring the channel catfish chemokine signalling pathways and their roles in immune responses to infection.

Immune effects observed after the injection of plasmids coding for rainbow trout (Oncorhynchus mykiss) CK5B, CK6 and CK7A chemokines demonstrate their immunomodulatory capacity and reveal CK6 as a major interferon inducer

In the current study, we have determined the immune effects of the intramuscular injection of eukaryotic expression plasmids coding for rainbow trout (Oncorhynchus mykiss) CK5B, CK6 or CK7A CC chemokines (pCK5B, pCK6 and pCK7A) as a first step towards the establishment of their biological role. We have studied the levels of expression of several immune genes in the spleen and head kidney by real-time PCR in comparison to the levels observed in animals injected with the empty plasmid. Concerning the levels of expression of these CC chemokines and the CXC chemokine, interleukin 8 (IL-8), each plasmid induced up-regulation on expression levels of its coded chemokine in the head kidney and spleen, but also affected the expression of other chemokines. Both pCK6 and pCK7A induced the expression of the other two CC chemokines, while pCK5B induced CK7A but not CK6. Both pCK5B and pCK7A induced IL-8 as well. pCK6 was the only plasmid that induced IL-1beta in the head kidney, whereas in the spleen, this occurred only with pCK5B. Different effects on the head kidney and spleen were also visible for tumour necrosis factor alpha (TNF-alpha), since the three plasmids induced this cytokine in the head kidney, but only pCK5B and pCK6 in the spleen. Concerning the effects on type I interferon (IFN), again pCK6 induced the strongest enhancement in the head kidney, while in the spleen it was pCK5B. However, the levels of expression of the Mx gene, know to be induced by type I IFN correlated with the CK6-induced IFN levels in the head kidney, but not with the CK5B-induced IFN in head kidney or spleen, suggesting an inhibition of Mx mRNA levels independent of IFN due to CK5B. The clear effect of pCK6 on the levels of expression of IFN-gamma and its strong effects on type I IFN, in contrast with its recent adscription to the CCL17/22 group linked to Th2 responses, were verified by studying the in vitro effects of recombinant CK6 on head kidney leukocytes. Again in this case, recombinant CK6 strongly induced type I IFN, Mx and IFN-gamma to a lesser extent, revealing CK6 as a potent IFN inducer in contrast to its mammalian homologues. Finally, effects on major histocompatibility complex (MHC)-IIalpha, CD4 and CD8alpha expression demonstrate that the three chemokines are able to mobilize antigen-presenting cells, CD4(+) and CD8(+) lymphocytes.

NOD-like subfamily of the nucleotide-binding domain and leucine-rich repeat containing family receptors and their expression in channel catfish

The NLRs (nucleotide-binding domain and leucine-rich repeat containing family receptors) are a recently identified family of pattern recognition receptors in vertebrates. Several subfamilies of NLRs have been characterized in human, mouse, and zebrafish, but studies of NLRs in other species, especially teleost species, have been lacking. Here we report characterization of five NLRs from channel catfish: NOD1, NOD2, NLRC3, NLRC5, and NLRX1. Structural analysis indicated that the genes were organized in a similar fashion as in the mammals and in zebrafish. Phylogenetic analysis suggested that they were orthologous to the NOD-like subfamily of NLRs. All five NOD-like genes exist as a single copy gene in the catfish genome. Hybridization of gene-specific probes allowed mapping of three NLR genes to the catfish physical map, laying a foundation for genome characterization and for establishing orthologies with NLR genes from other species. These genes are widely expressed in various tissues and leukocyte cell lines. While the majority of the NLR genes appeared to be constitutively expressed, NOD1 was induced after infection with a bacterial pathogen, Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish (ESC), suggesting its involvement in immunity against the intracellular pathogen.

Will advances in fish immunology change vaccination strategies?

This review will discuss some of the recent advances in discovering immune genes in fish, in terms of their relevance to vaccine design and development. Particular emphasis will be placed on the many cytokine and costimulatory molecules now known, with examples drawn from the mammalian literature as to their potential value for fish vaccinology. A new area of vaccine research will also be touched upon, where efficacious responses are elicited by inhibiting the natural negative regulators of immune responses, such as Treg cell products and SOCS proteins.

Interleukin 8 and CK-6 chemokines specifically attract rainbow trout (Oncorhynchus mykiss) RTS11 monocyte-macrophage cells and have variable effects on their immune functions

In the current work, we have demonstrated that both rainbow trout (Oncorhynchus mykiss) interleukin 8 (IL-8), a CXC chemokine, and CK-6, a CC chemokine, are able of efficiently attracting RTS11, a rainbow trout established macrophage-monocyte-like cell line. Interestingly, two sub-populations of non-adherent cells are distinguishable by flow cytometry that could be identified as immature monocyte- and mature macrophage-like populations, respectively, and the two chemokines studied exert their effects on different populations. Although IL-8 specifically attracts the monocyte-like sub-population, CK-6 specifically attracts the macrophage-like cell sub-population. We have also determined the effects of both of these chemokines on RTS11 phagocytosis, respiratory burst and the expression of other immune-related genes. We found that IL-8 inhibited the phagocytosis capacity of RTS11 cells belonging to the macrophage-like profile. No effect was observed, however, on the respiratory burst, immune function that has been considerably affected throughout the establishment of the cell culture. Concerning the effect that IL-8 and CK-6 have on the expression of other immune genes, we found that IL-8 significantly induced the levels of expression of CK-6, IL-8, pro-inflammatory cytokines such as IL-1beta and tumour necrosis factor alpha (TNF-alpha) of RTS11 cells. On the other hand, CK-6 induced the levels of expression of IL-8, iNOS and the integrin CD-18, while it had very faint effect on pro-inflammatory cytokines. These results constitute one of the very few studies in which the effect of IL-8, a CXC chemokine, on monocyte-like cells is described. Moreover, it demonstrates that different monocyte-macrophage sub-populations have different reactivity to different chemokines.

Extensive expansion and diversification of the chemokine gene family in zebrafish: identification of a novel chemokine subfamily CX

Background

The chemokine family plays important roles in cell migration and activation. In humans, at least 44 members are known. Based on the arrangement of the four conserved cysteine residues, chemokines are now classified into four subfamilies, CXC, CC, XC and CX3C. Given that zebrafish is an important experimental model and teleost fishes constitute an evolutionarily diverse group that forms half the vertebrate species, it would be useful to compare the zebrafish chemokine system with those of mammals. Prior to this study, however, only incomplete lists of the zebrafish chemokine genes were reported.

Results

We systematically searched chemokine genes in the zebrafish genome and EST databases, and identified more than 100 chemokine genes. These genes were CXC, CC and XC subfamily members, while no CX3C gene was identified. We also searched chemokine genes in pufferfish fugu and Tetraodon, and found only 18 chemokine genes in each species. The majority of the identified chemokine genes are unique to zebrafish or teleost fishes. However, several groups of chemokines are moderately similar to human chemokines, and some chemokines are orthologous to human homeostatic chemokines CXCL12 and CXCL14. Zebrafish also possesses a novel species-specific subfamily consisting of five members, which we term the CX subfamily. The CX chemokines lack one of the two N-terminus conserved cysteine residues but retain the third and the fourth ones. (Note that the XC subfamily only retains the second and fourth of the signature cysteines residues.) Phylogenetic analysis and genome organization of the chemokine genes showed that successive tandem duplication events generated the CX genes from the CC subfamily. Recombinant CXL-chr24a, one of the CX subfamily members on chromosome 24, showed marked chemotactic activity for carp leukocytes. The mRNA was expressed mainly during a certain period of the embryogenesis, suggesting its role in the zebrafish development.

Conclusion

The phylogenic and genomic organization analyses suggest that a substantial number of chemokine genes in zebrafish were generated by zebrafish-specific tandem duplication events. During such duplications, a novel chemokine subfamily termed CX was generated in zebrafish. Only two human chemokines CXCL12 and CXCL14 have the orthologous chemokines in zebrafish. The diversification observed in the numbers and sequences of chemokines in the fish may reflect the adaptation of the individual species to their respective biological environment.

Characterization of a BAC library from channel catfish Ictalurus punctatus: indications of high levels of chromosomal reshuffling among teleost genomes

The CHORI-212 bacterial artificial chromosome (BAC) library was constructed by cloning EcoRI/EcoRI partially digested DNA into the pTARBAC2.1 vector. The library has an average insert size of 161 kb, and provides 10.6-fold coverage of the channel catfish haploid genome. Screening of 32 genes using overgo or cDNA probes indicated that this library had a good representation of the genome as all tested genes existed in the library. We previously reported sequencing of approximately 25,000 BAC ends that generated 20,366 high-quality BAC end sequences (BES) and identified a large number of sequences similar to known genes using BLASTX searches. In this work, particular attention was given to identification of BAC mate pairs with known genes from both ends. When identified, comparative genome analysis was conducted to determine syntenic regions of the catfish genome with the genomes of zebrafish and Tetraodon. Of the 141 mate pairs with known genes from channel catfish, conserved syntenies were identified in 34 (24.1%), with 30 conserved in the zebrafish genome and 14 conserved in the Tetraodon genome. Additional analysis of three of the 34 conserved syntenic groups by direct sequencing indicated conserved gene contents in all three species. This indicates that comparative genome analysis may provide shortcuts to genome analysis in catfish, especially for short genomic regions once the conserved syntenies are identified.

The warm temperature acclimation protein Wap65 as an immune response gene: its duplicates are differentially regulated by temperature and bacterial infections

The warm temperature acclimation related 65kDa protein (Wap65) in teleost fish shares high structural similarities with mammalian hemopexins. Recent studies using microarray analysis indicated that this temperature acclimation protein may also be involved in immune responses. To provide evidence of its potential involvement in immune responses after bacterial infections, we have identified and characterized two types of Wap65 genes in channel catfish, referred to as Wap65-1 and Wap65-2, respectively. While Wap65-1 and Wap65-2 are both structurally similar to the mammalian hemopexins, they exhibit highly differential patterns of spatial expression. Wap65-1 was expressed in a wide range of tissues, whereas Wap65-2 was only expressed in the liver. Their regulation with warm temperature and bacterial infections was also highly different: Wap65-1 was constitutively expressed, whereas Wap65-2 was highly regulated by both warm temperature and bacterial infections, and warm temperature and bacterial infections appeared to synergistically induce the expression of Wap65-2. The great contrast of expression patterns and regulation of the two catfish Wap65 genes suggested both neofunctionalization and partitioning of their functions. Phylogenetic analysis indicated that the duplicated catfish Wap65 genes were evolved not only from whole genome duplication, but also from tandem, intrachromosomal gene duplications. Taken together, the results of this study suggest that Wap65 genes are not only important for its classical role as a warm temperature acclimation protein, but more importantly, may also function as an immune response protein.

A BAC-based physical map of the channel catfish genome

Catfish is the major aquaculture species in the United States. To enhance its genome studies involving genetic linkage and comparative mapping, a bacterial artificial chromosome (BAC) contig-based physical map of the channel catfish (Ictalurus punctatus) genome was generated using four-color fluorescence-based fingerprints. Fingerprints of 34,580 BAC clones (5.6x genome coverage) were generated for the FPC assembly of the BAC contigs. A total of 3307 contigs were assembled using a cutoff value of 1x10(-20). Each contig contains an average of 9.25 clones with an average size of 292 kb. The combined contig size for all contigs was 0.965 Gb, approximately the genome size of the channel catfish. The reliability of the contig assembly was assessed by both hybridization of gene probes to BAC clones contained in the fingerprinted assembly and validation of randomly selected contigs using overgo probes designed from BAC end sequences. The presented physical map should greatly enhance genome research in the catfish, particularly aiding in the identification of genomic regions containing genes underlying important performance traits.