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Molecular Genetics and Genomics

, Volume 279, Issue 4, pp 385–401 | Cite as

Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants

  • Fabrício Ramon Lopes
  • Marcelo Falsarella Carazzolle
  • Gonçalo Amarante Guimarães Pereira
  • Carlos Augusto Colombo
  • Claudia Marcia Aparecida Carareto
Original Paper

Abstract

Transposable elements are major components of plant genomes and they influence their evolution, acting as recombination hot spots, acquiring specific cell functions or becoming part of protein-coding regions. The latter is the subject of the present analysis. This study is a report on the annotation of transposable elements (TEs) in expressed sequences of Coffea arabica, Coffea canephora and Coffea racemosa, showing the occurrence of 383 ESTs and 142 unigenes with TE fragments in these three Coffea species. Based on selected unigenes, it was possible to suggest 26 putative proteins with TE-cassette insertions, demonstrating a likely contribution to protein variability. The genes for two of those proteins, the fertility restorer (FR) and the pyrophosphate-dependent phosphofructokinase (PPi-PFKs) genes, were selected for evaluating the impact of TE-cassettes on host gene evolution of other plant genomes (Arabidopsis thaliana, Oryza sativa and Populus trichocarpa). This survey allowed identifying a FR gene in O. sativa harboring multiple insertions of LTR retrotransposons that originated new exons, which however does not necessarily mean a case of molecular domestication. A possible transduction event of a fragment of the PPi-PFK β-subunit gene mediated by Helitron ATREPX1 in Arabidopsis thaliana was also highlighted.

Keywords

Transposable elements Coffea genome Protein diversity Molecular domestication Gene transduction 

Notes

Acknowledgments

We thank V.V. Kapitonov (GIRINST, Mountain View, USA) for valuable suggestions, L.M. Almeida (University of Alberta, Edmonton, Canada) for the drawing of Fig. 1 and three anonymous referees for critically reviewing the manuscript. This work was supported by grants provided by the Brazilian agencies FAPESP (fellowship 05/57212-3 to F.R.L) and CNPq (to C.M.A.C and G.A.G.P.).

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Fabrício Ramon Lopes
    • 1
  • Marcelo Falsarella Carazzolle
    • 2
  • Gonçalo Amarante Guimarães Pereira
    • 2
  • Carlos Augusto Colombo
    • 3
  • Claudia Marcia Aparecida Carareto
    • 1
  1. 1.Laboratory of Molecular Evolution, Department of BiologyUNESP, São Paulo State UniversitySão José do Rio PretoBrazil
  2. 2.Laboratory of Genomics and Expression, Department of Genetics and Evolution, Institute of BiologyUNICAMP, State University of CampinasCampinasBrazil
  3. 3.IAC, Agronomic Institute of CampinasCampinasBrazil

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