Table of Contents
International Journal of Evolutionary Biology
Volume 2011 (2011), Article ID 358412, 9 pages
http://dx.doi.org/10.4061/2011/358412
Research Article

Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow

1IRD, UMR DIADE, Centre IRD de Montpellier, BP 64501, 34394 Montpellier Cedex 5, France
2UMR ECOFOG INRA, BP 709, 97387 Kourou Cedex, Guyane Française, France
3FOFIFA, BP 1444, Ambatobe, Antananarivo 101, Madagascar

Received 1 March 2011; Accepted 16 July 2011

Academic Editor: A. Rus Hoelzel

Copyright © 2011 Christine Dubreuil-Tranchant et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S.-J. Kwon, K. L. Ju, S. W. Hong, Y. J. Park, K. L. McNally, and N. S. Kim, “Genetic diversity and phylogenetic relationship in AA Oryza species as revealed by Rim2/Hipa CACTA transposon display,” Genes and Genetic Systems, vol. 81, no. 2, pp. 93–101, 2006. View at Publisher · View at Google Scholar · View at Scopus
  2. K. Takagi, H. Nagano, Y. Kishima, and Y. Sano, “MITE-transposon display efficiently detects polymorphisms among the Oryza AA-genome species,” Breeding Science, vol. 53, no. 2, pp. 125–132, 2003. View at Google Scholar · View at Scopus
  3. S. J. Wheelan, L. Z. Scheifele, F. Martinez-Murillo, R. A. Irizarry, and J. D. Boeke, “Transposon insertion site profiling chip (TIP-chip),” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 47, pp. 17632–17637, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  4. Z. J. Xu and W. Ramakrishna, “Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history,” Gene, vol. 412, no. 1-2, pp. 50–58, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  5. M. Calonje et al., “Non-coding nuclear DNA markers in phylogenetic reconstruction,” Plant Systematics and Evolution, vol. 282, no. 3-4, pp. 257–280, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. J. M. Casacuberta and N. Santiago, “Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes,” Gene, vol. 311, no. 1-2, pp. 1–11, 2003. View at Publisher · View at Google Scholar · View at Scopus
  7. D. Grzebelus et al., “Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula,” Gene, vol. 448, no. 2, pp. 214–220, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  8. R. J. Mason-Gamer, “Multiple homoplasious insertions and deletions of a Triticeae (Poaceae) DNA transposon: a phylogenetic perspective,” BMC Evolutionary Biology, vol. 7, article 92, 2007. View at Publisher · View at Google Scholar · View at PubMed
  9. C. Feschotte, N. Jiang, and S. R. Wessler, “Plant transposable elements: where genetics meets genomics,” Nature Reviews Genetics, vol. 3, no. 5, pp. 329–341, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  10. A. M. Casa, S. E. Mitchell, O. S. Smith, J. C. Register, S. R. Wessler, and S. Kresovich, “Evaluation of Hbr (MITE) markers for assessment of genetic relationships among maize (Zea mays L.) inbred lines,” Theoretical and Applied Genetics, vol. 104, no. 1, pp. 104–110, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  11. S. R. Wessler, T. E. Bureau, and S. E. White, “LTR-retrotransposons and MITEs: important players in the evolution of plant genomes,” Current Opinion in Genetics and Development, vol. 5, no. 6, pp. 814–821, 1995. View at Publisher · View at Google Scholar · View at Scopus
  12. A. Benjak, S. Boue, A. Forneck, and J. M. Casacuberta, “Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.),” Genome Biology and Evolution, vol. 1, pp. 75–84, 2009. View at Google Scholar
  13. O. Maurin, A. P. Davis, M. Chester, E. F. Mvungi, Y. Jaufeerally-Fakim, and M. F. Fay, “Towards a phylogeny for Coffea (Rubiaceae): identifying well-supported lineages based on nuclear and plastid DNA sequences,” Annals of Botany, vol. 100, no. 7, pp. 1565–1583, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  14. R. Waugh, K. McLean, A. J. Flavell et al., “Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP),” Molecular and General Genetics, vol. 253, no. 6, pp. 687–694, 1997. View at Publisher · View at Google Scholar · View at Scopus
  15. R. Kalendar, T. Grob, M. Regina, A. Suoniemi, and A. Schulman, “IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques,” Theoretical and Applied Genetics, vol. 98, no. 5, pp. 704–711, 1999. View at Publisher · View at Google Scholar · View at Scopus
  16. A. J. Flavell, M. R. Knox, S. R. Pearce, and T. H. N. Ellis, “Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis,” Plant Journal, vol. 16, no. 5, pp. 643–650, 1998. View at Publisher · View at Google Scholar · View at Scopus
  17. R. Guyot et al., “Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes,” BMC Plant Biology, vol. 9, no. 1, article 22, 2009. View at Publisher · View at Google Scholar · View at PubMed
  18. P. Cubry et al., “Diversity in coffee assessed with SSR markers: structure of the genus Coffea and perspectives for breeding,” Genome, vol. 51, no. 1, pp. 50–63, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  19. C. Gomez, S. Dussert, P. Hamon, S. Hamon, A. de Kochko, and V. Poncet, “Current genetic differentiation of Coffea canephora pierre ex a. Froehn in the guineo-Congolian african zone: cumulative impact of ancient climatic changes and recent human activities,” BMC Evolutionary Biology, vol. 9, no. 1, article 167, 2009. View at Publisher · View at Google Scholar · View at PubMed
  20. P. Musoli, P. Cubry, P. Aluka et al., “Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda,” Genome, vol. 52, no. 7, pp. 634–646, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  21. P. Hamon et al., “Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae),” Molecular Genetics and Genomics, vol. 285, no. 6, pp. 447–460, 2011. View at Publisher · View at Google Scholar · View at PubMed
  22. E. L. L. Sonnhammer and R. Durbin, “A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis,” Gene, vol. 167, no. 1-2, pp. GC1–GC10, 1995. View at Google Scholar
  23. P. Hamon, S. Siljak-Yakovlev, S. Srisuwan et al., “Physical mapping of rDNA and heterochromatin in chromosomes of 16 Coffea species: a revised view of species differentiation,” Chromosome Research, vol. 17, no. 3, pp. 291–304, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  24. A. P. Davis, R. Govaerts, D. M. Bridson, and P. Stoffelen, “An annotated taxonomic conspectus of the genus Coffea (Rubiaceae),” Botanical Journal of the Linnean Society, vol. 152, no. 4, pp. 465–512, 2006. View at Publisher · View at Google Scholar · View at Scopus
  25. C. Gomez et al., “Favourable habitats for Coffea inter-specific hybridization in central New Caledonia: combined genetic and spatial analyses,” Journal of Applied Ecology, vol. 47, no. 1, pp. 85–95, 2010. View at Publisher · View at Google Scholar · View at Scopus