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At least 55 records · Page 3Linked to original sources
PubMed1996

Conservation of synteny between the genome of the pufferfish (Fugu rubripes) and the region on human chromosome 14 (14q24.3) associated with familial Alzheimer disease (AD3 locus)

The genome of the pufferfish (Fugu rubripes) (400 Mb) is approximately 7.5 times smaller than the human genome, but it has a similar gene repertoire to that of man. If regions of the two genomes exhibited conservation of gene order (i.e., were syntenic), it should be possible to reduce dramatically the effort required for identification of candidate genes in human disease loci by sequencing syntenic regions of the compact Fugu genome. We have demonstrated that three genes (dihydrolipoamide succinyltransferase, S31iii125, and S20i15), which are linked to FOS in the familial Alzheimer disease focus (AD3) on human chromosome 14, have homologues in the Fugu genome adjacent to Fugu cFOS. The relative gene order of cFOS, S31iii125, and S20i15 was the same in both genomes, but in Fugu these three genes lay within a 12.4-kb region, compared to >600 kb in the human AD3 locus. These results demonstrate the conservation of synteny between the genomes of Fugu and man and highlight the utility of this approach for sequence-based identification of genes in human disease loci.

Acyltransferases↗
PubMed2004

Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes.

With about 24,000 extant species, teleosts are the largest group of vertebrates. They constitute more than 99% of the ray-finned fishes (Actinopterygii) that diverged from the lobe-finned fish lineage (Sarcopterygii) about 450 MYA. Although the role of genome duplication in the evolution of vertebrates is now established, its role in structuring the teleost genomes has been controversial. At least two hypotheses have been proposed: a whole-genome duplication in an ancient ray-finned fish and independent gene duplications in different lineages. These hypotheses are, however, based on small data sets and lack adequate statistical and phylogenetic support. In this study, we have made a systematic comparison of the draft genome sequences of Fugu and humans to identify paralogous chromosomal regions ("paralogons") in the Fugu that arose in the ray-finned fish lineage ("fish-specific"). We identified duplicate genes in the Fugu by phylogenetic analyses of the Fugu, human, and invertebrate sequences. Our analyses provide evidence for 425 fish-specific duplicate genes in the Fugu and show that at least 6.6% of the genome is represented by fish-specific paralogons. We estimated the ages of Fugu duplicate genes and paralogons using the molecular clock. Remarkably, the ages of duplicate genes and paralogons are clustered, with a peak around 350 MYA. These data strongly suggest a whole-genome duplication event early during the evolution of ray-finned fishes, probably before the origin of teleosts.

Animals↗
PubMed1996

A functional role for some Fugu introns larger than the typical short ones: the example of the gene coding for ribosomal protein S7 and snoRNA U17.

The compact genome of Fugu rubripes, with its very small introns, appears to be particularly suitable to study intron-encoded functions. We have analyzed the Fugu gene for ribosomal protein S7 (formerly S8, see Note), whose Xenopus homolog contains in its introns the coding sequences for the small nucleolar RNA U17. Except for intron length, the organization of the Fugu S7 gene is very similar to that of the Xenopus counterpart. The total length of the Fugu S7 gene is 3930 bp, compared with 12691 bp for Xenopus. This length difference is uniquely due to smaller introns. Although short, the six introns are longer than the approximately 100 bp size of most Fugu introns, as they host U17 RNA coding sequences. While four of the six U17 sequences are 'canonical', the remaining two represent diverged U17 pseudocopies. In fact, microinjection in Xenopus oocytes of in vitro synthesized Fugu transcripts containing the 'canonical' U17f sequence results in efficient production of mature U17 RNA, while injection of a transcript containing the U17 psi b sequence does not.

Animals↗
PubMed2002

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.

Animals↗
PubMed2004

Extensive expansion of the claudin gene family in the teleost fish, Fugu rubripes.

In humans, the claudin superfamily consists of 19 homologous proteins that commonly localize to tight junctions of epithelial and endothelial cells. Besides being structural tight-junction components, claudins participate in cell-cell adhesion and the paracellular transport of solutes. Here, we identify and annotate the claudin genes in the whole-genome of the teleost fish, Fugu rubripes (Fugu), and determine their phylogenetic relationships to those in mammals. Our analysis reveals extensive gene duplications in the teleost lineage, leading to 56 claudin genes in Fugu. A total of 35 Fugu claudin genes can be assigned orthology to 17 mammalian claudin genes, with the remaining 21 genes being specific to the fish lineage. Thus, a significant number of the additional Fugu genes are not the result of the proposed whole-genome duplication in the fish lineage. Expression profiling shows that most of the 56 Fugu claudin genes are expressed in a more-or-less tissue-specific fashion, or at particular developmental stages. We postulate that the expansion of the claudin gene family in teleosts allowed the acquisition of novel functions during evolution, and that fish-specific novel members of gene families such as claudins contribute to a large extent to the distinct physiology of fishes and mammals.

Animals↗
PubMed2002

Comparative analysis of somitogenesis related genes of the hairy/Enhancer of split class in Fugu and zebrafish.

BACKGROUND: Members of a class of bHLH transcription factors, namely the hairy (h), Enhancer of split (E(spl)) and hairy-related with YRPW motif (hey) (h/E(spl)/hey) genes are involved in vertebrate somitogenesis and some of them show cycling expression. By sequence comparison, identified orthologues of cycling somitogenesis genes from higher vertebrates do not show an appropriate expression pattern in zebrafish. The zebrafish genomic sequence is not available yet but the genome of Fugu rubripes was recently published. To allow comparative analysis, the currently known Her proteins from zebrafish were used to screen the genomic sequence database of Fugu rubripes. RESULTS: 20 h/E(spl)/hey-related genes were identified in Fugu, which is twice the number of corresponding zebrafish genes known so far. A novel class of c-Hairy proteins was identified in the genomes of Fugu and Tetraodon. A screen of the human genome database with the Fugu proteins yielded 10 h/E(spl)/hey-related genes. By analysing the upstream sequences of the c-hairy class genes in zebrafish, Fugu and Tetraodon highly similar sequence stretches were identified that harbour Suppressor of hairless paired binding sites (SPS). This motif was also discovered in the upstream sequences of the her1 gene in the examined fish species. Here, the Su(h) sites are separated by longer intervening sequences. CONCLUSIONS: Our study indicates that not all her homologues in zebrafish have been isolated. Comparison to the human genome suggests a selective duplication of h/E(spl) genes in pufferfish or loss of members of these genes during evolution to the human lineage.

Journal Article↗
PubMed2003

Analysis of the conservation of synteny between Fugu and human chromosome 12.

BACKGROUND: The pufferfish Fugu rubripes (Fugu) with its compact genome is increasingly recognized as an important vertebrate model for comparative genomic studies. In particular, large regions of conserved synteny between human and Fugu genomes indicate its utility to identify disease-causing genes. The human chromosome 12p12 is frequently deleted in various hematological malignancies and solid tumors, but the actual tumor suppressor gene remains unidentified. RESULTS: We investigated approximately 200 kb of the genomic region surrounding the ETV6 locus in Fugu (fETV6) in order to find conserved functional features, such as genes or regulatory regions, that could give insight into the nature of the genes targeted by deletions in human cancer cells. Seven genes were identified near the fETV6 locus. We found that the synteny with human chromosome 12 was conserved, but extensive genomic rearrangements occurred between the Fugu and human ETV6 loci. CONCLUSION: This comparative analysis led to the identification of previously uncharacterized genes in the human genome and some potentially important regulatory sequences as well. This is a good indication that the analysis of the compact Fugu genome will be valuable to identify functional features that have been conserved throughout the evolution of vertebrates.

Animals↗
PubMed2004

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 http://anz.anu.edu.au:8080/Fugu_rubripes/ 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.

Amino Acid Sequence↗
PubMed1999

Genomic structure and comparative analysis of nine Fugu genes: conservation of synteny with human chromosome Xp22.2-p22.1.

The pufferfish Fugu rubripes has a compact 400-Mb genome that is approximately 7.5 times smaller than the human genome but contains a similar number of genes. Focusing on the distal short arm of the human X chromosome, we have studied the evolutionary conservation of gene orders in Fugu and man. Sequencing of 68 kb of Fugu genomic DNA identified nine genes in the following order: (SCML2)-STK9, XLRS1, PPEF-1, KELCH2, KELCH1, PHKA2, AP19, and U2AF1-RS2. Apart from an evolutionary inversion separating AP19 and U2AF1-RS2 from PHKA2, gene orders are identical in Fugu and man, and all nine human homologs map to the Xp22 band. All Fugu genes were found to be smaller than their human counterparts, but gene structures were mostly identical. These data suggest that genomic sequencing in Fugu is a powerful and economical strategy to predict gene orders in the human genome and to elucidate the structure of human genes.

Amino Acid Sequence↗
PubMed2004

Fugu immunoglobulin D: a highly unusual gene with unprecedented duplications in its constant region.

We have isolated and characterized the cDNA that encodes IgD of fugu (Takifugu rubripes). Though the splicing of micro1 with the delta1 domain was similar to those reported for teleost IgDs, highly unusual and unprecedented domain duplications were found in the constant region of the fugu IgD. The structure of the fugu IgD is like VDJ-micro1-(delta1-delta2-delta3-delta4-delta5-delta6)(2)-delta7-deltam1-deltam2. Genomic sequence analysis of the fugu IgD gene supported the results of cDNA sequencing that the first six delta domains in the constant region are duplicated. Such a novel duplication pattern has not been reported in any other vertebrates. However, IgD secretory domains could not be identified in this study. The deduced amino acid sequence of the fugu IgD constant region showed high identity (35-55%) to the sequences of previously reported teleost IgDs. Gene expression analyses based on RT-PCR demonstrated that the IgD gene is preferentially expressed in presumptive lymphoid tissues; moreover, in situ hybridization showed that IgD-positive cells are distributed throughout the spleen and head kidney. The expression pattern is similar to that of IgM, corroborating the hypothesis that IgD plays an important role in the humoral immune system of this species.

Alternative Splicing↗
PubMed2001

Molecular cloning and genomic structure of a gene encoding interferon regulatory factor in the pufferfish (Fugu rubripes).

Interferon regulatory factors (IRFs) are a large family of transcription factors involved in regulating the transcriptional response of vertebrates to interferons and viral infection. In this report we describe the cloning and genomic organization of an IRF gene from the pufferfish (Fugu rubripes). The fugu IRF gene spans 2.7 kb from the transcription start site to the polyadenylation signal. It consists of 10 exons and 9 introns and encodes a protein of 296 amino acids. The overall amino acid sequence of fugu IRF displays 55% identity to flounder IRF and approximately 44% identity to avian and mammalian IRF-1 and IRF-2. On the basis of the genomic structure and the absence of a transcriptional repression domain, we conclude that the fugu IRF is a member of the IRF-1 family. The fugu IRF gene is expressed in a wide range of tissues. While a single transcript of 1.4 kb was detected in most tissues, several larger transcripts generated using alternative polyadenylation signals were found in the gills.

Journal Article↗
PubMed1995

Analysis of the dopamine receptor family in the compact genome of the puffer fish Fugu rubripes.

The genome of the puffer fish, Fugu rubripes (Fugu), is approximately 400 Mb, 7.5 times smaller than that of human. We have isolated four dopamine receptor-like genes from Fugu genomic DNA. These genes show high sequence and structural homology to the known dopamine receptor genes, although, in contrast to previously described genes from this species, the intron size is comparable to that in human. The 5' noncoding exons of the D2/D3 dopamine receptor-like genes is described and compared to that in human. The high gene density of Fugu is shown by the close proximity of a cystatin-like gene 1503 bp from the dopamine receptor gene D222. We propose that the compact genome of Fugu can serve as a model for identifying gene family members directly from genomic DNA.

Amino Acid Sequence↗
PubMed2004

Characterization of the zebrafish vascular endothelial growth factor A gene: comparison with vegf-A genes in mammals and Fugu.

Vascular endothelial growth factor (VEGF-A) is a key angiogenic growth factor which regulates vertebrate embryonic vascularization, adult physiology such as wound healing and reproduction as well as many human diseases. To understand the evolution and regulation of this gene in vertebrates, we have isolated and characterized the zebrafish vegf-A gene and compared it with VEGF-A genes of human, mouse as well as an in silico isolated VEGF-A homologue from pufferfish. Our results indicate that the zebrafish vegf-A gene is organized similarly to mammalian and Fugu VEGF-A genes, with eight exons interrupted by seven introns. However, zebrafish vegf-A introns are generally larger than mammalian introns while Fugu VEGF-A introns are much smaller. Furthermore, zebrafish exon 6 (z6) has a unique sequence while Fugu's exon 6 is highly homologous to the mammalian counterparts. Alternative splicing generates multiple vegf-A mRNA isoforms in zebrafish with Vegf(121) as the dominant isoform in adult and Vegf(165) as the dominant isoform in early embryos. The exon z6 containing isoform Vegf(12345z678) is only detected in heart, muscle, and early embryos while another isoform Vegf-A(1234577)(a)(8) is only detected in heart. Furthermore, no conserved 5' flanking sequences between zebrafish and Fugu were observed while numerous conserved regions exist between human and mouse in this area. These results suggest both conserved and diverged functions of VEGF-A from fish to mammals since the separation of these two groups from their common ancestor about 450 million years ago and a diverged regulation of this gene since the separation of zebrafish from Fugu. These data will be valuable for future studies of VEGF-A gene regulation and function in different vertebrates.

Amino Acid Sequence↗
PubMed2004

Origin and diversity of the SOX transcription factor gene family: genome-wide analysis in Fugu rubripes.

The SOX family of transcription factors are found throughout the animal kingdom and are important in a variety of developmental contexts. Genome analysis has identified 20 Sox genes in human and mouse, which can be subdivided into 8 groups, based on sequence comparison and intron-exon structure. Most of the SOX groups identified in mammals are represented by a single SOX sequence in invertebrate model organisms, suggesting a duplication and divergence mechanism has operated during vertebrate evolution. We have now analysed the Sox gene complement in the pufferfish, Fugu rubripes, in order to shed further light on the diversity and origins of the Sox gene family. Major differences were found between the Sox family in Fugu and those in humans and mice. In particular, Fugu does not have orthologues of Sry, Sox15 and Sox30, which appear to be specific to mammals, while Sox19, found in Fugu and zebrafish but absent in mammals, seems to be specific to fishes. Six mammalian Sox genes are represented by two copies each in Fugu, indicating a large-scale gene duplication in the fish lineage. These findings point to recent Sox gene loss, duplication and divergence occurring during the evolution of tetrapod and teleost lineages, and provide further evidence for large-scale segmental or a whole-genome duplication occurring early in the radiation of teleosts.

Animals↗
PubMed2004

Multiple gene organization of pufferfish Fugu rubripes tropomyosin isoforms and tissue distribution of their transcripts.

The Japanese pufferfish, torafugu (Fugu rubripes), has a haploid genome of about 400 Mb in size, which has been sequenced to approximately 90% coverage. Here we identified six Fugu tropomyosin (TPM) gene sequences by using the BLASTN program and the sequence of the white croaker TPM1 gene in our collection against the draft assembly of the Fugu genomic sequence database. TPM2, TPM3 and TPM4 genes were identified together with a set of two potentially duplicated genes of TPM1 (TPM1-1 and TPM1-2) as described in our previous report and TPM4 (TPM4-1 and TPM4-2) newly found in this study. The expression patterns of these Fugu TPM genes were determined by reverse transcription polymerase chain reaction (RT-PCR). A phylogenetic tree was constructed using the deduced amino acid sequences, which were encoded by the exons common to all vertebrate TPM genes. This indicated that the Fugu TPM1 and TPM4 genes had resulted from a gene duplication in the fish evolutionary lineage.

Alternative Splicing↗
PubMed2004

Identification of the putative collagen X gene from the pufferfish Fugu rubripes.

The type X collagen gene is the classical marker of hypertrophic chondrocytes. Mutations in the human collagen X gene cause metaphyseal chondrodysplasia type Schmid (MCDS). In order to gain insight into the evolution of collagen X genes, we identified a putative collagen X gene from the pufferfish Fugu rubripes. We demonstrated expression of the putative Fugu collagen X gene by reverse transcription-polymerase chain reaction (RT-PCR) with primers spanning intron 1. The Fugu collagen X gene shares a common gene structure and high amino acid identity with mammalian and chicken collagen X genes. Interestingly, we have found that most of the residues mutated in human MCDS are highly conserved in the Fugu gene. The availability of the Fugu collagen X gene sequence will be of value in the identification of functionally important residues within the protein and for delineating regulatory elements that control collagen X gene expression in chondrocytes.

5' Flanking Region↗
PubMed2004

The 350-fold compacted Fugu parkin gene is structurally and functionally similar to human Parkin.

Mutations in the human parkin gene (huParkin) are the predominant genetic cause of familial parkinsonism. The huParkin locus, spanning about 1.4 Mb, is one of the largest in the human genome. Despite its huge size, huParkin codes for a rather short transcript of about 4.5 kb. To gain an insight into the structure, function and evolutionary history of huParkin, we have characterized the pufferfish [Fugu rubripes (Fugu)] ortholog of huParkin. A remarkable feature of the Fugu parkin gene (fuparkin) is its unusually compact size. It spans only about 4 kb and is thus 350-fold smaller than its human ortholog. The Fugu and human parkin genes are otherwise highly similar in their genomic organization and expression pattern. Furthermore, like human Parkin, Fugu parkin also functions as an ubiquitin ligase. These shared features between fuparkin and huParkin suggest that the physiological function and regulation of the parkin gene are conserved during the evolution of vertebrates. Conceivably, the compact locus of fuparkin could serve as a useful model to understand the transcriptional regulation of huParkin.

Amino Acid Sequence↗
PubMed1997

Molecular cloning of 5-hydroxytryptamine (5-HT) type 1 receptor genes from the Japanese puffer fish, Fugu rubripes.

To characterize the structure of Fugu G-protein coupled receptor family and its evolutionary divergence, we have cloned and sequenced the Fugu 5-HT type 1 receptor genes by Polymerase Chain Reaction (PCR) with degenerate primers followed by phage library screening. The analysis of the deduced amino acid sequences showed that F1A alpha and F1A beta have the highest homology to the human 5-HT1A receptor (71.5% and 63.7%, respectively). Another clone, F1D, showed highest (70.5%) homology to the human type 1D receptor. The amino acid residues that are important for ligand binding have been conserved in these Fugu genes. The phylogenetic tree analysis suggests that the duplication event of the Fugu type 1A receptor may have occurred after the divergence of Fugu and the tetrapod lineage.

Amino Acid Sequence↗