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MpSaci is a widespread gypsy-Ty3 retrotransposon highly represented by non-autonomous copies in the Moniliophthora perniciosa genome

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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 sha** its genome. In this work, we aimed the characterization of a new gypsy/Ty3 retrotransposon species, named MpSaci, in the M. perniciosa 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. Approximately, all of the copies are non-autonomous as shifts in 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 elements containing small sequences with or without interruptions 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 findings 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.

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Acknowledgments

We are grateful to CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico), CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior), SEAGRI (Secretaria de Agricultura, Irrigação e Reforma Agrária do Estado da Bahia), CARGILL/FUNCAMP/UNICAMP convenium, and FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) for financial support. We also would like to acknowledge the contributions of the Center for Computational Engineering and Sciences at Universidade Estadual de Campinas, SP, Brazil (FAPESP/CEPID project #2013/08293-7).

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Authors and Affiliations

  1. Embrapa Trigo, Passo Fundo, RS, CEP 99001-970, Brazil

    Jorge F. Pereira

  2. Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, CEP 36570-000, Brazil

    Elza F. Araújo, Casley B. Queiroz & Marisa V. Queiroz

  3. Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, CEP 36570-000, Brazil

    Sérgio H. Brommonschenkel

  4. Departamento de Genética e Evolução, Universidade Estadual de Campinas, Campinas, SP, CEP 13083-970, Brazil

    Gustavo G. L. Costa, Marcelo F. Carazzolle & Gonçalo A. G. Pereira

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  1. Jorge F. Pereira
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  2. Elza F. Araújo
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  3. Sérgio H. Brommonschenkel
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  4. Casley B. Queiroz
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  5. Gustavo G. L. Costa
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  6. Marcelo F. Carazzolle
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  7. Gonçalo A. G. Pereira
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  8. Marisa V. Queiroz
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Corresponding author

Correspondence to Marisa V. Queiroz.

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Communicated by G. Goldman.

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Pereira, J.F., Araújo, E.F., Brommonschenkel, S.H. et al. MpSaci is a widespread gypsy-Ty3 retrotransposon highly represented by non-autonomous copies in the Moniliophthora perniciosa genome. Curr Genet 61, 185–202 (2015). https://doi.org/10.1007/s00294-014-0469-3

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  • DOI: https://doi.org/10.1007/s00294-014-0469-3

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