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 ,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.Access to entire genome sequences is revolutionizing our understanding of how genetic information is stored and organized in DNA, and how it has evolved over time. The sequence of a genome provides exquisite detail of the gene catalogue within a species, and the recent analysis of near-complete genome sequences of three mammals (human 1 , mouse 2 and rat 3 ) shows the acceleration in the search for causal links between genotype and phenotype, which can then be related to physiological, ecological and evolutionary observations. The partial sequence of the compact puffer fish Takifugu rubripes genome was obtained recently and this survey provided a preliminary catalogue of fish genes 4 . However, the Takifugu assembly is highly fragmented and as a result important questions could not be addressed.Here, we describe and analyse the genome sequence of the freshwater puffer fish Tetraodon nigroviridis with long-range linkage and extensive anchoring to chromosomes. Tetraodon resembles Takifugu in that it possesses one of the smallest known vertebrate genomes, but as a popular aquarium fish it is readily available and is easily maintained in tap water (see Supplementary Notes for naming conventions, natural habitat and phylogeny). The two puffer fish diverged from a common ancestor between 18-30 million years (Myr) ago and from the common ancestor with mammals about 450 Myr ago 5 . This long evolutionary distance provides a good contrast to distinguish conserved features from neutrally evolving DNA by sequence comparison. Tetraodon sequences in fact had an important role in providing a reliable estimate of the number of genes in the human genome 6 . There has been a vigorous and unresolved debate as to whether a whole-genome duplication (WGD) occurred in the ray-finned fish (actinopterygians) lineage after its separation from tetrapods [7][8][9] . By exploiting the extensive anchoring of the Tetraodon sequence to chromosomes, we provide a definitive answer to this question. The distribution of duplicated genes in t...

We identified DNA markers linked to sex determining genes in six closely related species of tilapiine fishes. The mode of sex determination differed among species. In Oreochromis karongae and Tilapia mariae the sex-determining locus is on linkage group (LG) 3 and the female is heterogametic (WZ-ZZ system). In O. niloticus and T. zillii the sex-determining locus is on LG1 and the male is heterogametic (XX-XY system). A more complex pattern was observed in O. aureus and O. mossambicus, in which markers on both LG1 and LG3 were associated with sex. We found evidence for sex-linked lethal effects on LG1, as well as interactions between loci in the two linkage groups. Comparison of genetic and physical maps demonstrated a broad region of recombination suppression harboring the sex-determining locus on LG3. Sex-specific recombination suppression was found in the female heterogametic sex. Sequence analysis showed the accumulation of repetitive elements in this region. Phylogenetic analysis suggests that at least two transitions in the mode of sex determination have occurred in this clade. This variation in sex determination mechanisms among closely related species makes tilapias an excellent model system for studying the evolution of sex chromosomes in vertebrates.

Abstract:The non-long terminal repeat retrotransposons Rex1 and Rex3 were identified in 13 species of Antarctic fishes from five families of the suborder Notothenioidei. Partial reverse transcriptase gene sequences were characterized for Notothenia coriiceps, Trematomus newnesi and Dissostichus mawsoni (Nototheniidae), and Gymnodraco acuticeps (Bathydraconidae). Rex1 and Rex3 both formed a notothenioidspecific monophyletic group compared to the corresponding elements from other fishes. They globally evolved under purifying selection, showing their activity during notothenioid evolution. Fluorescence in situ hybridization analysis of the chromosomal distribution of Rex1 and Rex3 was performed for several notothenioid fish species. Rex1 was generally less abundant than Rex3, which was widely scattered on the chromosomes with more intense hybridization patterns in some specific zones. Particularly, Rex3 accumulated in Chionodraco hamatus in pericentromeric areas, short arms of some pairs as well as in an intercalary band in the long arm of the Y chromosome similarly to a previously described DNA transposon. Such pattern similarities suggest the presence of autosomal and gonosomal regions of preferential accumulation for different types of repeated elements in notothenioid genomes. To the best of our knowledge, this report is the first description and analysis of retrotransposable elements in Antarctic fish genomes.