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Journal of Botany
Volume 2011 (2011), Article ID 646198, 10 pages
http://dx.doi.org/10.1155/2011/646198
Review Article

The Genomes of All Angiosperms: A Call for a Coordinated Global Census

1School of Plant Sciences and Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA
2Department of Genetics, University of Georgia, Athens, GA 30602, USA
3Department of Biology, University of Missouri-St Louis, St Louis, MO 63121-4400, USA
4Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA
5Florida Museum of Natural History and The Genetics Institute, University of Florida, Gainesville, FL 32611, USA

Received 1 June 2011; Accepted 22 August 2011

Academic Editor: Andrew Wood

Copyright © 2011 David W. Galbraith 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. R. F. Thorne, “How many species of seed plants are there?” Taxon, vol. 51, no. 3, pp. 511–512, 2002. View at Google Scholar · View at Scopus
  2. A. J. Paton, N. Brummitt, R. Govaerts et al., “Towards target 1 of the global strategy for plant conservation: a working list of all known plant species—progress and prospects,” Taxon, vol. 57, no. 2, pp. 602–611, 2008. View at Google Scholar · View at Scopus
  3. B. Bremer, K. Bremer, M. W. Chase et al., “An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG III,” Botanical Journal of the Linnean Society, vol. 161, no. 2, pp. 105–121, 2009. View at Publisher · View at Google Scholar · View at Scopus
  4. D. Bramwell, “How many plant species are there?” Plant Talk, vol. 28, pp. 32–34, 2002. View at Google Scholar
  5. T. J. Davies, T. G. Barraclough, M. W. Chase, P. S. Soltis, D. E. Soltis, and V. Savolainen, “Darwin's abominable mystery: insights from a supertree of the angiosperms,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 7, pp. 1904–1909, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  6. R. Dirzo and P. H. Raven, “Global state of biodiversity and loss,” Annual Review of Environment and Resources, vol. 28, pp. 137–167, 2003. View at Publisher · View at Google Scholar · View at Scopus
  7. N. E. Stork, “Re-assessing current extinction rates,” Biodiversity and Conservation, vol. 19, no. 2, pp. 357–371, 2010. View at Publisher · View at Google Scholar · View at Scopus
  8. A. D. Barnosky, N. Matzke, S. Tomiya et al., “Has the Earth's sixth mass extinction already arrived?” Nature, vol. 471, no. 7336, pp. 51–57, 2011. View at Google Scholar
  9. American Museum of Natural History, “National survey reveals biodiversity crisis—scientific experts believe we are in midst of fastest mass extinction in Earth's history,” 1998, http://www.amnh.org/museum/ press/feature/biofact.html/.
  10. D. W. Galbraith, K. R. Harkins, and S. Knapp, “Systemic endopolyploidy in Arabidopsis thaliana,” Plant Physiology, vol. 96, no. 3, pp. 985–989, 1991. View at Google Scholar · View at Scopus
  11. M. Barow and A. Meister, “Endopolyploidy in seed plants is differently correlated to systematics, organ, life strategy and genome size,” Plant, Cell and Environment, vol. 26, no. 4, pp. 571–584, 2003. View at Publisher · View at Google Scholar · View at Scopus
  12. M. D. Bennett and I. J. Leitch, “Nuclear DNA amounts in angiosperms: targets, trends and tomorrow,” Annals of Botany, vol. 107, no. 3, pp. 467–590, 2011. View at Publisher · View at Google Scholar · View at PubMed
  13. J. L. Bennetzen, J. Ma, and K. M. Devos, “Mechanisms of recent genome size variation in flowering plants,” Annals of Botany, vol. 95, no. 1, pp. 127–132, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  14. N. Chantret, J. Salse, F. Sabot et al., “Molecular basis of evolutionary events that shaped the Hardness locus in diploid and polyploid wheat species (Triticum and Aegilops),” Plant Cell, vol. 17, no. 4, pp. 1033–1045, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  15. K. M. Devos, J. K. M. Brown, and J. L. Bennetzen, “Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis,” Genome Research, vol. 12, no. 7, pp. 1075–1079, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  16. K. Ilic, P. J. SanMiguel, and J. L. Bennetzen, “A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 21, pp. 12265–12270, 2003. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  17. E. Isidore, B. Scherrer, B. Chalhoub, C. Feuillet, and B. Keller, “Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels,” Genome Research, vol. 15, no. 4, pp. 526–536, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  18. J. Ma and J. L. Bennetzen, “Rapid recent growth and divergence of rice nuclear genomes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 34, pp. 12404–12410, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  19. J. Ma and J. L. Bennetzen, “Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 2, pp. 383–388, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  20. R. T. Gaeta and J. C. Pires, “Homoeologous recombination in allopolyploids: the polyploid ratchet,” New Phytologist, vol. 186, no. 1, pp. 18–28, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  21. C. Vitte and J. L. Bennetzen, “Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 47, pp. 17638–17643, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  22. I. J. Leitch, D. E. Soltis, P. S. Soltis, and M. D. Bennett, “Evolution of genome size in the angiosperms,” American Journal of Botany, vol. 90, no. 11, pp. 1596–1603, 2003. View at Google Scholar · View at Scopus
  23. I. J. Leitch, D. E. Soltis, P. S. Soltis, and M. D. Bennett, “Evolution of DNA amounts across land plants (embryophyta),” Annals of Botany, vol. 95, no. 1, pp. 207–217, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  24. D. W. Galbraith, J. Bartos, and J. Dolezel, “Flow cytometry and cell sorting in plant biotechnology,” in Flow Cytometry in Biotechnology, L. A. Sklar, Ed., pp. 291–322, Oxford University Press, New York, NY, USA, 2005. View at Google Scholar
  25. M. D. Bennett and I. J. Leitch, “Plant DNA C-values database,” 2010, http://data.kew.org/cvalues/.
  26. D. W. Galbraith, K. R. Harkins, J. M. Maddox et al., “Rapid flow cytometric analysis of the cell cycle in intact plant tissues,” Science, vol. 220, no. 4601, pp. 1049–1051, 1983. View at Google Scholar · View at Scopus
  27. J. S. Johnston, M. D. Bennett, A. L. Rayburn, D. W. Galbraith, and H. J. Price, “Reference standards for determination of DNA content of plant nuclei,” American Journal of Botany, vol. 86, no. 5, pp. 609–613, 1999. View at Google Scholar · View at Scopus
  28. J. Doležel, J. Greilhuber, and J. Suda, “Estimation of nuclear DNA content in plants using flow cytometry,” Nature Protocols, vol. 2, no. 9, pp. 2233–2244, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  29. K. R. Chi, “Going with the flow,” The Scientist, vol. 25, no. 5, p. 57, 2011. View at Google Scholar
  30. D. W. Galbraith, “Simultaneous flow cytometric quantification of plant nuclear DNA contents over the full range of described angiosperm 2C values,” Cytometry A, vol. 75, no. 8, pp. 692–698, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  31. J. Suda and P. Travnicek, “Reliable DNA ploidy determination in dehydrated tissues of vascular plants by DAPI flow cytometry—new prospects for plant research,” Cytometry A, vol. 69, no. 4, pp. 273–280, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  32. A. V. Roberts, “The use of bead beating to prepare suspensions of nuclei for flow cytometry from fresh leaves, herbarium leaves, petals and pollen,” Cytometry A, vol. 71, no. 12, pp. 1039–1044, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  33. D. Haussler, S. J. O'Brien, O. A. Ryder et al., “Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species,” Journal of Heredity, vol. 6, pp. 659–674, 100. View at Google Scholar
  34. J. Greilhuber, T. Borsch, K. Muller, A. Worberg, S. Porembski, and W. Barthlott, “Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size,” Plant Biology, vol. 8, no. 6, pp. 770–777, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  35. B. J. M. Zonneveld, “New record holders for maximum genome size in eudicots and monocots,” Journal of Botany, Article ID 527357, 4 pages, 2010. View at Publisher · View at Google Scholar
  36. P. SanMiguel, A. Tikhonov, Y.-K. Jin et al., “Nested retrotransposons in the intergenic regions of the maize genome,” Science, vol. 274, no. 5288, pp. 765–768, 1996. View at Publisher · View at Google Scholar · View at Scopus
  37. C. Vitte, O. Panaud, and H. Quesneville, “LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss,” BMC Genomics, vol. 8, article 218, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  38. D. W. Galbraith, “The grand challenges in enabling data-intensive biological research,” Frontiers in Genomic Assay Technology, vol. 2, no. 26, 2011. View at Publisher · View at Google Scholar
  39. P. Green, “2x genomes—does depth matter?” Genome Research, vol. 17, no. 11, pp. 1547–1549, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  40. D. A. Rasmussen and M. A. F. Noor, “What can you do with 0.1× genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae),” BMC Genomics, vol. 10, article 382, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  41. P. R. Steele and J. C. Pires, “Biodiversity assessment: state-of-the-art techniques in phylogenomics and species identification,” American Journal of Botany, vol. 98, no. 3, pp. 415–425, 2011. View at Publisher · View at Google Scholar · View at PubMed
  42. J. DeBarry, R. Liu, and J. L. Bennetzen, “Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the assisted automated assembler of repeat families (AAARF) algorithm,” BMC Bioinformatics, vol. 9, article 235, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  43. Y. Jiao, N. J. Wickett, S. Ayyampalayam et al., “Ancestral polyploidy in seed plants and angiosperms,” Nature, vol. 473, no. 7345, pp. 97–100, 2011. View at Publisher · View at Google Scholar · View at PubMed
  44. M. D. Ermolaeva, M. Wu, J. A. Eisen, and S. L. Salzberg, “The age of the Arabidopsis thaliana genome duplication,” Plant Molecular Biology, vol. 51, no. 6, pp. 859–866, 2003. View at Publisher · View at Google Scholar · View at Scopus
  45. L. E. Flagel and J. F. Wendel, “Gene duplication and evolutionary novelty in plants,” New Phytologist, vol. 183, no. 3, pp. 557–564, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  46. J. Eid, A. Fehr, J. Gray et al., “Real-time DNA sequencing from single polymerase molecules,” Science, vol. 323, no. 5910, pp. 133–138, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  47. B. J. Strasser, “Collecting, comparing, and computing sequences: the making of margaret O. Dayhoff's Atlas of Protein Sequence and Structure, 1954–1965,” Journal of the History of Biology, vol. 43, no. 4, pp. 623–660, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  48. J. Loureiro, E. Rodriguez, J. Doležel, and C. Santos, “Two new nuclear isolation buffers for plant DNA flow cytometry: a test with 37 species,” Annals of Botany, vol. 100, no. 4, pp. 875–888, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  49. K. H. Keeler, B. Kwankin, P. W. Barnes, and D. W. Galbraith, “Polyploid polymorphism in big bluestem (Andropogon gerardii Vitman),” Genome, vol. 29, no. 2, pp. 374–379, 1987. View at Google Scholar
  50. G. Bharathan, G. M. Lambert, and D. W. Galbraith, “Nuclear DNA content of monocotyledons and related taxa,” American Journal of Botany, vol. 81, no. 3, pp. 381–386, 1994. View at Google Scholar · View at Scopus
  51. E. Sliwinska, I. Pisarczyk, A. Pawlik, and D. W. Galbraith, “Measuring genome size of desert plants using dry seeds,” Botany, vol. 87, no. 2, pp. 127–135, 2009. View at Publisher · View at Google Scholar · View at Scopus
  52. J. Suda, J. Loureiro, P. Travnicek et al., “Flow cytometry and its applications in plant population biology, ecology and biosystematics: new prospects for the cape flora,” South African Journal of Botany, vol. 75, no. 2, pp. 389–389, 2009. View at Google Scholar
  53. J. Loureiro, D. Kopecky, S. Castro, C. Santos, and P. Silveira, “Flow cytometric and cytogenetic analyses of Iberian Peninsula Festuca spp,” Plant Systematics and Evolution, vol. 269, no. 1-2, pp. 89–105, 2007. View at Publisher · View at Google Scholar · View at Scopus
  54. S. Siljak-Yakovlev, F. Pustahija, E. M. Solic et al., “Towards a genome size and chromosome number database of balkan flora: C-values in 343 taxa with novel values for 242,” Advanced Science Letters, vol. 3, no. 2, pp. 190–213, 2010. View at Publisher · View at Google Scholar