Molecular characterization and expression of the teleost cytosolic DNA sensor genes cGAS, LSm14A, DHX9, and DHX36 in Japanese medaka, Oryzias latipes

Numerous cytosolic DNA sensors (CDSs), which are very important for recognizing cytosolic dsDNA derived from intracellular viruses and bacteria, exist in mammals. However, teleost CDSs are poorly understood. In this study, four CDSs, including the cyclic GMP-AMP synthase (cGAS), Sm-like protein 14 homolog A (LSm14A), DEAH-box helicase (DHX) 9, and DHX36 genes were identified in Japanese medaka, Oryzias latipes, and their expression patterns were elucidated. The expression of these genes was upregulated in the intestines and kidney of CpG-ODN-stimulated medaka. The cGAS and LSm14A genes were significantly induced in the intestines, kidney, and spleen of formalin-killed Edwardsiella tarda-treated medaka; the DHX9 and DHX36 genes were not. cGAS gene expression was induced only in the intestines of live E. tarda-treated medaka. These results suggest that the transcription of four CDS genes of medaka responds to dsDNA stimulation, and cGAS is probably more important for the immune response against E. tarda infection.

Evolution of the sex-determining gene in the teleostean genus Oryzias

In the genetic sex determination of vertebrates, the gonadal sex depends on the combination of sex chromosomes that a zygote possesses. Despite the discovery of the sex-determining gene (SRY/Sry) in mammals in 1990s, the sex-determining gene in non-mammalian vertebrates remained an enigma for over a decade. In most mammals, the male-inducing master sex-determining gene is located on the Y chromosome and is therefore absent from XX females. A second sex-determining gene, Dmy, was described in the Oryzias latipes in 2002 and has a DNA-binding motif that is different from the motif in the mammalian sex-determining gene SRY or Sry. Dmy is also located on the Y chromosome and is therefore absent in XX females. Seven other sex-determining genes, including candidate genes, are now known in birds, a frog species, and 5 fish species. These findings over the past twenty years have increased our knowledge of sex-determining genes and sex chromosomes among vertebrates. Here, we review recent advances in our understanding of sex-determining genes and genetic sex determination systems in fish, especially those of the Oryzias species, which are described in detail. The facts suggest some patterns of how new sex-determining genes emerged and evolved. We believe that these facts are common not only in Oryzias but also in other fish species. This knowledge will help to elucidate the conserved mechanisms from which various sex-determining mechanisms have evolved.

Steroid responsive regulation of IFNγ2 alternative splicing and its possible role in germ cell proliferation in medaka

Interferon gamma (IFNγ) is an active player in estrogen dependent immuno-regulation of fish. The present work was aimed to characterize the alternatively spliced isoforms of IFNγ2 in the gonadal sex development in medaka. Phylogenetic analysis demonstrated that IFNγ2a and 2b were clustered with fish specific interferon gamma. Our in vitro promoter and mini-genome analysis data confirmed that alternative splicing of IFNγ2 is regulated by estrogens and androgens. Tissue distribution, quantitative PCR and ISH data demonstrated ubiquitous expression of IFNγ2a, while IFNγ2b was only expressed predominantly in female germ cells than males. This was further confirmed by germ cell specific GFP signals in the IFNγ2b-GFP over-expressed embryos and specific induction of IFNγ2b expression in the BrdU positive cells. All together our data suggest that steroid responsive alternatively spliced IFNγ2b isoforms might have some indirect roles in germ cell proliferation and thus can be an important candidate for immuno-reproductive interaction studies.

Toxicity of the veterinary sulfonamide antibiotic sulfamonomethoxine to five aquatic organisms

The purpose of this study was to investigate the acute and chronic toxicity of sulfamonomethoxine (SMM) to aquatic organisms to evaluate its impact at different trophic levels in the ecosystem. Regarding the growth inhibition of microalgae, SMM exhibited 72-h median effective concentration (EC50) values of 5.9mgL(-1) for freshwater Chlorella vulgaris and 9.7mgL(-1) for marine Isochrysis galbana. In a study on the cladocerans, SMM exhibited acute toxicity and 48-h median lethal concentrations of 48mgL(-1) for Daphnia magna and 283mgL(-1) for D. similis. An examination of chronic toxicity revealed that SMM inhibited the brook production of the cladocerans and exhibited 21-day EC50 values of 14.9mgL(-1) for D. magna and 41.9mgL(-1) for D. similis. This study investigated the potentially adverse effects of SMM on aquatic organisms and revealed that microalgae exhibited higher sensitivity to SMM than cladocerans did. The residue of SMM in water is recommended to be carefully evaluated to reduce ecological impacts after applied to cultured animals.

Cloning and developmental expression of kinesin superfamily7 (kif7) in the brackish medaka (Oryzias melastigma), a close relative of the Japanese medaka (Oryzias latipes)

kif7 is a member of the kinesin superfamily members which are molecular motor proteins that move along microtubules in a highly regulated manner through ATP hydrolysis. In this paper, we report on the cloning of the Oryziasmelastigmakif7 (omkif7) using primers designed according to the Japanese medaka (Oryziaslatipes) database. The cloned omkif7 has an open reading frame of 3762bp and is deduced to encode a polypeptide of 1254 amino acids that possesses the putative ATP-binding and microtubule-binding motifs in its motor domain at the N-terminal region. We characterized the cloned omkif7 by comparison with the zebrafish kif7. Both omkif7 and zebrafish kif7 are shown to be expressed in all embryonic stages and adult tissues examined with higher expression level in the testis and ovary. Whole-mount in situ hybridization revealed that the expression of omkif7 is ubiquitous during the early stages of embryonic development, but became more restrictive and localized to the brain, fin bud and eye at later development. This study suggested that the brackish O.melastigma can serve as a good seawater model organism for developmental studies by utilizing the resources developed from its close relative of the Japanese medaka.

The medaka draft genome and insights into vertebrate genome evolution

Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approximately 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.

Differential expression of anti-Müllerian hormone (amh) and anti-Müllerian hormone receptor type II (amhrII) in the teleost medaka

In mammals, the anti-Müllerian hormone (Amh) is responsible for the regression of the Müllerian ducts; therefore, Amh is an important factor of male sex differentiation. The amh gene has been cloned in various vertebrates, as well as in several teleost species. To date, all described species show a sexually dimorphic expression of amh during sex differentiation or at least in differentiated juvenile gonads. We have identified the medaka amh ortholog and examined its expression pattern. Medaka amh shows no sexually dimorphic expression pattern. It is expressed in both developing XY male and XX female gonads. In adult testes, amh is expressed in the Sertoli cells and in adult ovaries in granulosa cells surrounding the oocytes, like in mammals. To better understand the function of amh, we cloned the anti-Müllerian hormone receptor type II (amhrII) ortholog and compared its expression pattern with amh, aromatase (cyp19a1), and scp3. During gonad development, amhrII is coexpressed with medaka amh in somatic cells of the gonads and shows no sexually dimorphic expression. Only the expression level of the Amh type II receptor gene was decreased noticeably in adult female gonads. These results suggest that medaka Amh and AmhrII are involved in gonad formation and maintenance in both sexes.

Conservation and divergence of Bmp2a, Bmp2b, and Bmp4 expression patterns within and between dentitions of teleost fishes

The diversity of tooth location in teleost fishes provides an excellent system for comparing genetic divergence between teeth in different species (phylogenetic homologs) with divergence between teeth within one species (iterative homologs). We have chosen to examine the expression of three members of the bone morphogenetic protein (Bmp) family because they are known to play multiple roles in tooth development and evolution in tetrapod vertebrates. We characterized expression of Bmp2a, Bmp2b, and Bmp4 during the development of oral and pharyngeal dentitions in three species of teleost fishes, the zebrafish (Danio rerio), Mexican tetra (Astyanax mexicanus), and Japanese medaka (Oryzias latipes). We found that expression in teleosts is generally highly conserved, with minor differences found among both iteratively homologous and phylogenetically homologous teeth. Expression of orthologous genes differs in several ways between the teeth of teleost fishes and those of the mouse, but between these vertebrate groups the summed expression pattern of Bmp genes is highly conserved. Significantly, the toothless oral region of the zebrafish lacks Bmp expression domains found in teleosts with oral teeth, implicating these genes in evolutionary tooth loss. We conclude that Bmp expression has been largely conserved in vertebrate tooth development over evolutionary time, and that loss of Bmp expression is correlated with region-specific loss of the dentition in a major group of fishes.

Genetic structure of korean wild populations of the Medaka Oryzias latipes inferred from allozymic variation

Previous allozymic studies have revealed that Korean wild populations of Oryzias latipes have differentiated regionally, and are composed of two distinct groups, the East Korean Population and the China-West Korean Population. Recently, mitochondrial DNA (mtDNA) sequencing and restriction fragment length polymorphism (RFLP) analyses have confirmed these two groups, and shown that the distribution ranges of the two groups overlap in western Korea. In order to describe the detailed distributions of the two groups and the gene flow between them, genotypes of 13 allozymic loci were determined in 444 specimens from 96 localities in Korea. The two major groups were supported by remarkable allele frequency differences at six diagnostic loci: ACP*, AMY*, CK-A*, LDH-A*, PGM* and TF*. Individuals with the typical "eastern" genotype were mainly distributed in eastern and southern areas. In contrast, fish with the "western" genotype were predominant in the western area, and were further divided into two subgroups (the Han River and Geum River Subpopulations) by unique alleles at the ADH* locus. In the western coast, two distinct (eastern and western) genotypes were distributed in a mosaic fashion. This distribution pattern was identical to those from mtDNA analyses. Although the distribution patterns of the alleles at three loci (GPI-A*, LDH-C* and SOD*) showed introgressive conditions between the two groups, each population was nearly fixed as either the eastern or western genotype at all six diagnostic loci despite the proximity among samples. Therefore, it is suggested that some reproductive isolation mechanisms exist between the two groups in natural habitats.

Molecular phylogeny of the medaka fishes genus Oryzias (Beloniformes: Adrianichthyidae) based on nuclear and mitochondrial DNA sequences

The phylogenetic relationships among medaka fishes of 2 genera, Oryzias and Xenopoecilus, were studied using the nuclear tyrosinase and mitochondrial 12S and 16S rRNA genes. Of the 23 species currently described for these genera, 13 species of Oryzias and 2 species of Xenopoecilus were examined. The tree topologies obtained from the nuclear and mitochondrial data were consistent, indicating that Xenopoecilus is a polyphyletic genus nested within Oryzias. This result suggested the necessity for a systematic study and taxonomic revision of Xenopoecilus. The combined data analysis of all data partitions resulted in a well-resolved tree, with most internal branches supported by high statistical values. Based on our combined data phylogeny, we divided the Oryzias species into three major species groups, namely the latipes, javanicus, and celebensis groups. These three groups corresponded to the three chromosomal groups (biarmed, monoarmed, and fused chromosome groups) previously proposed from karyological analyses. The phylogeographic pattern suggests historical vicariance between Sulawesi Island and the continental shelf.

Novel evolutionary relationship among four fish model systems

Knowledge of the correct phylogenetic relationships among animals is crucial for the valid interpretation of evolutionary trends in biology. Zebrafish, medaka, pufferfish and cichilds are fish models for development, genomics and comparative genetics studies, although their phylogenetic relationships have not been tested rigorously. The results of phylogenomic analysis based on 20 nuclear protein-coding genes confirmed the basal placement of zebrafish in the fish phylogeny but revealed an unexpected relationship among the other three species, contrary to traditionally held systematic views based on morphology. Our analyses show that medaka (Beloniformes) and cichlids (Perciformes) appear to be more closely related to each other than either of them is to pufferfish (Tetraodontiformes), suggesting that a re-interpretation of some findings in comparative biology might be required. In addition, phylogenomic analyses show that fish typically have more copies of nuclear genes than land vertebrates, supporting the fish-specific genome duplication hypothesis.

Oryzias curvinotus has DMY, a gene that is required for male development in the medaka, O. latipes

DMY is a Y-specific DM-domain gene required for male development and appears to be the sex-determining gene in the teleost fish medaka, Oryzias latipes. Although the genomic region containing DMY appears to have originated through duplication of the DMRT1 region, it is unknown when the duplication occurred. Here we show that O. curvinotus also has the DMY gene on the Y chromosome, which is homologous to the Y chromosome of medaka, and that DMY is expressed in XY embryos. A phylogenetic tree based on the amino acid sequence including the DM-domain shows that DMY was derived from DMRT1 immediately before speciation of O. latipes and O. curvinotus.

Evidence for recent invasion of the medaka fish genome by the Tol2 transposable element

Tol2 is a transposable element of the terminal-inverted-repeat class, residing in the genome of the medaka fish Oryzias latipes. The genus Oryzias contains more than 10 species for which phylogenetic relationships have previously been estimated. To infer the history of Tol2 in this genus we performed genomic Southern blots and PCR analyses of 10 of the species. It was revealed that Tol2 occurs in 2 of the 10 species (O. curvinotus and O. latipes) and that the length and the restriction map structure of Tol2 are identical in the two cases. Further, sequencing analysis revealed an extremely low level of divergence compared with that in a nuclear gene. These results suggest recent incorporation of Tol2 into one or both of the two species, implying horizontal transfer of Tol2 from one species to the other or into them both from a common source.

Molecular cloning and linkage analysis of the Japanese medaka fish complement Bf/C2 gene

Evolutionary studies of complement factor B (Bf) and C2 in lower vertebrates have revealed the presence of the Bf/C2 common ancestor-like molecule in lamprey (cyclostome) and the Bf molecule encoded by the duplicated genes closely linked to the major histocompatibility complex (MHC) in Xenopus (amphibian). To further define when Bf/C2 gene duplication occurred and when linkage between the Bf/C2 gene and the MHC was established, we amplified the Bf/C2 sequences in teleost, the Japanese medaka (Oryzias latipes), by reverse transcription - polymerase chain reaction with primers corresponding to the common amino acid sequences shared by mammalian Bf and C2. Only a single molecular species has been amplified, and the corresponding cDNA clones were isolated from the liver cDNA library. The longest insert contained 2384 nucleotides with an open reading frame of 754 residues. The deduced amino acid sequence showed 33.6% and 34.1% overall identity with the human Bf and C2 sequences, respectively, hence this clone was named medaka Bf/C2. The single-copy medaka Bf/C2 gene had exactly the same exon-intron organization as the mammalian Bf and C2 genes, and spanned about 8 kilobases. The Bf/C2 locus was mapped to the close proximity (2.9 cM) of the superoxide dismutase locus on the linkage group XX by the use of a restriction site polymorphism between two inbred strains of the medaka.