Genome-Wide Comparative Analysis of pogo-Like Transposable Elements in Different Fusarium Species Marie Dufresne • Olivier Lespinet • Marie-Jose ´e Daboussi • Aure ´lie Hua-Van Received: 24 May 2011 / Accepted: 7 November 2011 / Published online: 18 November 2011 Ó Springer Science+Business Media, LLC 2011 Abstract The recent availability of genome sequences of four different Fusarium species offers the opportunity to perform extensive comparative analyses, in particular of repeated sequences. In a recent work, the overall content of such sequences in the genomes of three phylogenetically related Fusarium species, F. graminearum, F. verticillio- ides, and F. oxysporum f. sp. lycopersici has been esti- mated. In this study, we present an exhaustive characterization of pogo-like elements, named Fots, in four Fusarium genomes. Overall 10 Fot and two Fot-related miniature inverted-repeat transposable element families were identified, revealing a diversification of multiple lin- eages of pogo-like elements, some of which accompanied by a gain of introns. This analysis also showed that such elements are present in an unusual high proportion in the genomes of F. oxysporum f. sp. lycopersici and Nectria haematococca (anamorph F. solani f. sp. pisi) in contrast with most other fungal genomes in which retroelements are the most represented. Interestingly, our analysis showed that the most numerous Fot families all contain potentially active or mobilisable copies, thus conferring a mutagenic potential of these transposable elements and consequently a role in strain adaptation and genome evolution. This role is strongly reinforced when examining their genomic distri- bution which is clearly biased with a high proportion (more than 80%) located on strain- or species-specific regions enriched in genes involved in pathogenicity and/or adap- tation. Finally, the different reproductive characteristics of the four Fusarium species allowed us to investigate the impact of the process of repeat-induced point mutations on the expansion and diversification of Fot elements. Keywords Fusaria Á Fot transposons Á Phylogenetics Á Evolution Introduction In recent years, great progress has been made in the characterization, the genomic distribution, dispersion, and maintenance of transposable elements (TEs) in fungal species (for a review, see Daboussi and Capy 2003). Such studies have highlighted interesting features such as the prevalence of pogo-like elements among class II elements (or DNA transposons) in these organisms. An interesting feature of this family in fungal genomes is that it contains active members since several copies have been identified through their transposition in a target gene in F. oxysporum (Migheli et al. 1999; Trouvelot et al. 2002), Botrytis cinerea (Levis et al. 1997), Aspergillus niger (Nyysso ¨nen et al. 1996), and Magnaporte grisea (Kang et al. 2001). Most of these elements share common features with Fot1, the first active pogo-like element discovered in fungi (Daboussi et al. 1992). However, comparative analysis with other members of this family showed that they are Electronic supplementary material The online version of this article (doi:10.1007/s00239-011-9472-1) contains supplementary material, which is available to authorized users. M. Dufresne (&) Institut de Biologie des Plantes, Ba ˆt 630, Universite ´ Paris-Sud 11, UMR8618, 91405 Orsay cedex, France e-mail: marie.dufresne@u-psud.fr O. Lespinet Á M.-J. Daboussi Institut de Ge ´ne ´tique et Microbiologie, Universite ´ Paris-Sud 11, UMR8621, 91405 Orsay, France A. Hua-Van Laboratoire Evolution, Ge ´nomes et Spe ´ciation, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France 123 J Mol Evol (2011) 73:230–243 DOI 10.1007/s00239-011-9472-1