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

3. 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)

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

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

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

7. Arabidopsis thaliana 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

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

10. The Arabidopsis chromosome 2-4 complex

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

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

13. Chromosomal rearrangements inversionreciprocal translocation Many small duplicated regions may correspond to a single duplication event

14. Dating the duplication events A B D C E F 0 50100 150200 Mya

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

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

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

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

19. Why such gappy genomic alignments?

20. 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).

21. How to do comparative mapping among multiple taxa and in the presence of genome duplications? X BCDEFA BCDEFA duplication speciation Species XSpecies Y BCDEFA AEC XX FABD X F

22. 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

23. 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.

24. 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?

25. 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