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Plant genomes: phenotypes evolving by new rules

Plant genomes: phenotypes evolving by new rules. Todd J. Vision Department of Biology University of North Carolina at Chapel Hill. Functional conservation of genes across distantly related plants. GA1 (a dwarf gibberellin insensitive mutant from Arabidopsis )

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Plant genomes: phenotypes evolving by new rules

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  1. Plant genomes: phenotypes evolving by new rules Todd J. Vision Department of Biology University of North Carolina at Chapel Hill

  2. Functional conservation of genes across distantly related plants • GA1 (a dwarf gibberellin insensitive mutant from Arabidopsis) • GA1 protein sequence used to identify a homolog from the grass sequence database • Homolog shown to map to the Reduced height-1 loci in wheat and to the dwarf-8 locus in maize (Green Revolution genes)

  3. Comparative mapping for candidate genes Goff et al (2002) Science 296, 92

  4. Convergent genetic architectures? Genomic regions of foxtail millet, maize, and sorghum that carry genes for shattering of the infructescence (Devos, Plant Cell 2000)

  5. Fruit weight 2.2 and the domestication of Solanaceous fruit crops Frary et al (2000) Science 289, 85

  6. Arabidopsisthaliana as a hub for plant comparative maps • Compact genome • Fully sequenced • Well studied data from Arumuganathan & Earle (1991)Plant Mol Biol Rep 9:208-218

  7. Rice Medicago Arabidopsis Tomato Stevens, P.F. (2001 onwards). Angiosperm Phylogeny Website. Version 2 August 2001. http://www.mobot.org/MOBOT/research/APweb/.

  8. The Arabidopsis chromosome 2-4 complex

  9. Stacked genomic duplications in Arabidopsis Vision et al. (2000) Science 290:2114-7.

  10. Duplication vs. multiplication Multiple duplications generate abundant overlaps among homeologous regions

  11. Chromosomal rearrangements inversion reciprocal translocation Many small duplicated regions may correspond to a single duplication event

  12. A B C E F D Mya 50 100 0 150 200 Dating the duplication events

  13. Wikström et al (2001) Proc R Soc Lond B 268, 2211

  14. Loss of duplicated genes creates a network of synteny Bancroft (2001) TIG 17, 89 after Ku et al (2000) PNAS 97, 9121 Homologous genes may be in the minority, especially after multiple duplications

  15. Rice-Arabidopsis synteny Mayer et al. (2001) Genome Res. 11, 1167

  16. Divergence among duplicated genes in rice Goff et al. (2002) Science 296: 92

  17. Why such gappy genomic alignments?

  18. Gene deletion in new allopolyploids • Some gene loss in duplicated genomes appears to occur gradually • But there is now convincing evidence for gene loss (not merely silencing) immediately following synthetic tetraploidization in wheat (Kashkush et al, 2002, Genetics 160, 1651).

  19. How to do comparative mapping among multiple taxa and in the presence of genome duplications? Species X Species Y X A X C X E F A B X D F A B C D E F duplication A B C D E F speciation A B C D E F

  20. Phytome:an online plant comparative mapping resource • Integrating: • Organismal phylogeny • Gene family sequences, alignments, phylogenies • Genetic and physical maps • Goals • Centralize • Data collection • Computation • Provide • Comprehensive analysis of comparative mapping data • An enabling interface

  21. Dispersed gene duplications • In our analysis, 85% of the dispersed duplicated gene pairs were not found in duplicated blocks. • Dispersed duplications tended to co-occur on the same chromosome, and closer together, than they would if dispersed randomly. • Lynch & Conery (2001) estimate the duplication frequency in Arabidopsis to be 2x10-3 per gene per MY and the half-life of duplicate pairs to be 23 MY. This estimate combines tandem and dispersed duplicates.

  22. Gene order repatterning – the unknown consequences • We know very little… • Are there blocks of gene order being actively maintained by selection? • Self-incompatibility loci • Coordinately regulated stress-response genes • How much phenotypic evolution is due to gene expression changes brought about by gene order rearrangements?

  23. Acknowledgements • collaborators • Daniel Brown (U Waterloo) • Peter Calabrese (U Southern California) • Brandon Gaut (U California Irvine) • Steven Tanksley (Cornell U) • Liqing Zhang (U Chicago) • students • Sugata Chakravarti (UNC-CH) • Luke Huan (UNC-CH) • Dihiu Liu (UNC-CH) • support • USDA-ARS, NSF Plant Genome

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