1 3 Curr Genet DOI 10.1007/s00294-014-0469-3 RESEARCH ARTICLE MpSaci is a widespread gypsy-Ty3 retrotransposon highly represented by non-autonomous copies in the Moniliophthora perniciosa genome Jorge F. Pereira · Elza F. Araújo · Sérgio H. Brommonschenkel · Casley B. Queiroz · Gustavo G. L. Costa · Marcelo F. Carazzolle · Gonçalo A. G. Pereira · Marisa V. Queiroz Received: 10 April 2014 / Revised: 21 November 2014 / Accepted: 22 December 2014 © Springer-Verlag Berlin Heidelberg 2015 the reading frame and stop codons were detected. Only two elements (MpSaci6 and MpSaci9) code for GAG and POL proteins that possess functional domains. Conserved domains that are typically not found in retrotransposons were detected and could potentially impact the expression of neighbor genes. Solo LTRs and several LARDs (large retrotransposon derivative) were detected. Unusual ele- ments containing small sequences with or without interrup- tions that are similar to gag or different pol domains and presenting LTRs with different levels of similarities were identified. Methylation was observed in MpSaci reverse transcriptase sequences. Distribution analysis indicates that MpSaci elements are present in high copy number in the genomes of C-, S- and L-biotypes of M. perniciosa. In addition, C-biotype isolates originating from the state of Bahia have fragments in common with isolates from the Amazon region and two hybridization profiles related to two chromosomal groups. RT-PCR analysis reveals that the gag gene is constitutively expressed and that the expression is increased at least three-fold with nutrient depravation even though no new insertion were observed. These find- ings point out that MpSaci collaborated and, even though is primarily represented by non-autonomous elements, still might contribute to the generation of genetic variability in the most important cacao pathogen in Brazil. Abstract Transposons are an important source of genetic variation. The phytopathogen Moniliophthora perniciosa shows high level of variability but little is known about the role of class I elements in shaping its genome. In this work, we aimed the characterization of a new gypsy/Ty3 retrotransposon species, named MpSaci, in the M. perni- ciosa genome. These elements are largely variable in size, ranging from 4 to 15 kb, and harbor direct long terminal repeats (LTRs) with varying degrees of similarity. Approxi- mately, all of the copies are non-autonomous as shifts in Communicated by G. Goldman. Nucleotide sequence data reported are available in the DDBL/ EMBL/GenBank databases under the accession numbers: KJ526182 (MpSaci1), KJ526183 (MpSaci2), KJ526184 (MpSaci3), KJ526185 (MpSaci4), KJ526186 (MpSaci5), KJ526187 (MpSaci6), KJ526188 (MpSaci7), KJ526189 (MpSaci8), KJ526190 (MpSaci9), KJ526191 (MpSaci10), KJ526192 (MpSaci11), KJ526193 (MpSaci12), KJ526194 (MpSaci13), KJ526195 (MpSaci14), KJ526196 (MpSaci15), KJ526197 (MpSaci16), KJ526198 (MpSaci17), KJ526199 (MpSaci18), KJ526200 (MpSaci19), KJ526201 (MpSaci20), KJ526202 (MpSaci21), KJ526203 (MpSaci22), KJ526204 (MpSaci23), KJ526205 (MpSaci24), KJ526206 (MpSaci25), KJ526207 (MpSaci26), KJ526208 (MpSaci27), KJ526209 (MpSaci28), KJ526210 (MpSaci29), and KJ526211 (MpSaci30). Electronic supplementary material The online version of this article (doi:10.1007/s00294-014-0469-3) contains supplementary material, which is available to authorized users. J. F. Pereira Embrapa Trigo, Passo Fundo, RS CEP 99001-970, Brazil E. F. Araújo · C. B. Queiroz · M. V. Queiroz (*) Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG CEP 36570-000, Brazil e-mail: mvqueiro@ufv.br S. H. Brommonschenkel Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG CEP 36570-000, Brazil G. G. L. Costa · M. F. Carazzolle · G. A. G. Pereira Departamento de Genética e Evolução, Universidade Estadual de Campinas, Campinas, SP CEP 13083-970, Brazil