Mol Genet Genomics (2007) 277:83–95 DOI 10.1007/s00438-006-0174-0 123 ORIGINAL PAPER Molecular characterization and genomic distribution of Isis: a new retrotransposon of Drosophila buzzatii M. P. García Guerreiro · A. Fontdevila Received: 21 February 2006 / Accepted: 18 September 2006 / Published online: 13 October 2006  Springer-Verlag 2006 Abstract A new transposable element, Isis, is identi- Wed as a LTR retrotransposon in Drosophila buzzatii. DNA sequence analysis shows that Isis contains three long ORFs similar to gag, pol and env genes of retrovi- ruses. The ORF1 exhibits sequence homology to matrix, capsid and nucleocapsid gag proteins and ORF2 encodes a putative protease (PR), a reverse transcrip- tase (RT), an Rnase H (RH) and an integrase (IN) region. The analysis of a putative env product, encoded by the env ORF3, shows a degenerated protein contain- ing several stop codons. The molecular study of the putative proteins coded by this new element shows strik- ing similarities to both Ulysses and Osvaldo elements, two LTR retrotransposons, present in D. virilis and D. buzzatii, respectively. Comparisons of the predicted Isis RT to several known retrotransposons show strong phylogenetic relationships to gypsy-like elements, par- ticulary to Ulysses retrotransposon. Studies of Isis chro- mosomal distribution show a strong hybridization signal in centromeric and pericentromeric regions, and a scat- tered distribution along all chromosomal arms. The exis- tence of insertional polymorphisms between diVerent strains and high molecular weight bands by Southern blot suggests the existence of full-sized copies that have been active recently. The presence of euchromatic inser- tion sites coincident between Isis and Osvaldo could indicate preferential insertion sites of Osvaldo element into Isis sequence or vice versa. Moreover, the presence of Isis in diVerent species of the buzzatii complex indi- cates the ancient origin of this element. Keywords Transposable elements · Retrotransposons · Drosophila buzzatii · Isis · Genomic distribution Introduction Retrotransposons, or class I elements, are mobile ele- ments that transpose through an RNA intermediate. As a consequence of their replicative transposition mechanism, they are generally present in higher num- ber than transposable elements (TE) of other classes. These TE retrotransposons represent the largest pro- portion in Drosophila genome representing at least 15% (Kaminker et al. 2002). They also account for a large fraction of other eukaryotic genomes; for exam- ple, they represent more than 50% of the maize genome (SanMiguel et al. 1996, 1998) and nearly half (42%) of the human genome (IHGSC 2001). The Drosophila buzzatii species belong to the D. repl- eta group (Wasserman 1982) and shows a nonsatellite repetitive DNA content (19–26%) higher than that found in D. melanogaster (Marin et al. 1992). DiVerent TEs were isolated in this species including elements of class I (Fran- cino et al. 1993; Labrador and Fontdevila 1994; Pantazidis et al 1999; García Guerreiro and Fontdevila 2001) and class II (Cáceres et al. 1999; Casals et al. 2005). The best- characterized retrotransposon is the Osvaldo element, iso- lated from a recent insertion site, that constitutes a new Communicated by G. Reuter. Sequence data from this article have been deposited in the EMBL/GenBank Data Librairies with the accession number DQ408427. M. P. G. Guerreiro (&) · A. Fontdevila Departament de Genètica i Microbiologia, EdiWci C. Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain e-mail: mariapilar.garcia.guerreiro@uab.es