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.

There has been a significant body of literature on species flock definition but not so much about practical means to appraise them. We here apply the five criteria of Eastman and McCune for detecting species flocks in four taxonomic components of the benthic fauna of the Antarctic shelf: teleost fishes, crinoids (feather stars), echinoids (sea urchins) and crustacean arthropods. Practical limitations led us to prioritize the three historical criteria (endemicity, monophyly, species richness) over the two ecological ones (ecological diversity and habitat dominance). We propose a new protocol which includes an iterative fine-tuning of the monophyly and endemicity criteria in order to discover unsuspected flocks. As a result nine « full » species flocks (fulfilling the five criteria) are briefly described. Eight other flocks fit the three historical criteria but need to be further investigated from the ecological point of view (here called « core flocks »). The approach also shows that some candidate taxonomic components are no species flocks at all. The present study contradicts the paradigm that marine species flocks are rare. The hypothesis according to which the Antarctic shelf acts as a species flocks generator is supported, and the approach indicates paths for further ecological studies and may serve as a starting point to investigate the processes leading to flock-like patterning of biodiversity.

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Identification of the sex-determining genes of the Nile tilapia (Oreochromis niloticus) has important implications for commercial aquaculture. We previously identified an XX/XY sex-determining locus in this species within a 10cM interval between markers GM201 and UNH995 on linkage group one (LG1). In order to refine this region, we developed new AFLP markers using bulked segregant analysis of the mapping families. We identified three AFLP markers that showed a sex-specific pattern of segregation. All three mapped near, but just outside, the previously identified sex-determining region on LG1. Hybridization of BAC clones containing these markers to chromosome spreads confirmed that the XX/XY sex determining locus is on one of the small chromosomes in O. niloticus.

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The diploid-polyploid Squalius alburnoides complex resulted from interspecific hybridization. The chromosomal mapping of 28S and 5S ribosomal genes and of (TTAGGG)n telomeric repeats was performed on specimens from the complex and from the sympatric bisexual species S. pyrenaicus (the complex maternal ancestor) as part of an investigation of the evolutionary relationships between genomic constitutions and the consequences of the ongoing polyploidization process in terms of chromosome reshaping. Contrasting results were obtained. While results with 5S rDNA and telomeric probes gave an impression of genomic stability, the variability detected with 28S rDNA probe suggested quite the opposite. The 5S rDNA probe mapped constantly to three chromosomes per haploid genome with apparently conserved locations in morphologically similar chromosomes; conversely, prominent intra- and inter-individual variations of 28S rDNA and of syntenic sites with 5S rDNA were detected with regard to number, size and location. Hypotheses for the causes of such polymorphisms are discussed. The terminal position of most 28S rDNA sites and the absence of detectable interstitial telomeric sequences suggest a mechanism that does not involve major chromosomal rearrangements. These fishes share similar patterns for the studied cytogenetic markers which may be taken as evidence of an apparent stability that may be hiding extensive and subtle genome variations that are possibly related to an ongoing evolutionary process of genome tetraploidization and speciation.