Gonadal development and fertility of triploid grass puffer Takifugu niphobles induced by cold shock treatment

Tiger puffer Takifugu rubripes is one of the most valuable fish species in Japan; however, there has not been much progress in their selective breeding until recently despite their potential in aquaculture. Their long generation time and the large body size of their broodstock make breeding difficult. Recently, we made a surrogate broodstock, which produced gametes of different species in salmonids. Therefore, by using closely related recipients, which have small body sizes and short generation times, it is possible to accelerate breeding of the tiger puffer. Thus, we considered the grass puffer Takifugu niphobles, which has a short generation time and a small maturation size, as a potential recipient for gamete production of the tiger puffer. Furthermore, if sterile triploid individuals are used as recipients, the resulting surrogate broodstock would produce only donor-derived gametes. Therefore, we examined conditions for inducing triploidy by suppressing meiosis II to retain the second polar body in grass puffer. We found that cold shock treatment, which is 5°C for 30 min starting from 5 min after fertilization, is optimal to obtain high triploidization and hatching rates. Although the resulting triploid grass puffers produced small amounts of gametes in both sexes, the offspring derived from the gametes could not live for over 3 days. Furthermore, we found that triploid grass puffer showed normal plasma sex steroid levels compared with diploids. These are important characteristics of triploid grass puffer as surrogate recipients used for germ cell transplantation.

A trans-species missense SNP in Amhr2 is associated with sex determination in the tiger pufferfish, Takifugu rubripes (fugu)

Heterogametic sex chromosomes have evolved independently in various lineages of vertebrates. Such sex chromosome pairs often contain nonrecombining regions, with one of the chromosomes harboring a master sex-determining (SD) gene. It is hypothesized that these sex chromosomes evolved from a pair of autosomes that diverged after acquiring the SD gene. By linkage and association mapping of the SD locus in fugu (Takifugu rubripes), we show that a SNP (C/G) in the anti-Müllerian hormone receptor type II (Amhr2) gene is the only polymorphism associated with phenotypic sex. This SNP changes an amino acid (His/Asp384) in the kinase domain. While females are homozygous (His/His384), males are heterozygous. Sex in fugu is most likely determined by a combination of the two alleles of Amhr2. Consistent with this model, the medaka hotei mutant carrying a substitution in the kinase domain of Amhr2 causes a female phenotype. The association of the Amhr2 SNP with phenotypic sex is conserved in two other species of Takifugu but not in Tetraodon. The fugu SD locus shows no sign of recombination suppression between X and Y chromosomes. Thus, fugu sex chromosomes represent an unusual example of proto–sex chromosomes. Such undifferentiated X-Y chromosomes may be more common in vertebrates than previously thought.

Diverse systems of sex determination have evolved independently in the animal and plant kingdoms. In vertebrates, so far four master sex-determining (SD) genes, Sry, Dmrt1, Dmy, and Dm-W, have been identified. These genes code for transcription factors and are located on only one of the sex chromosomes surrounded by nonrecombining regions. It is hypothesized that these sex chromosomes evolved from a pair of homologous chromosomes that diverged after acquiring the SD gene. We investigated the SD locus in fugu by high-resolution genetic mapping and association mapping. We found that a SNP that changes an amino acid (His/Asp384) in the kinase domain of anti-Müllerian hormone receptor type II (Amhr2) is perfectly associated with phenotypic sex. A combination of the two alleles of the SNP (homozygous females and heterozygous males) is likely to be responsible for sex determination in fugu. While these alleles are conserved in two other species of Takifugu, they are absent in the freshwater pufferfish, Tetraodon. Furthermore, Fugu Amhr2 lies in a region that shows no evidence for recombination suppression between X and Y chromosomes. Thus, fugu sex chromosomes represent an unusual example of a pre-differentiated phase of sex chromosomes in vertebrates.

O2-filled swimbladder employs monocarboxylate transporters for the generation of O2 by lactate-induced root effect hemoglobin

The swimbladder volume is regulated by O₂ transfer between the luminal space and the blood In the swimbladder, lactic acid generation by anaerobic glycolysis in the gas gland epithelial cells and its recycling through the rete mirabile bundles of countercurrent capillaries are essential for local blood acidification and oxygen liberation from hemoglobin by the “Root effect.” While O₂ generation is critical for fish flotation, the molecular mechanism of the secretion and recycling of lactic acid in this critical process is not clear. To clarify molecules that are involved in the blood acidification and visualize the route of lactic acid movement, we analyzed the expression of 17 members of the H⁺/monocarboxylate transporter (MCT) family in the fugu genome and found that only MCT1b and MCT4b are highly expressed in the fugu swimbladder. Electrophysiological analyses demonstrated that MCT1b is a high-affinity lactate transporter whereas MCT4b is a low-affinity/high-conductance lactate transporter. Immunohistochemistry demonstrated that (i) MCT4b expresses in gas gland cells together with the glycolytic enzyme GAPDH at high level and mediate lactic acid secretion by gas gland cells, and (ii) MCT1b expresses in arterial, but not venous, capillary endothelial cells in rete mirabile and mediates recycling of lactic acid in the rete mirabile by solute-specific transcellular transport. These results clarified the mechanism of the blood acidification in the swimbladder by spatially organized two lactic acid transporters MCT4b and MCT1b.

Characterization and functional analysis of two PKR genes in fugu (Takifugu rubripes)

PKR (protein kinase R) is a serine-threonine kinase that inhibits protein synthesis by the phosphorylation of the eukaryotic translation initiation factor 2-alpha (eIF2α), and activates NFκB by inducing NFκB-inducing kinase and IκB (inhibitor of NFκB) kinase. This can lead to antiviral and anti-proliferative effects. In this study, the complete sequence and organization of two fugu PKR genes (fPKRs) were determined by in silico analysis and conventional PCR. The full-length fPKR1 and fPKR2 genes were 3832 bp and 4325 bp, which encoded 523 and 492 amino acids, respectively. Both encoded two dsRNA binding domains and a Serine/Threonine protein kinase domain, and showed very high similarity to green spotted puffer PKRs. Gene expression of the two fPKRs was measured by quantitative real-time PCR on tissue samples from healthy fish and peripheral blood leukocytes stimulated with polyinosinic:polycytidylic acid (PolyI:C) or lipopolysaccharides (LPS). The fPKRs were highly expressed in the skin and fPKR2 was significantly induced in PBLs by PolyI:C but not by LPS. The fPKRs inhibited translation of a luciferase reporter gene in a dose-dependent manner and induced transcriptional activity of a mammalian NFκB luciferase reporter. These results demonstrate that two PKRs in a single species can both be independently, but not equally, functional and support the hypothesis that fish PKRs have roles in the innate immune response similar to those of mammalian PKRs.

STATISTICAL INFORMATION CHARACTERIZATION OF CONSERVED NON-CODING ELEMENTS IN VERTEBRATES

Recently, a set of highly conserved non-coding elements (CNEs) has been derived from a comparison between the genomes of the puffer fish, Takifugu or Fugu rubripes, and man. In order to facilitate the identification of these conserved elements in silico, we characterize them by a number of statistical features.

We found a pronounced information pattern around CNE borders; although the CNEs themselves are AT rich and have high entropy (complexity), they are flanked by GC-rich regions of low entropy (complexity). We also identified the most abundant motifs within and around of CNEs, and identified those that group around their borders. Like in human promoter regions, the TBP, NF-Y and some other binding motifs are clustered around CNE boundaries, which may suggest a possible transcription regulatory function of CNEs.

Patterns of positive selection and neutral evolution in the protein-coding genes of Tetraodon and Takifugu

Recent genome-wide analyses have revealed patterns of positive selection acting on protein-coding genes in humans and mammals. To assess whether the conclusions drawn from these analyses are valid for other vertebrates and to identify mammalian specificities, I have investigated the selective pressure acting on protein-coding genes of the puffer fishes Tetraodon and Takifugu. My results indicate that the strength of purifying selection in puffer fishes is similar to previous reports for murids but stronger in hominids, which have a smaller population size. Gene ontology analyses show that more than half of the biological processes targeted by positive selection in mammals are also targeted in puffer fishes, highlighting general patterns for vertebrates. Biological processes enriched with positively selected genes that are shared between mammals and fishes include immune and defense responses, signal transduction, regulation of transcription and several of their descendent terms. Mammalian-specific processes displaying an excess of positively selected genes are related to sensory perception and neurological processes. The comparative analyses also revealed that, for both mammals and fishes, genes encoding extracellular proteins are preferentially targeted by positive selection, indicating that adaptive evolution occurs more often in the extra-cellular environment rather than inside the cell. Moreover, I present here the first genome-wide characterization of neutrally-evolving regions of protein-coding genes. This analysis revealed an unexpectedly high proportion of genes containing both positively selected motifs and neutrally-evolving regions, uncovering a strong link between neutral evolution and positive selection. I speculate that neutrally-evolving regions are a major source of novelties screened by natural selection.

Molecular cloning, functional characterization and phylogenetic analysis of TRAIL in Japanese pufferfish Takifugu rubripes

In this study, the complementary DNA (cDNA) of Japanese pufferfish Takifugu rubripes tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) was cloned by reverse-transcription PCR. The open reading frame of the TRAIL consisted of 870 bases. The deduced amino-acid sequence of the TRAIL showed a high homology with the sequences of other teleosts. Recombinant soluble TRAIL was fused with a small ubiquitin-related modifier gene to enhance the soluble expression level in Escherichia coli BL21 (DE3). In vitro, the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrasodium bromide (MTT) assay indicated that the purified soluble TRAIL was able to induce apoptosis of Jurkat and HeLa cells in a dose-dependent manner.

Molecular structure, expression and bioactivity characterization of TNF13B (BAFF) gene in mefugu, Takifugu obscurus

B-cell activating factor of the TNF family (BAFF) induces B-cell survival, proliferation, immunoglobulin secretion and plays a role in enhancing immune responses. In the present study, a BAFF homolog has been identified in mefugu Takifugu obscurus, and its biological activities have been characterized. The mefugu BAFF (fBAFF) cDNA is 789 bp in length and translates into a 262-aa protein. The fBAFF genomic sequence consists of six exons and five introns, is approximately 1.8 kb in size. Amino acid sequence comparison indicated that fBAFF possessed the TNF signatures, a transmembrane domain, a putative furin protease cleavage site and three cysteine residues, which were the typical characteristics of TNF gene in mammals and birds. The predicted three-dimensional (3D) structure of the fsBAFF monomer analyzed by comparative protein modeling revealed that it was very similar to its human counterpart. Real-time quantitative PCR (qPCR) analysis revealed that fBAFF was predominantly expressed in mefugu lymphoid tissue spleen. The SUMO-fsBAFF and GFP/fsBAFF efficiently expressed in Escherichia coli Rosetta (DE3) were confirmed by SDS-PAGE and Western blotting analysis. After purification, the GFP/fsBAFF fusion protein obtained similar fluorescence spectrum to those of GFP. Laser scanning confocal microscopy analysis showed GFP/fsBAFF could bind to its receptors. In vitro, the MTT assays and flow cytometric analysis indicated that SUMO-fsBAFF could promote the proliferation of mefugu splenocytes or mouse splenic B cells together with/without anti-mouse IgM. These findings indicate that SUMO-fsBAFF plays an important role in proliferation of mefugu B cells and has functional cross-reactivity among mefugu and other mammalians. Therefore, BAFF may be a potential immunologic factor for enhancing immunological efficacy in fish.

Effect of cadmium exposure on expression of antioxidant gene transcripts in the river pufferfish, Takifugu obscurus (Tetraodontiformes)

Cadmium (Cd) is a non-essential toxic heavy metal with the potential to induce oxidative stress. Cd toxicity and its capacity for accumulation in aquatic habitats have earned its recognition as a pollutant of immediate and widespread concern. To obtain a better understanding of oxidative stress-associated gene expression in different tissues, six antioxidant genes such as catalase (CAT), glutathione reductase (GR), glutathione peroxidase 1a (GPx1a), glutathione peroxidase 1b (GPx1b), Cu/Zn superoxide dismutase (Cu/Zn-SOD), and Mn superoxide dismutase (Mn-SOD) were cloned and fully sequenced in the river pufferfish, Takifugu obscurus. On tissue specific mRNA expression, the liver showed the highest expression when compared to other tissues, even though each antioxidant gene showed different modes of expression patterns in the examined tissues. Of the various antioxidant genes, GR was the most highly expressed in the liver, followed by CAT, GPx1, and Cu/Zn-SOD. For the time-course experiment, all the antioxidant genes were significantly induced over time except for Cu/Zn-SOD in the liver, and there was a 5-fold induction in hepatic GR, CAT, and Mn-SOD mRNA compared to the control. These findings indicate that the liver of T. obscurus has a robust antioxidant system. In addition, these results suggest that Cd exposure modulates the expression of antioxidant genes, and would indicate that the antioxidant genes would be a relevant biomarker of trace metal pollution such as Cd exposure in T. obscurus.

Characterization of a hypoxia-response element in the Epo locus of the pufferfish, Takifugu rubripes

Animals respond to hypoxia by increasing synthesis of the glycoprotein hormone erythropoietin (Epo) which in turn stimulates the production of red blood cells. The gene encoding Epo has been recently cloned in teleost fishes such as the pufferfish Takifugu rubripes (fugu) and zebrafish (Danio rerio). It has been shown that the transcription levels of Epo in teleost fishes increase in response to anemia or hypoxia in a manner similar to its human ortholog. However, the cis-regulatory element(s) mediating the hypoxia response of Epo gene in fishes has not been identified. In the present study, using the human hepatoma cell line (Hep3B), we have identified and characterized a hypoxia response element (HRE) in the fugu Epo locus. The sequence of the fugu HRE (ACGTGCTG) is identical to that of the HRE in the human EPO locus. However, unlike the HRE in the mammalian Epo locus, which is located in the 3' region of the gene, the fugu HRE is located in the 5' flanking region and on the opposite strand of DNA. This HRE is conserved in other teleosts such as Tetraodon and zebrafish in a similar location. A 365-bp fragment containing the fugu HRE was able to drive GFP expression in the liver of transgenic zebrafish. However, we could not ascertain if the expression of transgene is induced by hypoxia in vivo due to the low and variable levels of GFP expression in transgenic zebrafish. Our investigations also revealed that the Epo locus has experienced extensive rearrangements during vertebrate evolution.

Isolation of seven IL-17 family genes from the Japanese pufferfish Takifugu rubripes

In humans, the IL-17 family is composed of six members (A-F). The A, E and F forms have been extensively studied in numerous mammalian species. However, there are few reports regarding IL-17 expression in teleost. In this study, IL-17 family genes were isolated from the Japanese pufferfish (Fugu) and their structure and expression profile were analyzed. Screening of the Fugu genome database revealed the existence of five scaffolds containing IL-17 family homologous genes. Scaffold_1 contained three IL-17 family homologues including IL-17A/F1, 2 and C2, and IL-17A/F1 and two located in tandem. This was similar to the IL-17A/F1 and two genes in zebrafish and to human IL-17A and F. Other scaffolds 38, 143 and 430, contained IL-17 family homologous genes that were identical to IL-17D, A/F3 and C1 in Fugu, respectively. Moreover, IL-17 family homologues on scaffold_264 included a novel type of IL-17 family genes in teleost. These isolates contained four cysteine residues that were involved in the formation of a typical cysteine knot consisting of two disulphide linkages. However, IL-17A/F2 did not demonstrate any conservation at the second and fourth cysteine residues. The tissue distribution of the Fugu IL-17 family genes was also found to differ. In particular, IL-17 family genes were highly expressed in the head kidney and gill. Moreover, expression of IL-17 family genes was significantly up-regulated in the lipopolysaccharide-stimulated head kidney. These results suggested that Fugu IL-17 family members were involved in inflammatory responses.

Molecular cloning, phylogenetic analysis and expression of a MAPEG superfamily gene from the pufferfish Takifugu obscurus

The microsomal glutathione S-transferases (MGSTs) of membrane-associated proteins in eicosanoid and glutathione metabolism (MAPEG) superfamily play an important role in xenobiotics detoxification. Compared to mammals, there is limited information on MAPEGS from fish. We cloned a full length of cDNA sequence of a MGST gene from the river pufferfish (Takifugu obscurus), studied its phylogenetic relationship, and measured its expression in different tissues and in liver of fish exposed to cadmium. Phylogenetic analysis revealed that the identified gene encoded for MGST3. Liver showed the highest expression of MGST3 transcripts. When MSGT expression was compared with the expression of other GSTs (GST-Alpha, GST-Mu and GST-Theta), a similar pattern of highest expression was observed in the liver. Upon Cd exposure (5 ppm) for 96 h, the highest expression of MGST was observed at 24 h. GST-Mu also showed highest expression at 24 h. These findings indicate that MGSTs may be playing a role in detoxification of xenobiotics or free radicals generated by Cd-induced oxidative stress in fish.

Hormones and receptors in fish: do duplicates matter?

Modern fish are the result of major changes in evolution including three possible duplications of the whole genome. Retained duplicate genes are often involved with metabolism, transcription, neurogenic processes and development. Here we examine the consequences of the most recent (350 mya) teleost-specific duplication in five fishes (zebrafish, fugu, medaka, stickleback and rainbow trout) in regard to duplicate copies of hormones and receptors in the secretin superfamily. This subset of genes was selected as the superfamily is limited to ten hormones and their receptors and includes some important members: glucagon, growth hormone-releasing hormone (GHRH), pituitary adenylate cyclase-activating polypeptide (PACAP) and vasoactive intestinal polypeptide (VIP). We used reports from the literature and an extensive database search of the fish genomes to evaluate the status of the superfamily and its duplicate genes. We found that all five fish species have an almost complete set of orthologs with the human superfamily of hormones, although they lack secretin and its receptor. Receptor orthologs are present in zebrafish, fugu, medaka, stickleback and to a lesser extent in salmonids. Zebrafish retain duplicate copies for seven hormones and five receptors. Duplicated genes in fugu, medaka, stickleback and salmonids are also present, based mainly on genome annotation or mRNA transcription. Separate chromosome locations and synteny support zebrafish duplicates as the result of large-scale duplications. Novel changes in fish include the modification of a duplicate glucagon receptor to a GLP-1 receptor and, unlike humans, the presence of bioactive and specific PHI and GHRH-like peptide receptors. We conclude that fish duplicates in the secretin superfamily are a rich, mostly unexplored area for endocrine research.

Evolutionary patterns and selective pressures of odorant/pheromone receptor gene families in teleost fishes

Background

Teleost fishes do not have a vomeronasal organ (VNO), and their vomeronasal receptors (V1Rs, V2Rs) are expressed in the main olfactory epithelium (MOE), as are odorant receptors (ORs) and trace amine-associated receptors (TAARs). In this study, to obtain insights into the functional distinction among the four chemosensory receptor families in teleost fishes, their evolutionary patterns were examined in zebrafish, medaka, stickleback, fugu, and spotted green pufferfish.

Methodology/Principal Findings

Phylogenetic analysis revealed that many lineage-specific gene gains and losses occurred in the teleost fish TAARs, whereas only a few gene gains and losses have taken place in the teleost fish vomeronasal receptors. In addition, synonymous and nonsynonymous nucleotide substitution rate ratios (K_A/K_S) in TAARs tended to be higher than those in ORs and V2Rs.

Conclusions/Significance

Frequent gene gains/losses and high K_A/K_S in teleost TAARs suggest that receptors in this family are used for detecting some species-specific chemicals such as pheromones. Conversely, conserved repertoires of V1R and V2R families in teleost fishes may imply that receptors in these families perceive common odorants for teleosts, such as amino acids. Teleost ORs showed intermediate evolutionary pattern between TAARs and vomeronasal receptors. Many teleost ORs seem to be used for common odorants, but some ORs may have evolved to recognize lineage-specific odors.

GC content increased at CpG flanking positions of fish genes compared with sea squirt orthologs as a mechanism for reducing impact of DNA methylation

Background

Fractional DNA methylation in sea squirts evolved to global DNA methylation in fish. The impact of global DNA methylation is reflected by more CpG depletions and/or more A/T to G/C changes at CpG flanking positions due to context-dependent mutations of methylated CpG sites.

Methods and Findings

In this report, we demonstrate that the sea squirt genes have undergone more CpG to TpG/CpA substitutions than the fish orthologs using homologous fragments from orthologous genes among Ciona intestinalis, Ciona savignyi, fugufish and zebrafish. To avoid premature transcription, the TGA sites derived from CGA were largely converted to TGG in sea squirt genes. By contrast, a significant increment of GC content at CpG flanking positions was shown in fish genes. The positively selected A/T to G/C substitutions, in combination with the CpG to TpG/CpA substitutions, are the sources of the extremely low CpG observed/expected ratios in vertebrates. The nonsynonymous substitutions caused by the GC content increase have resulted in frequent amino acid replacements in the directions that were not noticed previously.

Conclusion

The increased GC content at CpG flanking positions can reduce CpG loss in fish genes and attenuate the impact of DNA methylation on CpG-containing codons, probably accounting for evolution towards vertebrates.

Ancient and modern duplication events and the evolution of stearoyl-CoA desaturases in teleost fishes

Stearoyl-CoA desaturases (SCDs) are key enzymes of fatty acid biosynthesis whose regulation underpins responses to dietary, thermal, and hormonal treatment. Although two isoforms are known to exist in the common carp and human and four in mouse, there is no coherent view on how this gene family evolved to generate functionally diverse members. Here we identify numerous new SCD homologs in teleost fishes, using sequence data from expressed sequence tag (EST) and cDNA collections and genomic model species. Phylogenetic analyses of the deduced coding sequences produced only partially resolved molecular trees. The multiple SCD isoforms were, however, consistent with having arisen by an ancient gene duplication event in teleost fishes together with a more recent duplication in the tetraploid carp and possibly also salmonid lineages. Critical support for this interpretation comes from comparison across all vertebrate groups of the gene order in the genomic environments of the SCD isoforms. Using syntenically aligned chromosomal fragments from large-insert clones of common carp and grass carp together with those from genomically sequenced model species, we show that the ancient and modern SCD duplication events in the carp lineage were each associated with large chromosomal segment duplications, both possibly linked to whole genome duplications. By contrast, the four mouse isoforms likely arose by tandem duplications. Each duplication in the carp lineage gave rise to differentially expressed SCD isoforms, either induced by cold or diet as previously shown for the recent duplicated carp isoforms or tissue specific as demonstrated here for the ancient duplicate zebrafish isoforms.

Transcript expression profiles of Takifugu rubripes spermatozoa and eggs by expressed sequence tag analysis

Two cDNA libraries from Takifugu rubripes spermatozoa and eggs were constructed and a total of 620 expressed sequence tag (EST) clones were generated from the two libraries: 300 clones are from the spermatozoa library and 320 clones are from the eggs library. The most abundant cDNA clones in the two libraries were identified. A total of 207 'contigs' (or single) EST clones were found to share significant sequence identity with known sequences in the GenBank database, representing at least 51 different genes. In order to understand the two types of germ cells further, the expression profiles of the identified clones in these cDNA libraries were analyzed. Furthermore, the presence of specific messenger RNAs in the spermatozoa and eggs has been demonstrated with BLAST analysis; the spermatozoa and egg library can supply unique and novel cDNA sequences in the Takifugu rubripes EST project. Another aim of this study is to identify cDNA clones that can be used as molecular markers for the analysis of the spermatogenesis and oogenesis in Takifugu rubripes. Six potential clones (S1-3 from spermatozoa and E1-3 from eggs) were selected to analyze their expression patterns by reverse transcription (RT)-PCR analyses. Half of these showed a specific expression in the expected tissue. Two of the clones were found by RT-PCR and in situ hybridization to be expressed specifically in the testis or ovary, and they maybe suitable molecular markers for the analysis of spermatogenesis and oogenesis.

Genomic characterization and tissue distribution of leptin receptor and leptin receptor overlapping transcript genes in the pufferfish, Takifugu rubripes

Full-length cDNAs encoding the leptin receptor (tfLEPR), leptin receptor overlapping transcript (tfLEPROT) and leptin receptor overlapping transcript-like 1 (tfLEPROTL1) were cloned and sequenced from the pufferfish, Takifugurubripes. The tfLEPR gene encoded an 1116-amino acid protein that includes almost all functionally important domains conserved among vertebrate LEPR such as three fibronectin type III domains, the immunoglobulin (Ig) C2-like domain and a pair of repeated tryptophan/serine motifs. The tfLEPR mRNA was abundantly expressed in the pituitary and ovary and moderately expressed in brain, eye, heart, kidney, liver and testis. Both tfLEPROT and tfLEPROTL1 genes encoded a 130-amino acid protein. Human LEPR gene shares the first and second exons with the LEPROT gene, and they are continuously located on chromosome 1p31. In contrast, TakifuguLEPR and LEPROT were located at different regions of the chromosome. However, both Takifugu regions showed genomic synteny with the human genome around LEPR gene on chromosome 1p31. This result could mean that the Takifugu chromosomes around LEPR and LEPROT genes are paralogous genomic regions derived from genome duplication early in the teleost lineage and the overlapping LEPR and LEPROT genes were subsequently lost.

Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: A comparative analysis of the protocadherin cluster

Cartilaginous fishes are the oldest living phylogenetic group of jawed vertebrates. Here, we demonstrate the value of cartilaginous fish sequences in reconstructing the evolutionary history of vertebrate genomes by sequencing the protocadherin cluster in the relatively small genome (910 Mb) of the elephant shark (Callorhinchus milii). Human and coelacanth contain a single protocadherin cluster with 53 and 49 genes, respectively, that are organized in three subclusters, Pcdhalpha, Pcdhbeta, and Pcdhgamma, whereas the duplicated protocadherin clusters in fugu and zebrafish contain >77 and 107 genes, respectively, that are organized in Pcdhalpha and Pcdhgamma subclusters. By contrast, the elephant shark contains a single protocadherin cluster with 47 genes organized in four subclusters (Pcdhdelta, Pcdhepsilon, Pcdhmu, and Pcdhnu). By comparison with elephant shark sequences, we discovered a Pcdhdelta subcluster in teleost fishes, coelacanth, Xenopus, and chicken. Our results suggest that the protocadherin cluster in the ancestral jawed vertebrate contained more subclusters than modern vertebrates, and the evolution of the protocadherin cluster is characterized by lineage-specific differential loss of entire subclusters of genes. In contrast to teleost fish and mammalian protocadherin genes that have undergone gene conversion events, elephant shark protocadherin genes have experienced very little gene conversion. The syntenic block of genes in the elephant shark protocadherin locus is well conserved in human but disrupted in fugu. Thus, the elephant shark genome appears to be less prone to rearrangements compared with teleost fish genomes. The small and "stable" genome of the elephant shark is a valuable reference for understanding the evolution of vertebrate genomes.

Molecular cloning and beta-naphthoflavone-induced expression of a cytochrome P450 1A (CYP1A) gene from an anadromous river pufferfish, Takifugu obscurus

In recent years, there has been a decline in the wild populations of river pufferfish, Takifugu obscurus. Besides overexploitation for commercial purposes, environmental pollution is believed to have contributed to its decline. However, almost no information exists about genes involved in metabolism of xenobiotics by this species. Nevertheless, there is interest in fugu fishes, since they possess the smallest genome among vertebrates. We cloned and characterized the full-length cDNA sequence of a cytochrome P450 1A (CYP1A) gene from T. obscurus. Phylogenic relationship of T. obscurus CYP1A was also compared to other fish species. The tissue distribution and time-dependant induction of CYP1A mRNA were studied by real-time PCR in T. obscurus exposed to an aryl hydrocarbon receptor (Ahr) agonist, beta-naphthoflavone (BNF). The greatest basal expression in livers of control as well as BNF-treated individuals. However, brain, gill, gonad, intestine, and kidney also expressed CYP1A. Muscles expressed the least CYP1A. The results of the time-course study revealed induction in brain and gills after 6h and at 12h in most tissues. Except for gills, all other organs retained induced expression of CYP1A mRNA up to 96h.

Structure of neurohypophysial hormone genes and changes in the levels of expression during spawning season in grass puffer (Takifugu niphobles)

Vasotocin (VT) has been shown to influence various aspects of social and sexual behaviors in a broad range of vertebrate species, but less is known about the mechanisms through which this peptide modulates behavior. Additionally, much less is known about roles of isotocin (IT) in regulation of behavior. Grass puffer, Takifugu niphobles, has unique spawning behavior; spawning occurs on beach only for several days around the spring tide and is conducted by a group of 10-60 individuals, of which one is female. As a first step toward investigating the roles of VT and IT in this species' spawning behavior, we determined the structures of the VT and IT genes from grass puffer using the genome resources of the closely related tiger puffer and green puffer. We then used these sequences to develop real-time PCR assays and examined changes in expression of the VT and IT genes over the spawning season. The structures of VT and IT genes are well conserved among three puffer species. Particularly, the sequence similarities between grass and tiger puffers were very high not only in the coding region (85-99%), but also in the non-coding regions (92-98%) that include the 5'-upstream regions. The levels of expression of VT gene increased in the brain of pre-spawning females. The levels of VT mRNA in the spawning females tended to be higher than that in the spawning males. In contrast, the levels of IT mRNA did not show such variation. The present results suggest that VT gene expression augments in the brain of females during the spawning period. The unique spawning behavior of grass puffer provides a useful model for studying the molecular mechanism of sexual behavior utilizing the genome resources of tiger puffer.

Description of a fugu CXC chemokine and two CXC receptor genes, and characterization of the effects of different stimulators on their expression

The primary structures of a CXC chemokine (CXCL8) and two CXC receptors (CXCR) have been characterized in fugu, Takifugu rubripes. Unlike mammalian and avian species, CXCL8 of teleosts including fugu lacks the ELR motif that appears to be important in ligand/receptor interactions on neutrophils. Genomic organization shows that fugu CXCL8 gene consists of four exons and three introns. As in other vertebrates, two CXCR genes isolated from fugu encode proteins CXCR1 and CXCR2 that possess characteristic seven transmembrane domains. Each receptor consists of two exons separated by an intron. Synteny analysis indicates that these two CXCRs were derived from whole genome duplication in teleosts, differing from mammalian CXCR1 and CXCR2. All of these genes are primarily expressed in the lymphoid tissues. Immune stimulation with PHA showed that the expression of both CXCL8 and CXCRs in PBL are upregulated even after only a short time period, but downregulated by LPS stimulation, implying that these genes are involved in the regulation of the immune response in fugu.

Comparative genomics using Fugu reveals insights into regulatory subfunctionalization

Fish-mammal genomic alignments were used to compare over 800 conserved non-coding elements that associate with genes that have undergone fish-specific duplication and retention, revealing a pattern of element retention and loss between paralogs indicative of subfunctionalization.

Background

A major mechanism for the preservation of gene duplicates in the genome is thought to be mediated via loss or modification of cis-regulatory subfunctions between paralogs following duplication (a process known as regulatory subfunctionalization). Despite a number of gene expression studies that support this mechanism, no comprehensive analysis of regulatory subfunctionalization has been undertaken at the level of the distal cis-regulatory modules involved. We have exploited fish-mammal genomic alignments to identify and compare more than 800 conserved non-coding elements (CNEs) that associate with genes that have undergone fish-specific duplication and retention.

Results

Using the abundance of duplicated genes within the Fugu genome, we selected seven pairs of teleost-specific paralogs involved in early vertebrate development, each containing clusters of CNEs in their vicinity. CNEs present around each Fugu duplicated gene were identified using multiple alignments of orthologous regions between single-copy mammalian orthologs (representing the ancestral locus) and each fish duplicated region in turn. Comparative analysis reveals a pattern of element retention and loss between paralogs indicative of subfunctionalization, the extent of which differs between duplicate pairs. In addition to complete loss of specific regulatory elements, a number of CNEs have been retained in both regions but may be responsible for more subtle levels of subfunctionalization through sequence divergence.

Conclusion

Comparative analysis of conserved elements between duplicated genes provides a powerful approach for studying regulatory subfunctionalization at the level of the regulatory elements involved.

Genomic organization and expression of CD8alpha and CD8beta genes in fugu Takifugu rubripes

We have cloned cDNAs encoding the alpha and beta chains of CD8 from the tiger pufferfish (fugu), Takifugu rubripes. The cDNA sequences encode a putative leader peptide, extracellular immunoglobulin variable region-like domain, stalk region, transmembrane region, and cytoplasmic tail. A protein tyrosine kinase p56lck binding motif was not found in the putative fugu CD8alpha cytoplasmic tail. O-linked glycosylation sites were found in the stalk of both CD8 chains, suggesting possible stalk formation. Phylogenetic analysis showed that fugu CD8alpha and CD8beta chains cluster with other vertebrate CD8alpha and CD8beta chains, respectively. The fugu CD8 genes comprise six exons separated by five introns. The genes are tandemly aligned 3.6 kb apart and are in the same transcription orientation. Quantitative RT-PCR analysis demonstrated that fugu CD8 is expressed predominantly in lymphoid tissues. In situ hybridization showed that fugu CD8 genes are expressed in thymocytes and lymphocytes within lymphoid organs. Molecular characterization of CD8 in fish provides the basis for development of specific antibodies to identify T-cell subsets, as well as potentially important insights into the evolution of CD8 and the adaptive immunity.

CG dinucleotide clustering is a species-specific property of the genome

Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters.