Euteleost fish genomes are characterized by expansion of gene families

Long-range control of gene expression: emerging mechanisms and disruption in disease

Transcriptional control is a major mechanism for regulating gene expression. The complex machinery required to effect this control is still emerging from functional and evolutionary analysis of genomic architecture. In addition to the promoter, many other regulatory elements are required for spatiotemporally and quantitatively correct gene expression. Enhancer and repressor elements may reside in introns or up- and downstream of the transcription unit. For some genes with highly complex expression patterns--often those that function as key developmental control genes--the cis-regulatory domain can extend long distances outside the transcription unit. Some of the earliest hints of this came from disease-associated chromosomal breaks positioned well outside the relevant gene. With the availability of wide-ranging genome sequence comparisons, strong conservation of many noncoding regions became obvious. Functional studies have shown many of these conserved sites to be transcriptional regulatory elements that sometimes reside inside unrelated neighboring genes. Such sequence-conserved elements generally harbor sites for tissue-specific DNA-binding proteins. Developmentally variable chromatin conformation can control protein access to these sites and can regulate transcription. Disruption of these finely tuned mechanisms can cause disease. Some regulatory element mutations will be associated with phenotypes distinct from any identified for coding-region mutations.

Expression and distribution of CB1 cannabinoid receptors in the central nervous system of the African cichlid fishPelvicachromis pulcher

Neuroanatomical investigation of the cannabinoid system in a lower vertebrate group such as teleost fishes might improve our understanding of the physiological role of such a signaling system. In the present study, the expression of a CB1 cannabinoid receptor has been demonstrated in the CNS of a teleost fish, the cichlid Pelvicachromis pulcher. Moreover, CB1-like immunoreactivity has been analyzed by using a purified antibody against the CB1 receptor amino-terminus. Immunostained neurons and varicosities were found through the telencephalon as well as in the preoptic area and lateral infundibular lobes of the hypothalamus. Stained cells were observed in the pituitary gland. Several cell bodies and nerve terminals containing an intense CB1-like immunoreactivity were found in the pretectal central nucleus and posterior tuberculum, both lying in a transitional region between diencephalon and mesencephalon. In the brainstem, the CB1 immunopositivity was more restricted than in the prosencephalon, with the exception of some large, intensely immunopositive nerve cells within the dorsal mesencephalic tegmentum, possibly motor neurons of the third cranial nerve. In the cerebellum, among a majority of immunonegative granule cells, a subset of them was immunostained. Some positive Purkinje cells were also observed. In the spinal cord, ventral gray matter, several alpha-motoneurons were stained. Similarities to and discrepancies from the CB1 receptor distributions in other vertebrate CNS are discussed, paying particular attention to the abundant CB1 immunoreactivity observed in the area encompassing the pretectum and glomerular nucleus, which is characterized by a peculiar differentiation in bony fishes.

Cloning, tissue distribution, pharmacology and three-dimensional modelling of melanocortin receptors 4 and 5 in rainbow trout suggest close evolutionary relationship of these subtypes

The rainbow trout (Oncorhynchus mykiss) is one of the most widely used fish species in aquaculture and physiological research. In the present paper, we report the first cloning, 3D (three-dimensional) modelling, pharmacological characterization and tissue distribution of two melanocortin (MC) receptors in rainbow trout. Phylogenetic analysis indicates that these receptors are orthologues of the human MC4 and MC5 receptors. We created 3D molecular models of these rainbow trout receptors and their human counterparts. These models suggest greater divergence between the two human receptors than between their rainbow trout counterparts. The pharmacological analyses demonstrated that ACTH (adrenocorticotropic hormone) had surprisingly high affinity for the rainbow trout MC4 and MC5 receptors, whereas alpha-, beta- and gamma-MSH (melanocyte-stimulating hormone) had lower affinity. In second-messenger studies, the cyclic MSH analogues MTII and SHU9119 acted as potent agonist and antagonist respectively at the rainbow trout MC4 receptor, indicating that these ligands are suitable for physiological studies in rainbow trout. Interestingly, we found that the rainbow trout MC4 receptor has a natural high-affinity binding site for zinc ions (0.5 microM) indicating that zinc may play an evolutionary conserved role at this receptor. Reverse transcription PCR indicates that the rainbow trout receptors are expressed both in peripheral tissues and in the central nervous system, including the telencephalon, optic tectum and hypothalamus. Overall, this analysis indicates that the rainbow trout MC4 and MC5 receptors have more in common than their mammalian counterparts, which may suggest that these two receptors have a closer evolutionary relationship than the other MC receptor subtypes.

Cloning and developmental expression of the cytochrome P450 aromatase gene (CYP19) in the European eel (Anguilla anguilla)

To characterize the involvement of the aromatase gene during the process of sex determination in the European eel (Anguilla anguilla), the expression of its gonadal form was determined during various developmental stages. The cloned cDNA from the European eel gonad (EeCYP19) contains an open reading frame of 1539 bp, encoding a deduced protein of 513 residues. The predicted amino acid sequence shows 97% identity with that of the Japanese eel, and 59-69% of identity with those of the CYP19 gonadal and brain forms of other teleost fish. Two potential initiation sites (ATG) were found downstream of the first ATG codon. A fluorescent-based method of real-time PCR was developed to quantify EeCYP19 expression. The expression levels of EeCYP19 in the gonads of adult males were approximately 12- and 30-fold lower than the levels in adult females and juvenile eels previously treated with E2, respectively. Expression of aromatase was found only in a single specimen in the control group. In contrast, no difference was found among sexes in the aromatase expression in the brain. Treatment with aromatase inhibitor (AI) of juvenile eel resulted in the total loss of aromatase expression in the gonads and brains. The results of this work revealed that AI treatment not only reduces the synthesis of estradiol, but reduces the expression levels of EeCYP19 as well. No evidence for the presence of a distinct extra-gonadal (brain) form of aromatase in the European eel could be provided.

C-type lectin-like domains in Fugu rubripes

Background

Members of the C-type lectin domain (CTLD) superfamily are metazoan proteins functionally important in glycoprotein metabolism, mechanisms of multicellular integration and immunity. Three genome-level studies on human, C. elegans and D. melanogaster reported previously demonstrated almost complete divergence among invertebrate and mammalian families of CTLD-containing proteins (CTLDcps).

Results

We have performed an analysis of CTLD family composition in Fugu rubripes using the draft genome sequence. The results show that all but two groups of CTLDcps identified in mammals are also found in fish, and that most of the groups have the same members as in mammals. We failed to detect representatives for CTLD groups V (NK cell receptors) and VII (lithostathine), while the DC-SIGN subgroup of group II is overrepresented in Fugu. Several new CTLD-containing genes, highly conserved between Fugu and human, were discovered using the Fugu genome sequence as a reference, including a CSPG family member and an SCP-domain-containing soluble protein. A distinct group of soluble dual-CTLD proteins has been identified, which may be the first reported CTLDcp group shared by invertebrates and vertebrates. We show that CTLDcp-encoding genes are selectively duplicated in Fugu, in a manner that suggests an ancient large-scale duplication event. We have verified 32 gene structures and predicted 63 new ones, and make our annotations available through a distributed annotation system (DAS) server and their sequences as additional files with this paper.

Conclusions

The vertebrate CTLDcp family was essentially formed early in vertebrate evolution and is completely different from the invertebrate families. Comparison of fish and mammalian genomes revealed three groups of CTLDcps and several new members of the known groups, which are highly conserved between fish and mammals, but were not identified in the study using only mammalian genomes. Despite limitations of the draft sequence, the Fugu rubripes genome is a powerful instrument for gene discovery and vertebrate evolutionary analysis. The composition of the CTLDcp superfamily in fish and mammals suggests that large-scale duplication events played an important role in the evolution of vertebrates.

Evolution and diversity of fish genomes

The ray-finned fishes ('fishes') vary widely in genome size, morphology and adaptations. Teleosts, which comprise approximately 23600 species, constitute >99% of living fishes. The radiation of teleosts has been attributed to a genome duplication event, which is proposed to have occurred in an ancient teleost. But more evidence is required to support the genome-duplication hypothesis and to establish a causal relationship between additional genes and teleost diversity. Fish genomes seem to be 'plastic' in comparison with other vertebrate genomes because genetic changes, such as polyploidization, gene duplications, gain of spliceosomal introns and speciation, are more frequent in fishes.

Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish

Teleosts are the most species-rich group of vertebrates, and a genome duplication (tetraploidization) event in ray-fin fish appears to have preceded this remarkable explosion of biodiversity. What is the relationship of the ray-fin genome duplication to the teleost radiation? Genome duplication may have facilitated lineage divergence by partitioning different ancestral gene subfunctions among co-orthologs of tetrapod genes in different teleost lineages. To test this hypothesis, we investigated gene expression patterns for Sox9 gene duplicates in stickleback and zebrafish, teleosts whose lineages diverged early in Euteleost evolution. Most expression domains appear to have been partitioned between Sox9a and Sox9b before the divergence of stickleback and zebrafish lineages, but some ancestral expression domains were distributed differentially in each lineage. We conclude that some gene subfunctions, as represented by lineage-specific expression domains, may have assorted differently in separate lineages and that these may have contributed to lineage diversification during teleost evolution.

Characterization of NF-kappa B/I kappa B proteins in zebra fish and their involvement in notochord development

Although largely involved in innate and adaptive immunity, NF-kappa B plays an important role in vertebrate development. In chicks, the inactivation of the NF-kappa B pathway induces functional alterations of the apical ectodermal ridge, which mediates limb outgrowth. In mice, the complete absence of NF-kappa B activity leads to prenatal death and neural tube defects. Here, we report the cloning and characterization of NF-kappa B/I kappa B proteins in zebra fish. Despite being ubiquitously expressed among the embryonic tissues, NF-kappa B/I kappa B members present distinct patterns of gene expression during the early zebra fish development. Biochemical assays indicate that zebra fish NF-kappa B proteins are able to bind consensus DNA-binding (kappa B) sites and inhibitory I kappa B alpha proteins from mammals. We show that zebra fish I kappa B alphas are degraded in a time-dependent manner after induction of transduced murine embryo fibroblasts (MEFs) and that these proteins are able to rescue NF-kappa B activity in I kappa B alpha(-/-) MEFs. Expression of a dominant-negative form of the murine I kappa B alpha (mI kappa B alpha M), which is able to block NF-kappa B in zebra fish cells, interferes with the notochord differentiation, generating no tail (ntl)-like embryos. This phenotype can be rescued by coinjection of the T-box gene ntl (Brachyury homologue), which is typically required for the formation of posterior mesoderm and axial development, suggesting that ntl lies downstream of NF-kappa B . We further show that ntl and Brachyury promoter regions contain functional kappa B sites and NF-kappa B can directly modulate ntl expression. Our study illustrates the conservation and compatibility of NF-kappa B/I kappa B proteins among vertebrates and the importance of NF-kappa B pathway in mesoderm formation during early embryogenesis.

Evolutionary Genomics of Nuclear Receptors: From Twenty-Five Ancestral Genes to Derived Endocrine Systems

Bilaterian animals are notably characterized by complex endocrine systems. The receptors for many steroids, retinoids, and other hormones belong to the superfamily of nuclear receptors, which are transcription factors regulating many aspects of development and homeostasis. Despite a diversity of regulatory mechanisms and physiological roles, nuclear receptors share a common protein organization. To obtain the broad picture of bilaterian nuclear hormone receptor evolution, we have characterized the complete set of nuclear receptor genes from nine animal genome sequences and analyzed it in a phylogenetic framework. In addition, expressed sequence tags from key lineages with no available genome sequence were also searched. This allows us to date the evolutionary events that led from an ancestral nuclear receptor gene, in an early metazoan, to present day diversity. We show that there were approximately 25 nuclear receptor genes in Urbilateria, the ancestor of bilaterians, at which point the fundamental diversity of the subfamily was already established. Surprisingly, differential gene loss played an important role in the evolution of different nuclear receptor sets in bilaterian lineages. The nuclear receptor distribution was also shaped by periods of gene duplication, essentially in vertebrates, as well as a lineage-specific duplication burst in nematodes. Our results imply that the genes for major receptors such as steroid receptors or thyroid hormone receptors were present in Urbilateria.

The duplication of the Hox gene clusters in teleost fishes

Higher teleost fishes, including zebrafish and fugu, have duplicated their Hox genes relative to the gene inventory of other gnathostome lineages. The most widely accepted theory contends that the duplicate Hox clusters orginated synchronously during a single genome duplication event in the early history of ray-finned fishes. In this contribution we collect and re-evaluate all publicly available sequence information. In particular, we show that the short Hox gene fragments from published PCR surveys of the killifish Fundulus heteroclitus, the medaka Oryzias latipes and the goldfish Carassius auratus can be used to determine with little ambiguity not only their paralog group but also their membership in a particular cluster.Together with a survey of the genomic sequence data from the pufferfish Tetraodon nigroviridis we show that at least percomorpha, and possibly all eutelosts, share a system of 7 or 8 orthologous Hox gene clusters. There is little doubt about the orthology of the two teleost duplicates of the HoxA and HoxB clusters. A careful analysis of both the coding sequence of Hox genes and of conserved non-coding sequences provides additional support for the "duplication early" hypothesis that the Hox clusters in teleosts are derived from eight ancestral clusters by means of subsequent gene loss; the data remain ambiguous, however, in particular for the HoxC clusters.Assuming the "duplication early" hypothesis we use the new evidence on the Hox gene complements to determine the phylogenetic positions of gene-loss events in the wake of the cluster duplication. Surprisingly, we find that the resolution of redundancy seems to be a slow process that is still ongoing. A few suggestions on which additional sequence data would be most informative for resolving the history of the teleostean Hox genes are discussed.

Cloning and developmental expression of five estrogen-receptor related genes in the zebrafish

Estrogen-receptor related receptors (ERRalpha, beta and gamma) are so-called orphan (i.e. for which no natural ligand has been identified to date) nuclear receptors that are closely related to the estrogen receptors. To gain insights into the possible functions of ERRs during early development, we have cloned their homologs in the zebrafish. Five err cDNA types were recovered in a PCR screen. Transient transfection experiments indicated that zebrafish ERRalpha, ERRgamma and ERRdelta display transcriptional activities that are identical to those of their mammalian counterparts. The expression patterns of err genes were determined during zebrafish development. Tissues such as the hindbrain or the pronephric tubes express several errs whereas others, such as the presumptive mesoderm at the level of the margin, specifically express a single err. Our analysis also points to tissues in which err expression is conserved through evolution, such as slow muscles that specifically express erralpha, suggesting important functions in these tissues.

Phylogenetic Dating and Characterization of Gene Duplications in Vertebrates: The Cartilaginous Fish Reference

Vertebrates originated in the lower Cambrian. Their diversification and morphological innovations have been attributed to large-scale gene or genome duplications at the origin of the group. These duplications are predicted to have occurred in two rounds, the "2R" hypothesis, or they may have occurred in one genome duplication plus many segmental duplications, although these hypotheses are disputed. Under such models, most genes that are duplicated in all vertebrates should have originated during the same period. Previous work has shown that indeed duplications started after the speciation between vertebrates and the closest invertebrate, amphioxus, but have not set a clear ending. Consideration of chordate phylogeny immediately shows the key position of cartilaginous vertebrates (Chondrichthyes) to answer this question. Did gene duplications occur as frequently during the 45 Myr between the cartilaginous/bony vertebrate split and the fish/tetrapode split as in the previous approximately 100 Myr? Although the time interval is relatively short, it is crucial to understanding the events at the origin of vertebrates. By a systematic appraisal of gene phylogenies, we show that significantly more duplications occurred before than after the cartilaginous/bony vertebrate split. Our results support rounds of gene or genome duplications during a limited period of early vertebrate evolution and allow a better characterization of these events.

Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution

The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish possess duplicated Hox clusters that have undergone considerable sequence evolution. Whether these changes are associated with the duplication(s) that produced extra Hox clusters is unresolved because comparison with basal lineages is unavailable. We sequenced and analyzed the HoxA cluster of the bichir (Polypterus senegalus), a phylogenetically basal actinopterygian. Independent lines of evidence indicate that bichir has one HoxA cluster that is mosaic in its patterns of noncoding sequence conservation and gene retention relative to the HoxA clusters of human and shark, and the HoxAalpha and HoxAbeta clusters of zebrafish, pufferfish, and striped bass. HoxA cluster noncoding sequences conserved between bichir and euteleosts indicate that novel cis-sequences were acquired in the stem actinopterygians and maintained after cluster duplication. Hence, in the earliest actinopterygians, evolution of the single HoxA cluster was already more dynamic than in human and shark. This tendency peaked among teleosts after HoxA cluster duplication.

Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates

It has been suggested that fish have more genes than humans. Whether most of these additional genes originated through a complete (fish-specific) genome duplication or through many lineage-specific tandem gene or smaller block duplications and family expansions continues to be debated. We analyzed the complete genome of the pufferfish Takifugu rubripes (Fugu) and compared it with the paranome of humans. We show that most paralogous genes of Fugu are the result of three complete genome duplications. Both relative and absolute dating of the complete predicted set of protein-coding genes suggest that initial genome duplications, estimated to have occurred at least 600 million years ago, shaped the genome of all vertebrates. In addition, analysis of >150 block duplications in the Fugu genome clearly supports a fish-specific genome duplication (approximately equal to 320 million years ago) that coincided with the vast radiation of most modern ray-finned fishes. Unlike the human genome, Fugu contains very few recently duplicated genes; hence, many human genes are much younger than fish genes. This lack of recent gene duplication, or, alternatively, the accelerated rate of gene loss, is possibly one reason for the drastic reduction of the genome size of Fugu observed during the past 100 million years or so, subsequent to the additional genome duplication that ray-finned fishes but not land vertebrates experienced.

Molecular cloning and developmental expression patterns of thyroid hormone receptors and T3 target genes in the turbot (Scophtalmus maximus) during post-embryonic development

Thyroid hormones (TH) are pleiotropic factors important for many developmental and physiological functions in vertebrates and particularly in amphibian metamorphosis. Their effects are mediated by two specific receptors (TRalpha and TRbeta), which are ligand-dependent transcription factors, members of the nuclear hormone receptor superfamily. Besides their pivotal role in amphibian metamorphosis, TH are also critical for fish metamorphosis. As this later role of TH is less studied, we analyzed their action in the turbot (Scophtalmus maximus), a metamorphosing flat fish. We describe the isolation of sequences for the turbot orthologs of a number of Xenopus genes, which are induced during amphibian metamorphosis. Developmental expression of these genes during turbot metamorphosis was studied by several methods and the expression patterns of these genes compared with those in Xenopus and flounder. We find that the period between the onset and the end of eye migration (day 22 to day 30 post-hatching) most likely corresponds to the metamorphic climax with either high TRalpha or high TH levels. Our results show that in contrast to amphibians, it is TRalpha and not TRbeta mRNA that is up-regulated during metamorphosis. Our results highlight the notion that TH regulates, through a rise of TR expression, a genetic cascade during turbot metamorphosis. The fact that TH regulates metamorphosis in amphibian and teleost fishes suggests that TH-regulated metamorphosis is a post-embryonic process conserved in most vertebrates.

Expression of peroxisome proliferator-activated receptors in the liver of gray mullet (Mugil cephalus)

During the last decade, peroxisome proliferation has emerged as a novel biomarker of exposure to certain organic chemical pollutants in aquatic organisms. Peroxisome proliferation is mediated by nuclear receptors, peroxisome proliferator-activated receptors (PPARs). Three PPAR subtypes have been described in mammals: PPAR alpha, PPAR beta and PPAR gamma. PPARs have also been discovered in several fish species. The aim of the present study was to investigate the expression of PPAR subtypes and their cellular distribution patterns in the liver of gray mullet Mugil cephalus, a fish species widely distributed in estuaries and coastal areas in Europe and used as sentinel of environmental pollution. For this purpose, antibodies were generated against the three subtypes of mouse PPARs and different protocols of antigen retrieval were used. In western blots, main bands were detected of approximately 44 kDa for PPAR alpha, two bands of 44 and 58 kDa for PPAR beta and a single band of 56 kDa for PPAR gamma. Similar results were obtained in mouse liver and may indicate antibody recognition of two forms of the protein in certain cases. PPAR alpha was the subtype most markedly expressed in gray mullet liver, being expressed mainly in melanomacrophages, nuclei of hepatocytes and sinusoidal cells and connective tissue surrounding bile ducts. PPAR beta was expressed in the same cell types but immunolabeling was generally weaker than for PPAR alpha. PPAR gamma showed very weak expression; positivity was mainly found in melanomacrophages and connective tissue surrounding bile ducts. Our results demonstrate that all the three PPAR subtypes are expressed in gray mullet liver but in different intensities. The cellular distribution patterns of PPAR subtypes in gray mullet liver resembled partly those found in mouse liver with PPAR alpha as the main subtype expressed in hepatocytes. The fact that melanomacrophages, cells of the immune system in fish, show strong expression of both PPAR alpha and PPAR beta whereas PPAR gamma expression is almost restricted to this cell type suggest a significant role of PPAR-mediated regulation of cell function in melanomacrophages.

Expression analysis of the Toll-like receptor and TIR domain adaptor families of zebrafish

The zebrafish genomic sequence database was analysed for the presence of genes encoding members of the Toll-like receptors (TLR) and interleukin receptors (IL-R) and associated adaptor proteins containing a TIR domain. The resulting predictions show the presence of one or more counterparts for the human TLR1, TLR2, TLR3, TLR4, TLR5, TLR7, TLR8, TLR9, IL-1R and IL-18R genes and one copy of the adaptor genes MyD88, MAL, TRIF and SARM. In contrast to data for the pufferfish Fugu rubripes, zebrafish has two genes that are highly similar to human TLR4. In addition, one fish-specific TLR group can be distinguished that is closely related to the Drosophila melanogaster Toll-9 gene. The sequence of cloned cDNAs for TLR4, TLR2 and MyD88 show the same intron-exon organisation as in the human counterparts. Expression analysis using reverse transcriptase-PCR (RT-PCR) shows that 17 of the predicted zebrafish TLR genes and all the genes encoding adaptor proteins are expressed in the adult stage. A subset of the TLR genes are expressed at higher levels in fish infected with the pathogen Mycobacterium marinum. The induced genes include the homologues of the human TLR1 and TLR2 genes, whose functions are associated with mycobacterial infections, underscoring the suitability of zebrafish as a model for analysis of the vertebrate innate immune system.

The xmrk oncogene can escape nonfunctionalization in a highly unstable subtelomeric region of the genome of the fish xiphophorus☆

The Xmrk oncogene involved in melanoma formation in the fish Xiphophorus was formed relatively recently by duplication of the epidermal growth factor co-orthologue egfrb. In the platyfish X. maculatus, Xmrk is located close to the major sex-determining locus in a subtelomeric region of the X and Y sex chromosomes that frequently undergoes duplications and other rearrangements. This region accumulates repetitive sequences: more than 80% of the 33-kb region 3' of Xmrk is constituted by retrotransposable elements. The high degree of nucleotide identity between X- and Y-linked sequences and the rarity of gonosome-specific rearrangements indicated that the instability observed was not a manifestation of gonosome-specific degeneration. Seven other duplicated genes were found, all corresponding, in contrast to Xmrk, to pseudogenes (nonfunctionalization). Functional persistence of Xmrk in a highly unstable region in divergent Xiphophorus species suggests a beneficial function under certain conditions for this dispensable and potentially injurious gene.

Multiple corticosteroid receptors in a teleost fish: distinct sequences, expression patterns, and transcriptional activities

Corticosteroid hormones, including the mineralocorticoids and the glucocorticoids, regulate diverse physiological functions in vertebrates. These hormones act through two classes of corticosteroid receptors (CR) that are ligand-dependent transcription factors: type I or mineralocorticoid receptor (MR) and type II or glucocorticoid receptor (GR). There is substantial overlap in the binding of these two receptor types to hormones and to DNA. In fish, the overlap in processes controlled by CRs may be different from that in other vertebrates, as fish are thought to synthesize only glucocorticoids, whereas they express both GR and MR. Here we describe the characterization of four CRs in a cichlid fish, Haplochromis burtoni: a previously undescribed GR (HbGR1), another GR expressed in two splice isoforms (HbGR2a and HbGR2b), and an MR (HbMR). Sequence comparison and phylogenetic analysis showed that these CRs sort naturally into GR and MR groups, and that the GR duplication we describe will probably be common to all teleosts. Quantitative PCR revealed differential patterns of CR tissue expression in organs dependent on corticosteroid action. Trans-activation assays demonstrated that the CRs were selective for corticosteroid hormones and showed that the HbMR was similar to mammalian MRs in being more sensitive to both cortisol and aldosterone than the GRs. Additionally, the two HbGR2 isoforms were expressed uniquely in different tissues and were functionally distinct in their actions on classical GR-sensitive promoters. The identification of four CR subtypes in teleosts suggests a more complicated corticosteroid signaling in fish than previously recognized.

Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution

The widely accepted notion that two whole-genome duplications occurred during early vertebrate evolution (the 2R hypothesis) stems from the fact that vertebrates often possess several genes corresponding to a single invertebrate homolog. However the number of genes predicted by the Human Genome Project is less than twice as many as in the Drosophila melanogaster or Caenorhabditis elegans genomes. This ratio could be explained by two rounds of genome duplication followed by extensive gene loss, by a single genome duplication, by sequential local duplications, or by a combination of any of the above. The traditional method used to distinguish between these possibilities is to reconstruct the phylogenetic relationships of vertebrate genes to their invertebrate orthologs; ratios of invertebrate-to-vertebrate counterparts are then used to infer the number of gene duplication events. The lancelet, amphioxus, is the closest living invertebrate relative of the vertebrates, and unlike protostomes such as flies or nematodes, is therefore the most appropriate outgroup for understanding the genomic composition of the last common ancestor of all vertebrates. We analyzed the relationships of all available amphioxus genes to their vertebrate homologs. In most cases, one to three vertebrate genes are orthologous to each amphioxus gene (median number=2). Clearly this result, and those of previous studies using this approach, cannot distinguish between alternative scenarios of chordate genome expansion. We conclude that phylogenetic analyses alone will never be sufficient to determine whether genome duplication(s) occurred during early chordate evolution, and argue that a "phylogenomic" approach, which compares paralogous clusters of linked genes from complete amphioxus and human genome sequences, will be required if the pattern and process of early chordate genome evolution is ever to be reconstructed.

Molecular markers of endocrine disruption in aquatic organisms

A wide range of organic contaminant compounds prevalent in the aquatic environment has been shown to exhibit hormone-disrupting activity. The actual potency of such compounds are low compared with endogenous hormones, such as 17beta-estradiol, but may still produce detrimental biological effects. Induced hormone levels are routinely measured using commercial testing kits, though these fail to relate to actual effects. Field and laboratory studies on the biological effects of environmental estrogens have, in the past, largely relied on assays of vitellogenin (vtg) induction in male fish, reduced growth in testes formation, and intersex incidence. Here, we critically review the current and potential application of molecular techniques in assessing the adverse biological reproductive effects of endocrine-disrupting chemicals in aquatic organisms. The role of fish (estrogen, androgen, and progestogen) hormone receptors and invertebrate (ecdysone) hormone receptor, egg production (vtg and chorion) proteins, steroid biosynthesis enzymes (aromatase, sulfotransferase, and hydroxysteroid dehydrogenase), DNA damage, apoptosis, and their potential development as biomarkers are discussed in turn. In each case, the sequences characterized are presented and homologies across species are highlighted. Molecular methods of gauging vtg and zona radiata (ZR) expression and protein concentrations have included immunoassay and reverse transcription polymerase chain reaction (RT-PCR). Suggestions for the isolation for key gene expression products (aromatase, ZR, and vtg, for instance), from a wider range of fish species using degenerate primers, are given. Endocrine disruption in invertebrates has received less attention compared with fish, partly because the knowledge regarding invertebrate endocrinology is limited. Here we review and suggest alternate isolation strategies for key players in the imposex induction process: vitellin (Vn), aromatase, and Ala-Pro-Gly-Trp (APGW) amide neurohormone. Current molecular-level techniques rely on ligand-binding assays, enzyme-linked immunosorbent assay (ELISA), and, more recently, gene expression. In the future, more reliance will be placed on the development of gene expression assays using reporter systems combined with cross-species PCR-based or polyclonal antibody-based assays. We discuss the use of recombinant receptors as a means of primary screening of environmental samples for estrogenicity and antiestrogenicity, which avoids species and seasonal variation in receptor response to ligand binding, a recognized problem of earlier bioassays. Most exciting is the potential that microarray and proteomics approaches have to offer. Such techniques are now used routinely in medical research to identify specific genes and proteins affected by treatment with endocrine disruptors, including estradiol. The technique has yet to be used to screen aquatic organisms, but it has the potential to implicate previously unsuspected estradiol-sensitive genes that may later become molecular markers of endocrine disruption.

Temperature and the expression of seven muscle-specific protein genes during embryogenesis in the Atlantic cod Gadus morhua L

Seven cDNA clones coding for different muscle-specific proteins (MSPs) were isolated from the fast muscle tissue of Atlantic cod Gadus morhua L. In situ hybridization using cRNA probes was used to characterize the temporal and spatial patterns of gene expression with respect to somite stage in embryos incubated at 4 degrees C, 7 degrees C and 10 degrees C. MyoD transcripts were first observed in the presomitic mesoderm prior to somite formation, and in the lateral compartment of the forming somites. MyoD expression was not observed in the adaxial cells that give rise to the slow muscle layer, and expression was undetectable by in situ hybridization in the lateral somitic mesoderm after the 35-somite stage, during development of the final approximately 15 somites. RT-PCR analysis, however, confirmed the presence of low levels of the transcript during these later stages. A phylogenetic comparison of the deduced aminoacid sequences of the full-length MyoD cDNA clone and those from other teleosts, and inference from the in situ expression pattern suggested homology with a second paralogue (MyoD2) recently isolated from the gilthead seabream Sparus aurata. Following MyoD expression, alpha-actin was the first structural gene to be switched on at the 16-somite stage, followed by myosin heavy chain, troponin T, troponin I and muscle creatine kinase. The final mRNA in the series to be expressed was troponin C. All genes were switched on prior to myofibril assembly. The troponin C sequence was unusual in that it showed the greatest sequence identity with the rainbow trout Oncorhynchus mykiss cardiac/slow form, but was expressed in the fast myotomal muscle and not in the heart. In addition, the third TnC calcium binding site showed a lower level of sequence conservation than the rest of the sequence. No differences were seen in the timing of appearance or rate of posterior progression (relative to somite stage) of any MSP transcripts between embryos raised at the different temperatures. It was concluded that myofibrillar genes are activated asynchronously in a distinct temporal order prior to myofibrillar assembly and that this process was highly canalized over the temperature range studied.

Are all fishes ancient polyploids?

Euteleost fishes seem to have more copies of many genes than their tetrapod relatives. Three different mechanisms could explain the origin of these 'extra' fish genes. The duplicates may have been produced during a fish-specific genome duplication event. A second explanation is an increased rate of independent gene duplications in fish. A third possibility is that after gene or genome duplication events in the common ancestor of fish and tetrapods, the latter lost more genes. These three hypotheses have been tested by phylogenetic tree reconstruction. Phylogenetic analyses of sequences from human, mouse, chicken, frog (Xenopus laevis), zebrafish (Danio rerio) and pufferfish (Takifugu rubripes) suggest that ray-finned fishes are likely to have undergone a whole genome duplication event between 200 and 450 million years ago. We also comment here on the evolutionary consequences of this ancient genome duplication.

Evolution of signal transduction by gene and genome duplication in fish

Fishes possess more genes encoding receptor tyrosine kinases from the epidermal growth factor receptor (EGFR) family than other organisms. Three of the four genes present in higher vertebrates have been duplicated early during the evolution of the ray-finned fish lineage possibly as a consequence of an event of whole genome duplication. In the fish Xiphophorus, a much more recent local event of gene duplication of the egfr co-orthologue egfr-b generated a eighth gene, the Xmrk oncogene. This duplicate acquired within a short time a constitutive activity and a pigment cell-specific overexpression responsible for the induction of melanoma in certain interspecific hybrids. Despite its frequent loss during evolution of the genus Xiphophorus, the maintenance of Xmrk in numerous species and its evolution under purifying selection suggest a so far unknown function under certain natural conditions. One of the known functions of Xmrk in tumor cells is the suppression of differentiation of melanocytes induced by the microphthalmia-associated transcription factor MITF. While only one gene with alternative 5' exons and promoters is present in higher vertebrates, two mitf genes were identified in fish. Subfunctionalization of mitf paralogues by differential degeneration of alternative exons and regulatory sequences led particularly to the formation of a mitf gene specifically expressed in the melanocyte lineage. These observations validate fish as an outstanding model to study the mechanisms and biological consequences of gene and genome duplication but underline the complexity of the fish model and the caution necessary in transferring knowledge from fish to higher vertebrates and vice versa.

Nuclear receptors are markers of animal genome evolution

Nuclear hormone receptors form one evolutionary related super-family of proteins, which mediate the interaction between hormones (or other ligands) and gene expression in animals. Early phylogenetic analyses showed two main periods of gene duplication which gave rise to present-day diversity in most animals: one at the origin of the family, and another specifically in vertebrates. Moreover this second period is composed itself by, probably, two rounds of duplication, as proposed by Susumu Ohno at the origin of vertebrates. There are indeed often two, three or four vertebrate orthologs of each invertebrate nuclear receptor, in accordance with this theory. The complete genome of Drosophila melanogaster contains 21 nuclear receptors, compared to 49 in the human genome. In addition, many nuclear receptors have more paralogs in the zebrafish than in mammals, and a genome duplication has been proposed at the origin of ray-finned fishes. Nuclear receptors are a very good model to investigate the dating and functional role of these duplications, since they are dispersed in the genome, allow robust phylogenetic reconstruction, and are functionnaly well characterized, with different adaptations for different paralogs. We illustrate this with examples from differents nuclear receptors and different groups of species.

Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters

Comparisons of DNA sequences among evolutionarily distantly related genomes permit identification of conserved functional regions in noncoding DNA. Hox genes are highly conserved in vertebrates, occur in clusters, and are uninterrupted by other genes. We aligned (PipMaker) the nucleotide sequences of the HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human, and mouse, which are separated by approximately 500 million years of evolution. In support of our approach, several identified putative regulatory elements known to regulate the expression of Hox genes were recovered. The majority of the newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac database). The regulatory intergenic regions located between the genes that are expressed most anteriorly in the embryo are longer and apparently more evolutionarily conserved than those at the other end of Hox clusters. Different presumed regulatory sequences are retained in either the Aalpha or Abeta duplicated Hox clusters in the fish lineages. This suggests that the conserved elements are involved in different gene regulatory networks and supports the duplication-deletion-complementation model of functional divergence of duplicated genes.

Functional divergence of two zebrafish midkine growth factors following fish-specific gene duplication

In mammals, the unique midkine (mdk) gene encodes a secreted heparin-binding growth factor with neurotrophic activity. Here, we show the presence of two functional mdk genes named mdka and mdkb in zebrafish and rainbow trout. Both midkine proteins are clearly different from the related pleiotrophin, which was also identified in zebrafish and other fishes. Zebrafish mdka and mdkb genes map to linkage groups LG7 and LG25, respectively, both presenting synteny to human chromosome 11, in which the unique human ortholog mdk is located. At least four other genes unique in mammals are also present as duplicates on LG7 and LG25. Phylogenetic and divergence analyses suggested that LG7/LG25 paralogs including mdka and mdkb have been formed at approximately the same time, early during the evolution of the fish lineage. Hence, zebrafish and rainbow trout mdka and mdkb might have been generated by an ancient block duplication, and might be remnants of the proposed fish-specific whole-genome duplication. In contrast to the ubiquitous expression of their mammalian counterpart, zebrafish mdka and mdkb are expressed in spatially restricted, mostly nonoverlapping patterns during embryonic development and strongly in distinct domains in the adult brain. Ectopic ubiquitous expression of both mdk genes in early zebrafish embryos caused completely distinct effects on neural crest and floorplate development. These data indicate that mdka and mdkb underwent functional divergence after duplication. This provides an outstanding model to analyze the molecular mechanisms that lead to differences in pathways regulating the formation of homologous embryonic structures in different vertebrates.

Application of comparative genomics in fish endocrinology

This review discusses the ways in which comparative genomics can contribute to the study of fish endocrinology. First, the phylogenetic position of fish and an overview of their specific endocrine systems are presented. The emphasis will be on teleosts because they are the most abundant fishes and because most data are available for this group. Second, the complexity of fish genomics is reviewed. With the vast array of genome sizes and ploidy levels, assignment of gene orthology is more difficult in fish, but this is an absolute prerequisite in functional analysis and it is important to be aware of such genome plasticity when cloning genes. The ease with which a gene is cloned at the genomic level is directly related to genome size and complexity, a factor that is not known in the majority of fish species. Finally, the methodology is presented along with specific examples of parathyroid hormone-related protein (PTHrP) (a previously unidentified hormone in fish), calcium-sensing receptor, and calcitonin (with a duplication of this particular ligand in Fugu rubripes). Preliminary data also suggest that there are further duplicated genes in the calcium regulatory system. Comparative genomics has provided a valuable approach for isolating and characterizing a range of fish genes involved in calcium regulation. However, for understanding the physiology and endocrine regulation of this system, particularly with regard to gene duplication, an alternative approach is required in which conventional endocrinology techniques will play a significant role.

Medaka dmY/dmrt1Y is not the universal primary sex-determining gene in fish

An outstanding candidate for a primary male-determining gene equivalent to Sry of mammals has been recently described from a non-mammalian vertebrate, the medaka fish (Oryzias latipes). However, the universality of dmY/dmrt1Y as the master sex-determining gene in fish is questionable. Phylogenetic analysis shows that dmY/dmrt1Y is an evolutionarily young Y chromosome-specific duplicate of a gene involved in testis development in vertebrates, and that this duplicate cannot be the primary sex-determining gene in most other fish species. Study of alternative fish models will probably uncover new genetic strategies controlling sexual dimorphism in vertebrates.

Comparative sequence and expression analyses of four mammalian VPS4 genes

The VPS4 gene is a member of the AAA-family; it codes for an ATPase which is involved in lysosomal/endosomal membrane trafficking. VPS4 genes are present in virtually all eukaryotes. Exhaustive data mining of all available genomic databases from completely or partially sequenced organisms revealed the existence of up to three paralogues, VPS4a, -b, and -c. Whereas in the genome of lower eukaryotes like yeast only one VPS4 representative is present, we found that mammals harbour two paralogues, VPS4a and VPS4b. Most interestingly, the Fugu fish contains a third VPS4 paralogue (VPS4c). Sequence comparison of the three VPS4 paralogues indicates that the Fugu VPS4c displays sequence features intermediate between VPS4a and VPS4b. Using complete mammalian VPS4a and VPS4b cDNA clones as probes, genomic clones of both VPS4 paralogues in human and mouse were identified and sequenced. The chromosomal loci of all four VPS4 genes were determined by independent methods. A BLAST search of the human genome database with the human VPS4A sequence yielded a double match, most likely due to a faulty assembly of sequence contigs in the human draft sequence. Fluorescent in situ hybridization and radiation hybrid analyses demonstrated that human and mouse VPS4A/a and VPS4B/b are located on syntenic chromosomal regions. Northern blot and semi-quantitative reverse transcription analyses showed that mouse VPS4a and VPS4b are differentially expressed in different organs, suggesting that the two paralogues have developed different functional properties since their divergence. To investigate the subcellular distribution of the murine VPS4 paralogues, we transiently expressed various fluorescent VPS4 fusion proteins in mouse 3T3 cells. All tested VPS4 fusion proteins were found in the cytosol. Expression of dominant-negative mutant VPS4 fusion proteins led to their concentration in the perinuclear region. Co-expression of VPS4a-GFP and VPS4b-dsRed fusion proteins revealed a partial co-localization that was most prominent with mutant VPS4a and VPS4b proteins. A physical interaction between the mouse paralogues was also supported by two-hybrid analyses.

ParaDB: a tool for paralogy mapping in vertebrate genomes

We present ParaDB (http://abi.marseille.inserm.fr/paradb/), a new database for large-scale paralogy studies in vertebrate genomes. We intended to collect all information (sequence, mapping and phylogenetic data) needed to map and detect new paralogous regions, previously defined as Paralogons. The AceDB database software was used to generate graphical objects and to organize data. General data were automatically collated from public sources (Ensembl, GadFly and RefSeq). ParaDB provides access to data derived from whole genome sequences (Homo sapiens, Mus musculus and Drosophila melanogaster): cDNA and protein sequences, positional information, bibliographical links. In addition, we provide BLAST results for each protein sequence, InParanoid orthologs and 'In-Paralogs' data, previously established paralogy data, and, to compare vertebrates and Drosophila, orthology data.

Neurogenin1 defines zebrafish cranial sensory ganglia precursors

Cells delaminate from epithelial placodes to form sensory ganglia in the vertebrate head. We describe the formation of cranial neurogenic placodes in the zebrafish, Danio rerio, using bHLH transcription factors as molecular markers. A single neurogenin gene, neurogenin1 (ngn1), is required for the development of all zebrafish cranial ganglia, which contrasts with other described vertebrates. Expression of ngn1 delineates zebrafish ganglionic placodes, including trigeminal, lateral line, and epibranchial placodes. In addition, ngn1 is expressed in a subset of cells within the otic vesicle that will delaminate to form the octaval (statoacoustic) ganglion. The trigeminal placode is the first to differentiate, and forms just lateral and adjacent to the neural crest. Expression of ngn1 is transient and prefigures expression of a related bHLH transcription factor, neuroD. Interfering with ngn1 function using a specific antisense morpholino oligonucleotide blocks differentiation of all cranial ganglia but not associated glial cells. Lateral line sensory neuromasts develop independently of ngn1 function, suggesting that two derivatives of lateral line placodes, ganglia and migrating primordia, are under separate genetic control.

Developmental functions of theDistal-less/Dlx homeobox genes

Distal-less is the earliest known gene specifically expressed in developing insect limbs; its expression is maintained throughout limb development. The homeodomain transcription factor encoded by Distal-less is required for the elaboration of proximodistal pattern elements in Drosophila limbs and can initiate proximodistal axis formation when expressed ectopically. Distal-less homologs, the Dlx genes, are expressed in developing appendages in at least six phyla, including chordates, consistent with requirements for Dlx function in normal appendage development across the animal kingdom. Recent work implicates the Dlx genes of vertebrates in a variety of other developmental processes ranging from neurogenesis to hematopoiesis. We review what is known about the invertebrate and vertebrate Dll/Dlx genes and their varied roles during development. We propose revising the vertebrate nomenclature to reflect phylogenetic relationships among the Dlx genes.

Thioester function is conserved in SpC3, the sea urchin homologue of the complement component C3

The amino acid sequence of the thioester site in the alpha chain of SpC3, the sea urchin homologue of C3, is conserved. This implies a conserved function of covalent bond formation with amine or hydroxyl groups on target molecules. When coelomic fluid (CF) was incubated with 14C-methylamine, a classic assay for thioester binding function, the alpha chain became labeled. When CF was treated to induce autolysis, peptide bond cleavage occurred at the thioester site. Autolysis could be blocked or reduced by pre-treating CF with either methylamine or yeast, both of which are known to bind to thioester sites C3 proteins from other organisms. The data suggest that SpC3 can bind to target cell surfaces, constituting indirect evidence that it can covalently bind to pathogen surfaces and function as an opsonin in vivo. This activity may be an important aspect of host defense in the sea urchin.

Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes

The ray-finned fishes (Actinopterygii) seem to have two copies of many tetrapod (Sarcopterygii) genes. The origin of these duplicate fish genes is the subject of some controversy. One explanation for the existence of these extra fish genes could be an increase in the rate of independent gene duplications in fishes. Alternatively, gene duplicates in fish may have been formed in the ancestor of all or most Actinopterygii during a complete genome duplication event. A third possibility is that tetrapods have lost more genes than fish after gene or genome duplication events in the common ancestor of both lineages. These three hypotheses can be tested by phylogenetic reconstruction. Previously, we found that a large number of anciently duplicated genes of zebrafish are sister sequences in evolutionary trees suggesting that they were produced in Actinopterygii after the divergence of Sarcopterygii [Phil. Trans. R. Soc. Lond. B 356 (2001) 119]. On the other hand, several well-supported trees showed one of the two fish genes as the sister sequence to a monophyletic clade that included the second fish gene and genes from frog, chicken, mouse and human. These so-called outgroup topologies suggest that the origin of many fish duplicates predates the divergence of the Sarcopterygii and Actinopterygii and support the hypothesis that tetrapods have lost duplicates that have been retained in fish. Here we show that many of these 'outgroup' tree topologies are erroneous and can be corrected when mutational saturation is taken into account. To this end, a Java-based application has been developed to visualize the amount of saturation in amino acid sequences. The program graphically displays the number of observed frequent and rare amino acid replacements between pairs of sequences against their overall evolutionary distance. Discrimination between frequent and rare amino acid replacements is based on substitution probability matrices (e.g. PAM and BLOSUM). Evolutionary distances between sequences can be computed from the fraction of unsaturated sites only and evolutionary trees inferred by pairwise distance methods. When trees are computed by omitting the saturated fraction of sites, most fish duplicates are sister sequences.

One melanocortin 4 and two melanocortin 5 receptors from zebrafish show remarkable conservation in structure and pharmacology

We report the cloning, genome mapping, functional expression, pharmacology and anatomical distribution of three melanocortin (MC) receptors from zebrafish (z). Phylogenetic analysis showed with high bootstrap support that these genes represent one MC4 receptor and two MC5 receptors. Chromosomal mapping showed conserved synteny between regions containing zMC4 and human (h) MC4 receptors, whereas the two zMC5 receptor genes map on chromosome segments in which the zebrafish has several genes with two orthologues of a single mammalian gene. It is likely that the two copies of zMC5 receptors arose through a separate duplication in the teleost lineage. The zMC4, zMC5a, and zMC5b receptors share 70-71% overall amino acid identity with the respective human orthologues and over 90% in three TM regions believed to be most important for ligand binding. All three zebrafish receptors also show pharmacological properties remarkably similar to their human orthologues, with similar affinities and the same potency order, when expressed and characterized in radioligand binding assay for the natural MSH) peptides alpha-, beta-, and gamma-MSH. Stimulation of transfected mammalian cells with alpha-MSH caused a dose-dependent increase in intracellular cAMP levels for all three zebrafish receptors. All three genes were expressed in the brain, eye, ovaries and gastrointestinal tract, whereas the zMC5b receptor was also found in the heart, as determined by RT-PCR. Our studies, which represent the first characterization of MC receptors in a nonamniote species, indicate that the MC receptor subtypes arose very early in vertebrate evolution. Important pharmacological and functional properties, as well as gene structure and syntenic relationships have been highly conserved over a period of more than 400 million years implying that these receptors participate in vital physiological functions.

Search for enhancers: teleost models in comparative genomic and transgenic analysis of cis regulatory elements

Homology searches between DNA sequences of evolutionary distant species (phylogenetic footprinting) offer a fast detection method for regulatory sequences. Because of the small size of their genomes, tetraodontid species such as the Japanese pufferfish and green spotted pufferfish have become attractive models for comparative genomics. A disadvantage of the tetraodontid species is, however, that they cannot be bred and manipulated routinely under laboratory conditions, so these species are less attractive for developmental and genetic analysis. In contrast, an increasing arsenal of transgene techniques with the developmental model species zebrafish and medaka are being used for functional analysis of cis regulatory sequences. The main disadvantage is the much larger genome. While comparison between many loci proved the suitability of phylogenetic footprinting using fish and mammalian sequences, fast rate of change in enhancer structure and gene duplication within teleosts may obscure detection of homologies. Here we discuss the contribution and potentials provided by different teleost models for the detection and functional analysis of conserved cis-regulatory elements.

Molecular characterization of three estrogen receptor forms in zebrafish: binding characteristics, transactivation properties, and tissue distributions

There are two estrogen receptor (ER) subtypes in fish, ERalpha and ERbeta, and increasing evidence that the ERbeta subtype has more than one form. However, there is little information on the characteristics and functional significance of these ERs in adults and during development. Here, we report the cloning and characterization of three functional ER forms, zfERalpha, zfERbeta1, and zfERbeta2, in the zebrafish. The percentages of identity between these receptors suggest the existence of three distinct genes. Each cDNA encoded a protein that specifically bound estradiol with a dissociation constant ranging from 0.4 nM (zfERbeta2) to 0.75 nM (zfERalpha and zfERbeta1). In transiently transfected cells, all three forms were able to induce, in a dose-dependent manner, the expression of a reporter gene driven by a consensus estrogen responsive element; zfERbeta2 was slightly more sensitive than zfERalpha and zfERbeta1. Tissue distribution pattern, analyzed by reverse transcription polymerase chain reaction, showed that the three zfER mRNAs largely overlap and are predominantly expressed in brain, pituitary, liver, and gonads. In situ hybridization was performed to study in more detail the distribution of the three zfER mRNAs in the brain of adult females. The zfER mRNAs exhibit distinct but partially overlapping patterns of expression in two neuroendocrine regions, the preoptic area and the mediobasal hypothalamus. The characterization of these zfERs provides a new perspective for understanding the mechanisms underlying estradiol actions in a vertebrate species commonly used for developmental studies.

Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q

Cosmid and BAC contig maps have been constructed across two Fugu genomic regions containing the orthologs of human genes mapping to human chromosome 20q. Contig gene contents have been assessed by sample sequencing and comparative database analyses. Contigs are centered around two Fugu topoisomerase1 (top1) genes that were initially identified by sequence similarity to human TOP1 (20q12). Two other genes (SNAI1 and KRML) mapping to human chromosome 20 are also duplicated in Fugu. The two contigs have been mapped to separate Fugu chromosomes. Our data indicate that these linkage groups result from the duplication of an ancestral chromosome segment containing at least 40 genes that now map to the long arm of human chromosome 20. Although there is considerable conservation of synteny, gene orders are not well conserved between Fugu and human, with only very short sections of two to three adjacent genes being maintained in both organisms. Comparative analyses have allowed this duplication event to be dated before the separation of Fugu and zebrafish. Our data (which are best explained by regional duplication, followed by substantial gene loss) support the hypothesis that there have been a large number of gene and regional duplications (and corresponding gene loss) in the fish lineage, possibly resulting from a single whole genome duplication event.

The evolution of morphological complexity in zebrafish stripes

The zebrafish pigment stripe pattern is a complex tissue containing iridophores, xanthophores and multiple melanocyte types. Mutational analysis reveals that both ancient and recent gene duplications are involved in the generation or maintenance of the pattern complexity. Receptor tyrosine kinases kit and fms, products of an ancient gene duplication, are required in distinct types of melanocytes and xanthophores. Transcription factors mitfa and mitfb, results of a teleost-specific duplication, partition gene expression and function between different sets of melanocytes. Understanding the roles of these duplicated genes in zebrafish allows us to predict roles for their precursors in ancestral vertebrates.

Genome and protein evolution in eukaryotes

The past year has seen the completion of the genome sequence of the flowering plant Arabidopsis thaliana and the initial sequence reports of the human genome. The availability of completely sequenced eukaryotic genomes from disparate phylogenetic lineages has opened the door to comparative analyses and a better understanding of the evolutionary processes shaping genomes. Complex many-to-many relationships between genes from different species appear to be the norm, suggesting that transfer of detailed functional annotation will not be straightforward. In addition to expansion and contraction of gene families, new genes evolve from recombination of pre-existing domains, although some domain families do appear to have evolved recently and to be specific to restricted phylogenetic lineages. The overall picture is of a huge diversity of gene content within eukaryotic genomes, reflecting different functional demands in different species.

NUREBASE: database of nuclear hormone receptors

Nuclear hormone receptors are an abundant class of ligand activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official nomenclature of nuclear receptors, we have developed NUREBASE, a database containing protein and DNA sequences, reviewed protein alignments and phylogenies, taxonomy and annotations for all nuclear receptors. The reviewed NUREBASE is completed by NUREBASE_DAILY, automatically updated every 24 h. Both databases are organized under a client/server architecture, with a client written in Java which runs on any platform. This client, named FamFetch, integrates a graphical interface allowing selection of families, and manipulation of phylogenies and alignments. NUREBASE sequence data is also accessible through a World Wide Web server, allowing complex queries. All information on accessing and installing NUREBASE may be found at http://www.ens-lyon.fr/LBMC/laudet/nurebase.html.

Wanda: a database of duplicated fish genes

Comparative genomics has shown that ray-finned fish (Actinopterygii) contain more copies of many genes than other vertebrates. A large number of these additional genes appear to have been produced during a genome duplication event that occurred early during the evolution of Actinopterygii (i.e. before the teleost radiation). In addition to this ancient genome duplication event, many lineages within Actinopterygii have experienced more recent genome duplications. Here we introduce a curated database named Wanda that lists groups of orthologous genes with one copy from man, mouse and chicken, one or two from tetraploid Xenopus and two or more ancient copies (i.e. paralogs) from ray-finned fish. The database also contains the sequence alignments and phylogenetic trees that were necessary for determining the correct orthologous and paralogous relationships among genes. Where available, map positions and functional data are also reported. The Wanda database should be of particular use to evolutionary and developmental biologists who are interested in the evolutionary and functional divergence of genes after duplication. Wanda is available at http://www.evolutionsbiologie.uni-konstanz.de/Wanda/.

The LN54 radiation hybrid map of zebrafish expressed sequences

To increase the density of a gene map of the zebrafish, Danio rerio, we have placed 3119 expressed sequence tags (ESTs) and cDNA sequences on the LN54 radiation hybrid (RH) panel. The ESTs and genes mapped here join 748 SSLp markers and 459 previously mapped genes and ESTs, bringing the total number of markers on the LN54 RH panel to 4226. Addition of these new markers brings the total LN54 map size to 14,372 cR, with 118 kb/cR. The distribution of ESTs according to linkage groups shows relatively little variation (minimum, 73; maximum, 201). This observation, combined with a relatively uniform size for zebrafish chromosomes, as previously indicated by karyotyping, indicates that there are no especially gene-rich or gene-poor chromosomes in this species. We developed an algorithm to provide a semiautomatic method for the selection of additional framework markers for the LN54 map. This algorithm increased the total number of framework markers to 1150 and permitted the mapping of a high percentage of sequences that could not be placed on a previous version of the LN54 map. The increased concentration of expressed sequences on the LN54 map of the zebrafish genome will facilitate the molecular characterization of mutations in this species.

Study of intrachromosomal duplications among the eukaryote genomes

Complete eukaryote chromosomes were investigated for intrachromosomal duplications of nucleotide sequences. The analysis was performed by looking for nonexact repeats on two complete genomes, Saccharomyces cerevisiae and Caenorhabditis elegans, and four partial ones, Drosophila melanogaster, Plasmodium falciparum, Arabidopsis thaliana, and Homo sapiens. Through this analysis, we show that all eukaryote chromosomes exhibit similar characteristics for their intrachromosomal repeats, suggesting similar dynamics: many direct repeats have their two copies physically close together, and these close direct repeats are more similar and shorter than the other repeats. On the contrary, there are almost no close inverted repeats. These results support a model for the dynamics of duplication. This model is based on a continuous genesis of tandem repeats and implies that most of the distant and inverted repeats originate from these tandem repeats by further chromosomal rearrangements (insertions, inversions, and deletions). Remnants of these predicted rearrangements have been brought out through fine analysis of the chromosome sequence. Despite these dynamics, shared by all eukaryotes, each genome exhibits its own style of intrachromosomal duplication: the density of repeated elements is similar in all chromosomes issued from the same genome, but is different between species. This density was further related to the relative rates of duplication, deletion, and mutation proper to each species. One should notice that the density of repeats in the X chromosome of C. elegans is much lower than in the autosomes of that organism, suggesting that the exchange between homologous chromosomes is important in the duplication process.

Duplicate mitf genes in zebrafish: complementary expression and conservation of melanogenic potential

Mutations in the zebrafish nacre/mitfa gene, expressed in all embryonic melanogenic cells, perturb only neural crest melanocytes, suggesting redundancy of mitfa with another gene in the zebrafish retinal pigment epithelium (RPE). Here, we describe a second zebrafish mitf gene, mitfb, which may fulfill this role. The proteins encoded by the two zebrafish mitf genes appear homologous to distinct isoforms generated by alternately spliced mRNAs of the single mammalian Mitf gene, suggesting specialization of the two zebrafish genes following a duplication event. Consistent with this hypothesis, expression of mitfa and mitfb is partially overlapping. mitfb is coexpressed with mitfa in the RPE at an appropriate time to compensate for loss of mitfa function in the nacre mutant but is not expressed in neural crest melanoblasts. Additionally, mitfb is expressed in the epiphysis and olfactory bulb where mitfa is not, and where Mitf expression has not previously been reported in other species. mitfb, but not a zebrafish ortholog of the closely related gene tfe3, can rescue neural crest melanophore development in nacre/mitfa mutant embryos when expressed via the mitfa promoter. These data suggest that mitfa and mitfb together may recapitulate the expression and functions of a single ancestral Mitf gene, and that mitfb may serve additional novel functions.