Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis

Tetraodon nigroviridis is a freshwater pufferfish 20-30 million years dista nt from Fugu rubripes. The genome of both tetraodontiforms is compact, most ly because intergenic and intronic sequences are reduced in size compared t o other vertebrate genomes. The previously uncharacterized Tetraodon genome is described here together with a detailed analysis of its repeat content and organization. We report the sequencing of 46 megabases of bacterial art ificial chromosome (BAC) end sequences, which represents a random DNA sampl e equivalent to 13% of the genome. The sequence and location of rRNA gene c lusters, centromeric and subtelocentric satellite sequences have been deter mined. Minisatellites and microsatellites have been cataloged and notable d ifferences were observed in comparison with microsatellites from Fugu. The genome contains homologies to all known families of transposable elements, including Ty3-gypsy, Tyl-copia, Line retrotransposons, DNA transposons, and retroviruses, although their overall abundance is <1%. This structural ana lysis is an important prerequisite to sequencing the Tetraodon genome.