Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.

Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.

Estimation of the extent of synteny between Tetraodon nigroviridis and Homo sapiens genomes.

This paper presents a genomic comparison between 20 sequenced BACs (or fragments of BACs) from Tetraodon nigroviridis and the human genome. A total of 199 fish genes were identified by informatics resources, together with their putative human orthologues. Comparisons of the localizations in both species led to the identification of 32 syntenic regions and a minimum of 131 rearrangements in these regions that occurred during independent evolution of these species. This made it possible to estimate the rate of genomic rearrangements that occurred per million years (and per megabase). This rate is comparable to that obtained by comparison of the Fugu rubripes shotgun sequence data to human data but is significantly higher that those obtained by comparing the human genome to mammalian genomes. Overall, it suggests that genomic evolution by rearrangement is not uniform within the vertebrate group.

An active non-LTR retrotransposon with tandem structure in the compact genome of the pufferfish Tetraodon nigroviridis.

The fish retrotransposable element Zebulon encodes a reverse transcriptase and a carboxy-terminal restriction enzyme-like endonuclease, and is related phylogenetically to site-specific non-LTR retrotransposons from nematodes. Zebulon was detected in the pufferfishes Tetraodon nigroviridis and Takifugu rubripes, as well as in the zebrafish Danio rerio. Structural analysis suggested that Zebulon, in contrast to most non-LTR retrotransposons, might be able to retrotranspose as a partial tandem array. Zebulon was active relatively recently in the compact genome of T. nigroviridis, in which it contributed to the extension of intergenic and intronic sequences, and possibly to the formation of genomic rearrangements. Accumulation of Zebulon together with other retrotransposons was observed in some heterochromatic chromosomal regions of the genome of T. nigroviridis that might serve as reservoirs for active elements. Hence, pufferfish compact genomes are not evolutionarily inert and contain active retrotransposons, suggesting the presence of mechanisms allowing accumulation of retrotransposable elements in heterochromatin, but minimizing their impact on euchromatic regions. Homologous recombination between partial tandem sequences eliminating active copies of Zebulon and reducing the size of insertions in intronic and intragenic regions might represent such a mechanism.

Analysis of 148 kb of genomic DNA of Tetraodon nigroviridis covering an amylase gene family.

We have sequenced and analysed a 148 kb genomic region of Tetraodon nigroviridis, a teleost fish with a compact genome. Several genes were identified by comparison with genomic or transcript sequences of other species, informatic prediction and screening of a cDNA library. As expected for a compact genome, sizes of the identified genes and introns are very small, and intergenic distances are short. Among identified genes, three code for amylases. As in mammals, these genes are linked, but they are found in a small region of less than 11 kb. These results represent the first description of a genomic sequence larger than 100 kb in this species. Synteny with the human genome is restricted to three regions corresponding to human 1p32.3, 1p13.3 and 1p21.1.

Conservation of the T-cell receptor alpha/delta linkage in the teleost fish Tetraodon nigroviridis.

T-cell specific receptors (TCR) are present in all groups] from the jawed vertebrates to the mammals. In teleosts, however, the genes encoding the gamma- and delta-chains have not yet been found, the alpha- and beta-chains have been characterized mainly at the expression level, and genomic organization of these loci remains largely unknown. Here we describe both the genomic organization of the TCR alpha/delta locus in Tetraodon nigroviridis and the transcription of TCRA and TCRD. The TCR alpha/delta locus consists of 13 V alpha/delta segments, a Calpha gene, and 12 Jalpha segments, followed by a Cdelta gene, two Jdelta segments, and several Ddelta segments. However, the genomic organization found in this teleost differs significantly from that which has been observed in mammals and birds: a common set of V segments is used to generate either an alpha- or a delta-chain by genomic inversion, and the size of the locus is small in this vertebrate.