Cloning and characterization of cDNA clones encoding CD9 from Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss)

Single-cell atlas of rainbow trout peripheral blood leukocytes and profiling of their early response to infectious pancreatic necrosis virus

The recent development of single cell sequencing technologies has revolutionized the state-of-art of cell biology, allowing the simultaneous measurement of thousands of genes in single cells. This technology has been applied to study the transcriptome of single cells in homeostasis and also in response to pathogenic exposure, greatly increasing our knowledge of the immune response to infectious agents. Yet the number of these studies performed in aquacultured fish species is still very limited. Thus, in the current study, we have used the 10x Genomics single cell RNA sequencing technology to study the response of rainbow trout (Oncorhynchus mykiss) peripheral blood leukocytes (PBLs) to infectious pancreatic necrosis virus (IPNV), an important trout pathogen. The study allowed us to obtain a transcriptomic profile of 12 transcriptionally distinct leukocyte cell subpopulations that included four different subsets of B cells, T cells, monocytes, two populations of dendritic-like cells (DCs), hematopoietic progenitor cells, non-specific cytotoxic cells (NCC), neutrophils and thrombocytes. The transcriptional pattern of these leukocyte subpopulations was compared in PBL cultures that had been exposed in vitro to IPNV for 24 h and mock-infected cultures. Our results revealed that monocytes and neutrophils showed the highest number of upregulated protein-coding genes in response to IPNV. Interestingly, IgM+IgD+ and IgT+ B cells also upregulated an important number of genes to the virus, but a much fainter response was observed in ccl4 + or plasma-like cells (irf4 + cells). A substantial number of protein-coding genes and genes coding for ribosomal proteins were also transcriptionally upregulated in response to IPNV in T cells and thrombocytes. Interestingly, although genes coding for ribosomal proteins were regulated in all affected PBL subpopulations, the number of such genes transcriptionally regulated was higher in IgM+IgD+ and IgT+ B cells. A further analysis dissected which of the regulated genes were common and which were specific to the different cell clusters, identifying eight genes that were transcriptionally upregulated in all the affected groups. The data provided constitutes a comprehensive transcriptional perspective of how the different leukocyte populations present in blood respond to an early viral encounter in fish.

Phylogeny and expression of tetraspanin CD9 paralogues in rainbow trout (Oncorhynchus mykiss)

CD9 is a member of the tetraspanin family, which is characterised by a unique domain structure and conserved motifs. In mammals, CD9 is found in tetraspanin-enriched microdomains (TEMs) on the surface of virtually every cell type. CD9 has a wide variety of roles, including functions within the immune system. Here we show the first in-depth analysis of the cd9 gene family in salmonids, showing that this gene has expanded to six paralogues in three groups (cd9a, cd9b, cd9c) through whole genome duplication events. We suggest that through genome duplications, cd9 has undergone subfunctionalisation in the paralogues and that cd9c1 and cd9c2 in particular are involved in antiviral responses in salmonid fish. We show that these paralogues are significantly upregulated in parallel to classic interferon-stimulated genes (ISGs) active in the antiviral response. Expression analysis of cd9 may therefore become an interesting target to assess teleost responses to viruses.

Expression of CD9 on porcine lymphocytes and its relation to T cell differentiation and cytokine production

In this work, we report on two novel monoclonal antibodies, specific for porcine CD9. CD9 is a tetraspanin that is expressed on a wide variety of cells. We phenotyped porcine immune cell subsets and found that CD9 was expressed on all monocytes as well as a subset of B cells. CD9 was variably expressed on T cells, with CD4 T cells containing the highest frequency of CD9⁺ cells. CD9 expression positively correlated with the frequency of central memory CD4 T cells in ex vivo PBMC. Therefore, we proceeded to explore CD9 as a marker of T cell function. Here we observed that CD9 was expressed on the vast majority of long-lived influenza A virus-specific effector cells that retained the capacity for cytokine production in response to in vitro recall antigen. Therefore, the new antibodies enable the detection of a cell surface molecule with functional relevance to T cells. Considering the importance of CD9 in membrane remodelling across many cell types, they will also benefit the wider field of swine biomedical research.

Two CD9 tetraspanin family members of Japanese flounder (Paralichthys olivaceus): characterization and comparative analysis of the anti-infectious immune function

CD9 is a glycoprotein of the transmembrane 4 superfamily that is involved in various cellular processes. Studies related to the immune functions and activities of CD9 in teleost fish are limited. In this study, we characterized two CD9 homologs, PoCD9.1 and PoCD9.3, from Japanese flounder (Paralichthys olivaceus). Sequence analysis showed that PoCD9.1 and PoCD9.3 possess characteristic transmembrane 4 superfamily (TM4SF) structures. PoCD9.1 shares 70.61% sequence identity with PoCD9.3. The expression of PoCD9.1 and PoCD9.3 in the three main immune tissues was significantly induced in a time-dependent manner by extracellular and intracellular pathogen infection, which indicates that the two CD9 homologs play an important role in the response to pathogenic infection. Following infection with the extracellular pathogen Vibrio anguillarum, the expression profiles of both PoCD9.1 and PoCD9.3 were similar. After infection with the intracellular pathogen Edwardsiella piscicida, the expression levels of PoCD9.1 and PoCD9.3 were different at different stages of infection, especially in the spleen. The spleen was the most important tissue for the PoCD9.1 and PoCD9.3 responses to pathogen infection among the three examined immune tissues. Knockdown of PoCD9.1 and PoCD9.3 attenuated the ability of host cells to eliminate pathogenic bacteria, and PoCD9.1 knockdown was more lethal than PoCD9.3 knockdown for host cells with E. piscicida infection. Overexpression of PoCD9.1 and PoCD9.3 promoted host or host cell defence against E. piscicida infection. These findings suggest that PoCD9.1 and PoCD9.3 serve as immune-related factors, play an important role in the immune defence system of Japanese flounder, and display different functions in response to different pathogens at different stages of infection.

Comparative analysis of the tetraspanin gene family in six teleost fishes

Tetraspanins are a family of membrane proteins, which play important roles in many aspects of cell biology and physiology via binding other tetraspanins or proteins. In this study, we identified 251 putative tetraspanin genes in 6 teleost fishes. Conserved gene organization and motif distribution suggested their functional relevance existing in each group. Synteny analyses implied conserved and dynamic evolution characteristics of this gene family in several vertebrates. We also found that some recombination events have accelerated the evolution of this gene family. Moreover, a few positive selection sites were identified. Expression patterns of some tetraspanins were further studied under organophosphorus stress using transcriptome sequencing. Functional network analyses identified some interacting genes that exhibited 174 interactions, which reflected the diversity of tetraspanin binding proteins. The results will provide a foundation for the further functional investigation of the tetraspanin genes in fishes.

Down-regulation of CD53 expression in Epinephelus coioides under LPS, poly (I:C), and cytokine stimulation

Tetraspanins are a group of cell surface molecules involved in cell adhesion, motility, metastasis, signal transduction, and immune cell activation. Members of the tetraspanin family include CD9, CD37, CD63, CD53, and others. However, few tetraspanins have been investigated in teleosts. In this study, we obtained the open reading frame of CD53 cDNA from orange spotted grouper (Epinephelus coioices), an economically important fish. The predicted amino acid structure contains four membrane-spanning domains and a conserved CCG motif. The amino acid identity between human and grouper CD53 was only 38%; however, both CD53 proteins share the same structure. Quantitative real-time PCR revealed that mRNA is abundant in immune organs, including the head and trunk kidneys, spleen, thymus, gill, and blood. Immunochemistry and immunofluorescence analyses further revealed that CD53 was majorly expressed in the leukocytes of various organs. Finally, mRNA and protein expression for CD53 was down-regulated in fish treated with immune stimulators, including LPS, Poly (I:C), Vibrio, recombinant grouper IL-6, and CCL4. Our results indicate that the expression of CD53 may play important roles in pathogen invasion and inflammation reaction.

Molecular characterization of CD9 and CD63, two tetraspanin family members expressed in trout B lymphocytes

Tetraspanins are a family of membrane-organizing proteins, characterized by the presence of four highly conserved transmembrane regions that mediate diverse physiological functions. In the current study, we have identified two novel tetraspanin members in rainbow trout (Oncorhynchus mykiss), homologs to mammalian CD9 and CD63. Both genes were expressed in muscle, skin, gills, hindgut, gonad, liver, spleen, head kidney, thymus and peripheral blood leukocytes. Throughout the early life cycle stages, CD9 mRNA levels significantly increased after first feeding, whereas CD63 transcription remained constant during all the developmental stages analyzed. In response to an experimental bath infection with viral hemorrhagic septicemia virus (VHSV), CD9 transcription was down-regulated in the gills, while CD63 mRNA levels were down-regulated in the head kidney. Instead, when the virus was intraperitoneally injected, the transcription of both genes was significantly up-regulated in peritoneal cells at several days post-infection. Additionally, both genes were transcriptionally up-regulated in the muscle of trout injected with a VHSV DNA vaccine. To gain insight on the relation of these tetraspanins with B cell activity we determined their constitutive expression in naive IgM(+) populations from different sources and observed that both molecules were being transcribed by IgM(+) cells in different tissues. Furthermore, CD9 transcription was significantly down-regulated in splenic IgM(+) cells in response to in vitro VHSV exposure. Our results provide insights on the potential role of these tetraspanins on teleost B cell and antiviral immunity.

The antiviral innate immune response in fish: evolution and conservation of the IFN system

Innate immunity constitutes the first line of the host defense after pathogen invasion. Viruses trigger the expression of interferons (IFNs). These master antiviral cytokines induce in turn a large number of interferon-stimulated genes, which possess diverse effector and regulatory functions. The IFN system is conserved in all tetrapods as well as in fishes, but not in tunicates or in the lancelet, suggesting that it originated in early vertebrates. Viral diseases are an important concern of fish aquaculture, which is why fish viruses and antiviral responses have been studied mostly in species of commercial value, such as salmonids. More recently, there has been an interest in the use of more tractable model fish species, notably the zebrafish. Progress in genomics now makes it possible to get a relatively complete image of the genes involved in innate antiviral responses in fish. In this review, by comparing the IFN system between teleosts and mammals, we will focus on its evolution in vertebrates.

Channel catfish, Ictalurus punctatus (Rafinesque), tetraspanin membrane protein family: identification, characterization and phylogenetic analysis of tetraspanin 3 and tetraspanin 7 (CD231) transcripts

Tetraspanins, a large cell surface protein superfamily characterized by having four transmembrane domains, play many critical roles in physiological and pathological processes. In this study, we report the identification, characterization and phylogenetic analysis of the channel catfish tetraspanin 3 and tetraspanin 7 (CD231) transcripts. The full-length nucleotide sequences of tetraspanin 3 and tetraspanin 7 cDNA have 1,453 and 1,842 base pairs, respectively. Analysis of the nucleotide sequences reveals that each has one open reading frame (ORF). The ORF of tetraspanin 3 appears to encode 241 amino acids with calculated molecular mass of 26.8 kDa, while the ORF of tetraspanin 7 potentially encodes 251 amino acids with calculated molecular mass of 27.9 kDa. By comparison with the human counterparts, the channel catfish tetraspanin 3 and tetraspanin 7 peptides have four transmembrane domains, three intracellular domains and two (small and large) extracellular domains. In addition, several characteristic features critical for structure and functions in mammalian tetraspanins are also conserved in channel catfish tetraspanin 3 and tetraspanin 7. The transcripts were detected by RT-PCR in restrictive organs. These results with those from our previous studies on other channel catfish tetraspanins provide important information for further investigating the roles of various tetraspanins in channel catfish infection with microorganisms.

Cloning of arctic lamprey Lethenteron camtschaticum cd9 with roles in the immune response

In this study, the cd9 gene, a member of the tetraspanin superfamily and involved in various cellular processes, was cloned from Lethenteron camtschaticum. Both real-time PCR and immunohistochemical assays showed broad distribution of cd9 in various L. camtschaticum tissues. In addition, expression levels of Cd9 mRNA were up-regulated in the liver and heart after stimulation by lipopolysaccharide. Flow cytometric analyses demonstrated that cd9 was detected on the leukocytes and that the expression level was higher on granulocytes than on lymphocytes, which implied that cd9 was mainly involved in innate immunity.

Early antiviral response and virus-induced genes in fish

In fish as in mammals, virus infections induce changes in the expression of many host genes. Studies conducted during the last fifteen years revealed a major contribution of the interferon system in fish antiviral response. This review describes the screening methods applied to compare the impact of virus infections on the transcriptome in different fish species. These approaches identified a "core" set of genes that are strongly induced in most viral infections. The "core" interferon-induced genes (ISGs) are generally conserved in vertebrates, some of them inhibiting a wide range of viruses in mammals. A selection of ISGs -PKR, vig-1/viperin, Mx, ISG15 and finTRIMs - is further analyzed here to illustrate the diversity and complexity of the mechanisms involved in establishing an antiviral state. Most of the ISG-based pathways remain to be directly determined in fish. Fish ISGs are often duplicated and the functional specialization of multigenic families will be of particular interest for future studies.

Viral hemorrhagic septicaemia virus (VHSV) up-regulates the cytotoxic activity and the perforin/granzyme pathway in the rainbow trout RTS11 cell line

A survey of immune-relevant genes that might be up-regulated in response to viral hemorrhagic septicaemia virus (VHSV) in the rainbow trout monocyte-macrophage cell line, RTS11, unexpectedly revealed an increased expression of perforin (PRF) and granzyme (GRZ) genes, which represent components of the major cytotoxic pathway. The natural killer-enhancing factor (NKEF), also known to modulate cytotoxic activity, was up-regulated at the gene but strikingly down-regulated at protein level. The expression of these genes was not affected in head kidney leukocytes (HKLs) infected with VHSV, leading us to evaluate the potential cytotoxic activity of RTS11 and HKLs. For the first time, the cytotoxic activity of RTS11 against xenogeneic targets has been demonstrated, although this was modest relative to HKLs. Yet the activity in RTS11 was significantly increased by VHSV, as in HKLs. This cytotoxic activity elicited by viral infection appeared to require viral gene expression because inactivated VHSV failed to increase RTS11 cytotoxic activity. As for other immune functions, RTS11 cells provide a model for further studying cytotoxic activities of fish monocyte-macrophages.

Identification and characterization of the first reptilian CD9, and its expression analysis in response to bacterial infection

In this study, a CD9 homologue in a reptile, Chinese soft-shelled turtle, has been cloned and identified for the first time. The full-length cDNA of turtle CD9 was 1146bp and contained a 672bp open reading frame (ORF) coding for a protein of 224 amino acids. Four transmembrane domains (TMs) divided the turtle CD9 into several parts: short N-, C-termini, an intracellular loop and two (small and large) extracellular loops (SEL and LEL). A CCG motif, a potential N-linked glycosylation site and 10 cysteine residues were well conserved. The deduced amino acid sequence analysis showed that the turtle CD9 shared 82% identity to duck CD9. Most of the differences were found in the LEL. Phylogenetic analysis showed that the turtle CD9 sequence clustered together with bird CD9 sequence. RT-PCR analysis showed that turtle CD9 was ubiquitously expressed in liver, spleen, kidney, heart, blood and intestine tissues of un-infected turtles. Real-time PCR analysis further indicated that after Aeromonas hydrophila infection, the turtle CD9 mRNA was up-regulated in various tissues at 8h, and significantly up-regulated during 8h to 7d. These results indicated that turtle CD9 may be involved in anti-bacterial immune response.

Characterization of rainbow trout CHK2 and its potential as a genotoxicity biomarker

Checkpoint kinase 2 (CHK2) plays a central and conserved role in the eukaryotic DNA damage response. Few cell cycle checkpoint proteins have been examined in aquatic organisms, and this study is the first to characterize CHK2 expression in a fish species. CHK2 was cloned from Oncorhynchus mykiss, the rainbow trout. The coding region extends over 5741 nucleotides in the genome, including 13 introns, and specifies a predicted 533 amino acid protein. Southern blot analysis revealed that CHK2 exists as a single copy in the rainbow trout genome. Recombinant protein representing the FHA domain was used to generate polyclonal anti-CHK2 antibodies. While CHK2 transcript levels were relatively low in gill and high in brain, the opposite was true for protein levels. Both gill and brain cell cultures were treated with bleomycin, which induces double-strand DNA breaks. There was no effect on levels of CHK2 in gill cells, suggesting that the protein is constitutively active in this tissue. In contrast, brain cells upregulated CHK2 in a dose-dependent manner. The tissue specific expression of CHK2 and its ability to respond to bleomycin treatment suggests that some checkpoint proteins may serve as suitable biomarkers for DNA damage in rainbow trout and other fish species.

Genes associated with an effective host response by Chinook salmon to Renibacterium salmoninarum

An effective host response to Renibacterium salmoninarum, the etiologic agent of bacterial kidney disease, is poorly characterized. Using suppression subtractive hybridization, we exploited the difference in early host response in the pronephros of fish challenged by an attenuated strain (MT239) or a virulent strain (ATCC 33209) of R. salmoninarum. Among the 132 expressed sequence tag (EST) clones that were sequenced, 20 were selected for expression analysis at 24 and 72h after challenge. ESTs matching two interferon inducible genes (IFN-inducible GBP and VLIG1), the ligand GAS6, and the kinase VRK2 were upregulated in fish exposed to MT239, but downregulated or unchanged in fish exposed to 33209. A second group of ESTs matching genes involved in apoptosis (caspase 8) and immune function (IkappaBalpha, p47(phoX), EMR/CD97) were more slowly upregulated in fish exposed to 33209 compared to fish exposed to MT239. The ESTs displaying elevated expression in MT239-exposed fish may represent important cellular processes to bacterial challenge, and may be useful indicators of an effective host response to R. salmoninarum infection.

Comprehensive gene expression profiling following DNA vaccination of rainbow trout against infectious hematopoietic necrosis virus

The DNA vaccine based on the glycoprotein gene of Infectious hematopoietic necrosis virus induces a non-specific anti-viral immune response and long-term specific immunity against IHNV. This study characterized gene expression responses associated with the early anti-viral response. Homozygous rainbow trout were injected intra-muscularly (I.M.) with vector DNA or the IHNV DNA vaccine. Gene expression in muscle tissue (I.M. site) was evaluated using a 16,008 feature salmon cDNA microarray. Eighty different genes were significantly modulated in the vector DNA group while 910 genes were modulated in the IHNV DNA vaccinate group relative to control group. Quantitative reverse-transcriptase PCR was used to examine expression of selected immune genes at the I.M. site and in other secondary tissues. In the localized response (I.M. site), the magnitudes of gene expression changes were much greater in the vaccinate group relative to the vector DNA group for the majority of genes analyzed. At secondary systemic sites (e.g. gill, kidney and spleen), type I IFN-related genes were up-regulated in only the IHNV DNA vaccinated group. The results presented here suggest that the IHNV DNA vaccine induces up-regulation of the type I IFN system across multiple tissues, which is the functional basis of early anti-viral immunity.

Molecular cloning and characterization of CD9 cDNA from cartilaginous fish, red stingray, Dasyatis akajei

CD9 is a glycoprotein of the transmembrane 4 superfamily (TM4SF) and is involved in various cellular processes. In this study, we describe the isolation of the full-length cDNA encoding for CD9 molecule (daCD9) of red stingray, Dasyatis akajei. This 1252 bp cDNA was isolated from leukocyte cDNA library and contains 681 bp open reading frame encoding 226 amino acid residues. Amino acid sequences analysis and structure prediction display approximately 50% identity to higher vertebrates with the presence of conserved structures, including the four transmembrane domains and certain characteristic residues. Southern blot analysis shows that daCD9 exists as a single copy gene. Northern blot analysis reveals that daCD9 is highly expressed in gill and spleen although its expression can be found in other tissues suggesting daCD9 might play an important role in immune defense in this fish.

Homologs of CD83 from elasmobranch and teleost fish

Dendritic cells are one of the most important cell types connecting innate and adaptive immunity, but very little is known about their evolutionary origins. To begin to study dendritic cells from lower vertebrates, we isolated and characterized CD83 from the nurse shark (Ginglymostoma cirratum (Gici)) and rainbow trout (Oncorhynchus mykiss (Onmy)). The open reading frames for Gici-CD83 (194 aa) and Onmy-CD83 (218 aa) display approximately 28-32% identity to mammalian CD83 with the presence of two conserved N-linked glycosylation sites. Identical with mammalian CD83 genes, Gici-CD83 is composed of five exons including conservation of phase for the splice sites. Mammalian CD83 genes contain a split Ig superfamily V domain that represents a unique sequence feature for CD83 genes, a feature conserved in both Gici- and Onmy-CD83. Gici-CD83 and Onmy-CD83 are not linked to the MHC, an attribute shared with mouse but not human CD83. Gici-CD83 is expressed rather ubiquitously with highest levels in the epigonal tissue, a primary site for lymphopoiesis in the nurse shark, whereas Onmy-CD83 mRNA expression largely paralleled that of MHC class II but at lower levels. Finally, Onmy-CD83 gene expression is up-regulated in virus-infected trout, and the promoter is responsive to trout IFN regulatory factor-1. These results suggest that the role of CD83, an adhesion molecule for cell-mediated immunity, has been conserved over 450 million years of vertebrate evolution.

Differential gene expression analysis in fish exposed to endocrine disrupting compounds

This review discusses various methodologies that can be used to understand, at the gene level, the consequences to fish upon exposure to endocrine disrupting compounds (EDCs). Several approaches for measuring expression of gene transcripts are discussed, including directed approaches, such as Northern blotting and quantitative reverse transcriptase polymerase chain reaction (RT-PCR) as well as open-ended approaches, such as differential display RT-PCR, subtractive hybridizations, and gene arrays. Each of these systems has advantages and disadvantages, strengths and weaknesses. Conducting experiments with each of these methods provides important information about the molecular mechanisms that result from exposure to EDCs, information which can be used in risk assessment of polluted sites found in the environment.

Granzyme M Mediates a Novel Form of Perforin-dependent Cell Death

Cell death is mediated by cytotoxic lymphocytes through various granule serine proteases released with perforin. The unique protease activity, restricted expression, and distinct gene locus of granzyme M suggested this enzyme might have a novel biological function or trigger a novel form of cell death. Herein, we demonstrate that in the presence of perforin, the protease activity of granzyme M rapidly and effectively induces target cell death. In contrast to granzyme B, cell death induced by granzyme M does not feature obvious DNA fragmentation, occurs independently of caspases, caspase activation, and perturbation of mitochondria and is not inhibited by overexpression of Bcl-2. These data raise the likelihood that granzyme M represents a third major and specialized perforin-dependent cell death pathway that plays a significant role in death mediated by NK cells.

Molecular cloning and characterization of calreticulin from rainbow trout ( Oncorhynchus mykiss)

Calreticulin (CRT) is a highly conserved, high-capacity, calcium-binding protein shared among vertebrates, invertebrates and higher plants. Its biological importance, highlighted by its highly conserved nature, is supported by its crucial physiological and immunological functions. Within the endoplasmic reticulum, CRT serves as a calcium modulator and a lectin-like chaperone for glycoproteins, especially class I major histocompatibility receptors. To date, CRT cDNA clones have been isolated from a wide range of phyla, yet little is known about this gene in fish species, the largest and most diverse group of jawed vertebrates. This report describes the cloning of a cDNA from a rainbow trout pronephros library that encodes a deduced 419-amino acid protein, which includes a predicted 20-amino acid signal peptide and has a 69% amino acid identity to both murine and human CRT. Like its mammalian counterparts, this cDNA contains conserved cysteine residues believed to form a disulphide bond, a proline-rich region which includes a potential N-glycosylation site, and a highly acidic C-terminal domain terminating with the endoplasmic reticulum retrieval sequence, KDEL. Reverse transcription tissue-distribution assays indicate it is ubiquitously expressed in all tissues tested with highest expression in liver, while Southern blotting indicates it is a single copy gene.

Genomic cloning of novel isotypes of the rainbow trout interleukin-8

A cDNA clone, designated IL-8nL, was obtained by suppression subtractive hybridisation between lipopolysaccharide-stimulated and non-stimulated populations of the rainbow trout macrophage-like cell line, RTS11. IL-8nL was similar but not identical to a recently published sequence of the gene encoding rainbow trout interleukin-8 (IL-8). Amplification of genomic DNA by the polymerase chain reaction (genomic PCR) using a single outbred trout with common primers in the 5' and 3' untranslated regions gave six distinct genomic sequences, including one ( IL-8A) almost identical to that of the published IL-8 gene and another identical to IL-8nL. The other four clones were termed IL-8B, IL-8C, IL-8D and IL-8E. The deduced amino acid sequences of IL-8A through IL-8E are all identical to the published IL-8, while the IL-8nL protein has a substitution of Arg87 to Lys. Analysis of ten outbred trout by genomic PCR of a repeat region in exon 4, which has three different sizes in the above alleles, revealed a shorter, fourth fragment termed IL-8X and another of the same size as IL-8nL, but with a different single nucleotide replacement, called IL-8nL2. These results, together with a Southern blot of the same ten individuals showing up to five bands, indicate that rainbow trout has at least four copies of the IL-8 gene. Like IL-8nL, IL-8X lacks the repeat sequence in exon 4 and encodes a protein identical to IL-8nL protein. Polymerase chain reaction of the repeat region was useful for typing rainbow trout into four categories, and the type III and IV fish have a new allele, IL-8F, which lacks one repeat unit compared with IL-8A.