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Linking the Genomes of Nonmodel Teleosts Through Comparative Genomics

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Recently the genomes of two more teleost species have been released: the medaka (Oryzias latipes), and the three-spined stickleback (Gasterosteus aculateus). The rapid developments in genomics of fish species paved the way to new and valuable research in comparative genetics and genomics. With the accumulation of information in model species, the genetic and genomic characterization of nonmodel, but economically important species, is now feasible. Furthermore, comparison of low coverage gene maps of aquacultured fish species against fully sequenced fish species will enhance the efficiency of candidate genes identification projected for quantitative trait loci (QTL) scans for traits of commercial interest. This study shows the syntenic relationship between the genomes of six different teleost species, including three fully sequenced model species: Tetraodon nigroviridis, Oryzias latipes, Gasterosteus aculateus, and three marine species of commercial and evolutionary interest: Sparus aurata, Dicentrarchus labrax, Oreochromis spp. All three commercial fish species belong to the order Perciformes, which is the richest in number of species (approximately 10,000) but poor in terms of available genomic information and tools. Syntenic relationships were established by using 800 EST and microsatellites sequences successfully mapped on the RH map of seabream. Comparison to the stickleback genome produced most positive BLAT hits (58%) followed by medaka (32%) and Tetraodon (30%). Thus, stickleback was used as the major stepping stone to compare seabass and tilapia to seabream. In addition to the significance for the aquaculture industry, this approach can encompass important ecological and evolutionary implications.

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The authors thank Marine Genomics Europe Network, and in particular Dr. Richard Reinhardt from the Max-Planck Institute of Berlin for providing cDNA sequences, Professor Hiroshi Mitani for having provided medaka marker sequences, Mr. Spiros Papadopoulos who helped with RH mapping, Mr, Jaque Lagnel for bulk primer design, and Dr. Kostas Tsigenopoulos and Dr. Benny Ron for reviewing a first version of this article.

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Correspondence to E. Sarropoulou.

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Sarropoulou, E., Nousdili, D., Magoulas, A. et al. Linking the Genomes of Nonmodel Teleosts Through Comparative Genomics. Mar Biotechnol 10, 227–233 (2008).

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