Evolution and discontinuous distribution of Rex3 retrotransposons in fish.

The fish non–long-terminal-repeat (non-LTR) retrotransposon Rex3 has recently been isolated from the platyfish Xiphophorus maculatus (Volff et al. 1999). Complete versions of Rex3 encode a reverse transcriptase (RT) and an apurinic/apyrimidinic endonuclease (fig. 1). Rex3 belongs to the RTE family of non-LTR retrotransposons (Malik and Eickbush 1998; Volff et al. 1999). From all autonomous fish retrotransposons reported to date, Rex3 has the widest distribution observed in teleosts and is present in fish species having diverged 150–200 MYA. We report here a large PCRand Southern blot–based survey of Rex3 evolution including 21 representative teleost species (fig. 1) and 115 Rex3 partial reverse transcriptase sequences (fig. 2). The species chosen include a panel of economically important fishes (salmon Salmo salar, trout Oncorhynchus mykiss, carp Cyprinus carpio, sturgeon Acipenser sturio, mandarin fish Siniperca chuatsi) and several small aquarium teleosts used as models for developmental biology, cancer research and evolutionary studies (zebrafish Danio rerio, medakafish Oryzias latipes, platyfish Xiphophorus maculatus, and other Poeciliidae), as well as the genome project fish, the Japanese pufferfish Fugu rubripes. Rex3 partial RT-encoding sequences could be amplified by PCR from the majority of fish species with at least one of the nine primer combinations tested, but not from the more divergent nonteleost Acipenser sturio (sturgeon) and not from both salmonid species tested (O. mykiss and S. salar) (fig. 1). Using cloned Rex3 probes from X. maculatus and from Anguilla anguilla (European eel) in Southern blot experiments, no specific signal could be detected in A. sturio, O. mykiss, and S. salar even under low-stringency conditions (not shown), confirming the PCR analysis results. According to classical morphological and molecular fish phylogenies (fig. 1; Nelson 1994; Forey et al. 1996; Orti and Meyer 1996), the distribution of Rex3 in teleosts is discontinuous. Hence, Rex3 was lost (or, alternatively, diverged extremely rapidly) in the Oncorhynchus/Salmo lineage after its divergence from the Esox lineage. There are about 1,000 Rex3 copies in the haploid genome of Xiphophorus species (Volff et al. 1999). All other Poeciliidae species included in this study and the related Fundulus displayed a high level of Rex3 reiteration as well (data not shown). Rex3 is present in high copy numbers in the genomes of O. latipes, Oreochrom-