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PubMed1999

Hox gene duplication in fish.

The study of Hox gene clusters continues to serve as a paradigm for those interested in vertebrate genome evolution. Recent exciting discoveries about Hox gene composition in fishes challenges conventional views about vertebrate Hox gene evolution, and has initiated lively debates concerning the evolutionary events making the divergence of the major vertebrate lineages. Comparative analyses indicate that Hox cluster duplications occurred in early vertebrate evolution, and again within the order Cypriniformes of teleost fish. Loss of Hox genes was more widespread than duplication during fish evolution.

Animals↗
PubMed1994

Evolutionary analysis of cytochrome b sequences in some Perciformes: evidence for a slower rate of evolution than in mammals.

To obtain information relative to the phylogenesis and microevolutionary rate of fish mitochondrial DNA, the nucleotide sequence of cytochrome b gene in seven fish species belonging to the order of Perciformes was determined. Sequence analysis showed that fish mitochondrial DNA has a nucleotide compositional bias similar to that of sharks but lower compared to mammals and birds. Quantitative evolutionary analysis, carried out by using a markovian stochastic model, clarifies some phylogenetic relationships within the Perciformes order, particularly in the Scombridae family, and between Perciformes, Gadiformes, Cypriniformes, and Acipenseriformes. The molecular clock of mitochondrial DNA was calibrated with the nucleotide substitution rate of cytochrome b gene in five shark species having divergence times inferred from paleontological estimates. The results of such analysis showed that Acipenseriformes diverged from Perciformes by about 200 MY, that the Perciformes common ancestor dates back to 150 MY, and that fish mitochondrial DNA has a nucleotide substitution rate three to five times lower than that of mammals.

Animals↗
PubMed1985

The structure of the kidney from the freshwater teleost Carassius auratus.

The structure of the kidney of the crucian carp (Carassius auratus; a freshwater teleost, Cypriniformes) was studied by means of reconstruction from serial paraffin and semithin sections. In C. auratus, the Wolffian duct traverses the entire kidney. At various levels collecting ducts of different length and thickness join the Wolffian duct at right angles. Each collecting duct accepts a large number of connecting tubules, which are established by the joining of many nephrons. A regular pattern concerning the distribution of nephrons and the fusion of renal tubules is not apparent. Four segments have been distinguished in renal tubules; 1) proximal tubule, 2) distal tubule, 3) connecting tubule and 4) collecting duct. A neck and an intermediate segment are absent. The proximal tubule is established by proximal tubule cells which bear a brush border and have a conspicuous apical cytoplasmic rim containing few cell organelles, ciliated cells, mucous cells and dark cells. In the first part of the proximal tubule the brush border and the apical cytoplasmic rim of proximal tubule cells are well developed. Ciliated cells are interposed between proximal tubule cells, decreasing in number toward the end of this part. In the second part ciliated cells are absent and dark cells are numerous. In the third part the brush border and the apical cytoplasmic rim of proximal tubule cells are scarcely developed. Ciliated cells reappear and increase in number toward the distal tubule. The distal and connecting tubule are similar in epithelial structure. Connecting tubules are joined distal tubules and thus they belong to two or more nephrons.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2006

Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs.

The power of comparative phylogenomic analyses also depends on the amount of data that are included in such studies. We used expressed sequence tags (ESTs) from fish model species as a proof of principle approach in order to test the reliability of using ESTs for phylogenetic inference. As expected, the robustness increases with the amount of sequences. Although some progress has been made in the elucidation of the phylogeny of teleosts, relationships among the main lineages of the derived fish (Euteleostei) remain poorly defined and are still debated. We performed a phylogenomic analysis of a set of 42 of orthologous genes from 10 available fish model systems from seven different orders (Salmoniformes, Siluriformes, Cypriniformes, Tetraodontiformes, Cyprinodontiformes, Beloniformes, and Perciformes) of euteleostean fish to estimate divergence times and evolutionary relationships among those lineages. All 10 fish species serve as models for developmental, aquaculture, genomic, and comparative genetic studies. The phylogenetic signal and the strength of the contribution of each of the 42 orthologous genes were estimated with randomly chosen data subsets. Our study revealed a molecular phylogeny of higher-level relationships of derived teleosts, which indicates that the use of multiple genes produces robust phylogenies, a finding that is expected to apply to other phylogenetic issues among distantly related taxa. Our phylogenomic analyses confirm that the euteleostean superorders Ostariophysi and Acanthopterygii are monophyletic and the Protacanthopterygii and Ostariophysi are sister clades. In addition, and contrary to the traditional phylogenetic hypothesis, our analyses determine that killifish (Cyprinodontiformes), medaka (Beloniformes), and cichlids (Perciformes) appear to be more closely related to each other than either of them is to pufferfish (Tetraodontiformes). All 10 lineages split before or during the fragmentation of the supercontinent Pangea in the Jurassic.

Animals↗
PubMed2000

Nonlinkage of major histocompatibility complex class I and class II loci in bony fishes.

In tetrapods, the functional (classical) class I and class II B loci of the major histocompatibility complex (Mhc) are tightly linked in a single chromosomal region. In an earlier study, we demonstrated that in the zebrafish, Danio rerio, order Cypriniformes, the two classes are present on different chromosomes. Here, we show that the situation is similar in the stickleback, Gasterosteus aculeatus, order Gasterosteiformes, the common guppy, Poecilia reticulata, order Cyprinodontiformes, and the cichlid fish Oreochromis niloticus, order Perciformes. These data, together with unpublished results from other laboratories suggest that in all Euteleostei, the classical class I and class II B loci are in separate linkage groups, and that in at least some of these taxa, the class II loci are in two different groups. Since Euteleostei are at least as numerous as tetrapods, in approximately one-half of jawed vertebrates, the class I and class II regions are not linked.

Animals↗
PubMed2001

Xiphophorus genetic linkage map: beginnings of comparative gene mapping in fishes.

The explosive expansion of gene maps of mouse and man has provided strong support for hypotheses first advanced from comparing fish and mammalian genomes that the vertebrate genome was derived from multiple ancestral tetraploidizations with subsequent preferential translocations among paralogous chromosomes. At least two genome duplication events have become widely accepted in lineages leading to vertebrates, and a third has been proposed either before, or after, divergence of fishes and tetrapods. Cytogenetic and comparative gene mapping studies suggest that teleost gene maps have diverged more slowly from gene arrangements in the vertebrate ancestor than have those of mammals. The recent assembly of extensive maps of >100 genes in three fish species, medaka (Beloniformes), Xiphophorus swordtails and platyfishes (Cyprinodontiformes), and zebrafish (Cypriniformes) and the development of less extensive maps in several other fish orders provides the first salient opportunity to assess homology of most or all chromosomes among fishes.

Journal Article↗
PubMed1984

Endocrine changes during natural spawning in the white sucker, Catostomus commersoni. I. Gonadotropin, growth hormone, and thyroid hormones.

White suckers (Catostomus commersoni; Cypriniformes, Teleosteii) spawning in a small stream in central Alberta were captured during different stages of their spawning migrations in 1981 and 1982, blood was sampled, and the fish were examined to determine their reproductive condition. Blood samples were analyzed for gonadotropin (GtH), growth hormone (GH), triiodothyronine (T3), and thyroxine (T4) by radioimmunoassay. GtH levels in both sexes were lowest prior to the onset of spawning, increased significantly in spawning males, females in which germinal vesicle migration had begun, and ovulated females and then dropped significantly in spent fish of both sexes. GH was lowest in prespawning females, increased significantly at ovulation, and remained high in spent females. In contrast, GH levels in males were relatively constant throughout spawning. In both sexes, highest T4 levels were found in prespawning fish, and T4 decreased significantly in spent fish. Although a similar decline was seen in T3 in 1981, in 1982 there were no T3 changes associated with changes in reproductive condition. No significant diurnal variations were detected in the levels of GtH or T3; T4 levels appeared to vary on a diurnal basis in prespawning males only. Spawning activity in both sexes therefore appears to be associated with increases in GtH occurring at ovulation in females and at the initiation of spawning in males. GH levels may also be related to reproductive condition in females, but not in males. The relationship of thyroid hormone levels to reproductive condition is less clear, however, and these levels may reflect both endocrine and environmental influences on thyroid function.

Animals↗
PubMed1996

Identification of two prolactin cDNA sequences from a goldfish pituitary cDNA library.

We have identified two different cDNA clones encoding for goldfish prolactin (gfPRL) from a pituitary cDNA library. The coding regions of these clones are predicted to encode for an identical amino acid (aa) sequence with four silent mutations. The 3'-untranslated regions (UTRs) of these clones show only 72% nucleotide (nt) sequence identity. The two genes each encoding gfPRL might have derived from recent gene duplication before the divergence of goldfish from other Cypriniforms. Genomic Southern blot analysis of goldfish DNA also demonstrated that there is a small family of two genes for prolactin in the genome of goldfish.

Amino Acid Sequence↗
PubMed1992

Ependymins from the cerebrospinal fluid of salmonid fish: gene structure and molecular characterization.

So far, ependymins (Epds) have been sequenced only from cypriniform fish, and in the past all attempts have failed to characterize, on a molecular level, homologous Epd proteins in higher vertebrates. Therefore, rainbow trout (Oncorhynchus mykiss) Epds, which represent the predominant proteins of the cerebrospinal fluid, have been N-terminally sequenced and the encoding cDNA subsequently cloned using the polymerase chain reaction. Surprisingly, only 40-42% of the amino acids are identical with the corresponding sequences from goldfish (Carassius auratus), and no convincing immunological cross-reactivity is observed with an antiserum raised against purified Epds from C. auratus. O. mykiss possesses two highly homologous genes encoding Epds (Om-I, Om-II), a feature typical of a quasi-tetraploid species. Western analysis, using two specific antibodies against Epds from O. mykiss, revealed a variety of different glycosylation variants. In contrast to C. auratus, Epds from O. mykiss probably do not form disulfide-linked dimers. The structure of one Epd gene and its flanking regions have been determined for the Atlantic salmon (Salmo salar). Six exons were deduced by comparison with the corresponding cDNA sequence from O. mykiss (almost 98% homology with Om-II).

Amino Acid Sequence↗
PubMed1994

Cloning and sequencing the genes encoding goldfish and carp ependymin.

Ependymins (EPNs) are brain glycoproteins thought to function in optic nerve regeneration and long-term memory consolidation. To date, epn genes have been characterized in two orders of teleost fish. In this study, polymerase chain reactions (PCR) were used to amplify the complete 1.6-kb epn genes, gf-I and cc-I, from genomic DNA of Cypriniformes, goldfish and carp, respectively. Amplified bands were cloned and sequenced. Each gene consists of six exons and five introns. The exon portion of gf-I encodes a predicted 215-amino-acid (aa) protein previously characterized as GF-I, while cc-I encodes a predicted 215-aa protein 95% homologous to GF-I.

Amino Acid Sequence↗
PubMed2005

Molecular cloning, expression and immunological characterization of pejerrey (Odontesthes bonariensis) growth hormone.

Growth hormone is an essential polypeptide required for normal growth and development of vertebrates. The pejerrey fish, Odontesthes bonariensis, is a South American atherinid freshwater fish considered as a promising species for aquaculture. Although growth hormone has been characterized in a number of fish, there are no published data on the structure of this hormone in atherinids, except that of a related species Odontesthes argentinensis. In this paper, the molecular cloning, expression and immunological characterization of pejerrey growth hormone (pjGH) is described. The predicted amino acid sequence of pjGH cDNA consisted of 204 amino acid residues with an estimated molecular mass of 23 kDa. Amino acid sequence was highly conserved among the two Atheriniformes where the growth hormone sequences are known (99% aa identity), highly to moderately conserve (75-92% aa identity) when compared to the other members of Acantopterigii superorder and clearly less conserved (49-66% identity) when compared to Salmoniformes (Protacanthopterygii), Cypriniformes and Siluriformes (Ostariophysi). A phylogenetic tree depicting the relationship of various teleost GH nucleotide sequences was inferred. Pejerrey GH was produced using recombinant DNA technology in a bacterial system, representing the first time an atherinid growth hormone protein was expressed as a recombinant protein in Escherichia coli. A specific antiserum of this hormone was raised in rabbits and its specificity tested by using Western blot and immunocytochemistry. The distribution of pjGH mRNA was also studied by RT-PCR and Southern blot analysis. The transcript was detected not only in the pituitary gland but also in the testis.

Amino Acid Sequence↗
PubMed2006

The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes.

The complete sequence of the 16,539 nucleotide mitochondrial genome from the single species of the catfish family Cranoglanididae, the helmet catfish Cranoglanis bouderius, was determined using the long and accurate polymerase chain reaction (LA PCR) method. The nucleotide sequences of C. bouderius mitochondrial DNA have been compared with those of three other catfish species in the same order. The contents of the C. bouderius mitochondrial genome are 13 protein-coding genes, two ribosomal RNA and 22 transfer RNA genes, and a non-coding control region, the gene order of which is identical to that observed in most other vertebrates. Phylogenetic analyses for 13 otophysan fishes were performed using Bayesian method based on the concatenated mtDNA protein-coding gene sequence and the individual protein-coding gene sequence data set. The competing otophysan topologies were then tested by using the approximately unbiased test, the Kishino-Hasegawa test, and the Shimodaira-Hasegawa test. The results show that the grouping ((((Characiformes, Gymnotiformes), Siluriformes), Cypriniformes), outgroup) is the most likely but there is no significant difference between this one and the other alternative hypotheses. In addition, the phylogenetic placement of the family Cranoglanididae among siluriform families was also discussed.

Animals↗
PubMed2005

Genomic structure of the sea lamprey growth hormone-encoding gene.

Growth hormone (GH) belongs to a family of pituitary hormones together with prolactin and somatolactin. In our previous study, GH and its cDNA were identified in the pituitary gland of the sea lamprey, Petromyzon marinus, an extant representative of the most ancient class of vertebrates, and isolated GH stimulated expression of insulin-like growth factor in the liver. The evidence suggests that GH is the ancestral hormone in the molecular evolution of the GH/PRL/SL family and that the endocrine mechanism for growth stimulation was established at an early stage in the evolution of vertebrates. To further understand the molecular evolution of the GH/PRL/SL gene family, we report the genomic structure of sea lamprey GH including its 5'-flanking region, being cloned by PCR using specific primers prepared from its cDNA. The sea lamprey GH gene consists of 13,604 bp, making it the largest of all the GH genes. The 5'-flanking region within 697 bp contains consensus sequences for a TATA box, two Pit-1/GHF-1, three TRE, and a CRE. The sea lamprey GH gene consists of five exons and four introns, the same as in mammals, birds, and teleosts such as cypriniforms and siluriforms with the exception of some teleosts such as salmoniforms, percififorms, and tetradontiforms, in which there is an additional intron in the 5th exon. The 5-exon-type gene organization might reflect the structure of the ancestral gene for the GH/PRL/SL gene family.

5' Flanking Region↗
PubMed2006

Molecular characterization and expression analysis of stanniocalcin-1 in turbot (Scophthalmus maximus).

Stanniocalcin-1 (STC-1) is an anti-hypercalcemic hormone that is produced by the corpuscles of Stannius (CS) in the teleost. The hormone is a homodimeric glycoprotein involved in the calcium and phosphate regulation in both teleost fish and mammals. In the present study, we have cloned and characterized a full-length cDNA of STC-1 from the turbot (Scophthalmus maximus) CS and examined its expression pattern in various tissues. The turbot STC cDNA (1,246 nucleotides) encodes a putative preprohormone of 248 amino acids (aa) with a signal peptide of 18 aa and a pro-sequence peptide of 14 aa followed by a mature protein of 216 aa. The deduced aa sequence of turbot STC-1 shows the highest sequence identity (86.3%) with that of European flounder STC-1 among the fish and mammalian STC-1. The aa sequence of turbot STC-1 showed moderate sequence identity with those of salmoniforms (chum salmon and rainbow trout), cypriniforms (zebrafish), ancient fish (gar and bowfin), and humans (43.7-66.9%), respectively, whereas it showed less identity with those of zebrafish and human STC-2 (23.8-25.4%). RT-PCR analysis revealed that the turbot STC-1 gene is expressed in the CS, pituitary, brain, kidney, liver, heart, muscle, and gonad. In a transient transfection of turbot STC-1 cDNA construct into human embryonic kidney 293T cells followed by Western blot analysis, a recombinant STC-1 secreted into a medium was detected as a single band of 28 kDa under reducing conditions and a 50 kDa protein under non-reducing conditions. Deglycosylation of the recombinant STC-1 led to a decrease in the molecular mass. Our data indicate that the turbot STC-1 gene is widely expressed and the secreted protein exists as a homodimeric glycoprotein.

Amino Acid Sequence↗
PubMed2006

Cloning of stanniocalcin (STC) cDNAs of divergent teleost species: Monomeric STC supports monophyly of the ancient teleosts, the osteoglossomorphs.

Molecular cloning of teleost stanniocalcin (STC) cDNAs was undertaken in two species of order Osteoglossiformes of subdivision Osteoglossomorpha and one species of each of orders Cypriniformes and Perciformes within the subdivision Euteleostei. The elephantnose (Gnathonemus petersii) and the butterflyfish (Pantadon buchholzi) are basal teleosts in different osteoglossiforme suborders yet their 218 amino acid (aa) mature hormones, from prehormones of 249 and 251aa, respectively, have only 10 cysteine residues. A substitution for cysteine at the intermonomeric disulfide linkage site, implies that their STCs exist as monomeric peptides, as is the case with STC from another osteoglossormorph, arawana [Amemiya, Y., Marra, L.E., Reyhani, N., Youson, J.H., 2002. Stanniocalcin from an ancient teleost: a monomeric form of the hormone and a possible extracorpuscular distribution. Mol. Cell. Endocrinol. 188, 141-150]. The STC cDNA of the generalized teleost and cyprinid, the white sucker (Catostomus commersoni), encodes a prehormone of 249aa with a signal peptide of 31aa and a mature protein of 218aa that possesses 11 cysteine residues. The latter feature is consistent with a previous analysis that white sucker mature STC is a glycosylated, homodimeric peptide [Amemiya, Y., Marra, L.E., Reyhani, N., Youson, J.H., 2002. Stanniocalcin from an ancient teleost: a monomeric form of the hormone and a possible extracorpuscular distribution. Mol. Cell. Endocrinol. 188, 141-150]. An open reading frame of the STC cDNA of the derived teleost and perciforme, the smallmouth bass (Micropterus dolomieui), encodes a prehormone of 255aa with a signal peptide of 33aa and a mature protein of 222aa. The position of the 11 cysteines in smallmouth bass STC suggests that it exists as a homodimeric peptide. A phylogenetic analysis, using the new STC-1 amino acid sequences and those in the gene data base provided strong support for monophyly of the Osteoglossomorpha and indicated, with positioning of white sucker and smallmouth bass, that this molecule has some utility as a taxonomic marker. This analysis also suggested that two STC-1 gene sequences exist in multiple fish genomes, and that they may be a product of the fish-specific genome duplication. The mutation in the osteoglossomorph STC likely occurred after the appearance of the first teleosts and before movement of the tectonic plates.

Amino Acid Sequence↗
PubMed2002

Identification and analysis of additional copies of the platelet-derived growth factor receptor and colony stimulating factor 1 receptor genes in fugu.

The receptors for the platelet-derived growth factor (PDGFRalpha and PDGFRbeta) belong to a subfamily of protein tyrosine kinase receptors that also includes kit and the colony stimulating factor-1 receptor (CSF1R). In mammals, the genes encoding PDGFRalpha and PDGFRbeta are tandemly linked to the kit and CSF1R genes, respectively. Based on the structural similarity and genomic organization of these four genes, it has been suggested that they arose from an ancestral protein tyrosine kinase receptor gene by two rounds of duplication. We have previously cloned the PDGFRbeta and CSF1R genes from the pufferfish, Fugu rubripes, and shown that they are tandemly linked like the mammalian genes [Genome Res. 6 (1996) 1185]. We have now cloned two additional members of this gene family, fPDGFRbeta2 and fCSF1R2 from the fugu and shown that these two genes are also tandemly linked. This indicates that the PDGFRbeta-CSF1R locus has been duplicated in the lineage leading to fugu. The fugu fPDGFRbeta2 and fCSF1R2 genes contain three and one extra introns, respectively, compared with other members of this family. Polymerase chain reaction cloning of a conserved region of PDGFRbeta gene from other ray-finned fishes identified two copies in the zebrafish (order Cypriniformes) and sunfish (order Tetraodontiformes). These results are discussed in the context of the proposed teleost lineage-specific whole genome duplication hypothesis.

Amino Acid Sequence↗
PubMed2003

Genome size and longevity in fish.

The wide variety of genome sizes (measured as C-value) observed across taxa is not related to organismal complexity or number of coding genes. Partial answers to this C-value enigma have been found by establishing associations between C-value and particular phenotypic characteristics. One such controversial association has been recently suggested between genome size and longevity in birds. In order to determine whether genome size is a general predictor of longevity, we have extended the analysis to the Actinoptergyian fish, a widely divergent group in terms of both longevity and genome size. We collected data on genome size, longevity and body mass for species covering fourteen orders of bony fish. Analysis of covariance using order as a cofactor shows a significant effect of genome size on longevity (corrected for body mass), with lifespan increasing as a function of genome size. Analysis of phylogenetically independent contrasts for orders with a large number of species with a well resolved phylogenetic relationship (Acipenseriformes, Cypriniformes, and Salmoniformes) found the same trend of longer lifespan with increases in genome size but the relationship was not significant. Our results consistently show an increase in lifespan for fish with larger genomes.

Analysis of Variance↗
PubMed2000

The distribution of neuropeptide Y-immunoreactive neurons and nerve fibers in the forebrain of the carp Cyprinus carpio L.

The present study reports the distribution of Neuropeptide Y (NPY)-immunoreactive neurons and fibers in the forebrain of the adult carp Cyprinus carpio L. Serial Nissl-stained sections were used for cytoarchitecture and identification of anatomical structures. Immunostaining of NPY-containing neurons and fibers was used as neurochemical marker and tool for comparison with other species, including the goldfish. The general outline of the cytoarchitecture of the carp forebrain is similar to that of other Cypriniformes. However, using NPY immunohistochemistry, we found several specific differences with the goldfish, especially in the diencephalon. In the hypothalamus of the carp NPY-immunoreactive (NPYir) neurons were identified in the n. dorsolateralis thalami, and in the n. ventralis lateralis thalami. In the same location, we observed the n. anterior hypothalami and the n. preglomerulosus pars lateralis, described in the goldfish, as parts of n. prerotundus. However, in the carp we were not able to identify a n. preglomerulosus pars medialis, a n. preglomerulosus pars medialis commissuralis and a n. glomerulosus. We describe a n. rotundus, in which we did not find substructures typical of the goldfish. Further differences with the goldfish, trout and salmon were also noted.

Animals↗