2. The dynamics of nuclear gene order in the eukaryotes

3. Genome archaeology in the angiosperms Todd Vision Department of Biology University of North Carolina at Chapel Hill

4. Comparative maps Spaghetti Diagram Crop Circle Livingstone et al 1999 Genetics 152:1183 Gale & Devos 1998 PNAS 95:1972

5. Arabidopsis as a hub for plant comparative maps data from Arumuganathan & Earle (1991)Plant Mol Biol Rep 9:208-218

6. Tomato-Arabidopsis synteny Bancroft (2001) TIG 17, 89 after Ku et al (2000) PNAS 97, 9121

7. Outline Ancient genome duplication –How can we reconstruct genomic history? Computational challenges Role of different classes of gene duplication in genome evolution

8. Outline Ancient genome duplication –How can we reconstruct genomic history? Computational challenges Role of different classes of gene duplication in genome evolution

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

10. Paleotetraploidy? The Arabidopsis Genome Initiative. 2000. Nature 408:796

11. Genomic dot-plot gene1 2 3 4 5 6 7 8 11 0 0 0 1 0 0 0 20 1 0 0 0 1 0 0 30 0 1 0 0 0 1 0 40 0 0 1 0 0 0 1 51 0 0 0 1 0 0 0 60 1 0 0 0 1 0 0 70 0 1 0 0 0 1 0 80 0 0 1 0 0 0 1 1234 5678 Chromosome copy 1 Chromosome copy 2

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

14. Vision et al. (2000) Science 290:2114-7. Segmental paralogy in Arabidopsis

15. A B D C E F Many duplicated segments but few duplication events 0 2 4 6 8 10 12 0.1.2.3.4.5.6.7.8.9 amino acid substitution frequency of blocks

16. Blanc, Hokamp, Wolfe (2003) Genome Res. 13, 137-144.

17. Arabidopsis tomato Angiosperm Phylogeny Website. Version 2 August 2001. http://www.mobot.org/MOBOT/research/APweb/. rice

18. Block 37 after Asterid-Rosid split Block 57 before monocot-dicot divergence Raes, Vandepoele, Saeys, Simillion, Van de Peer (2003) J. Struct. Func. Genomics 3, 117-129

19. Divergence of homeologs Homeologs from age class C and older share less than a third of their genes –Gene loss –Or subsequent gene movement? There is no evidence for uneven proportions of duplicated genes between homeologs

20. Redundant gene function: SHATTERPROOF Martin Yanofsky

21. Implications for comparative maps Networks of synteny Goodbye to pairwise comparisons

22. Outline Ancient genome duplication –How can we reconstruct genomic history? Computational challenges Role of different classes of gene duplication in genome evolution

23. Ghosts and Muggles Simillion, Vandepoele, Van Montagu, Zabeau, Van de Peer (2002) PNAS 99, 13627

24. Interspecies comparison can reveal Ghosts

25. Things needful Identification of highly diverged Muggles A systematic way to identify Ghosts Centralization of mapped and sequenced DNA markers from multiple species

26. FISH (Fast Identification of Segmental Homology) Identifies candidate segmental homologies –Dynamic programming Statistically evaluates candidates –Null model of transpositional duplication No permutations required Approaches limits to sensitivity

27. FISH under null model kobserved number standard error upper bound lower bound 245.80.0647.640.1 32.280.022.391.78 40.1130.0030.1200.079 50.0060.0010.0060.004 60.00030.00020.00030.0002

28. eAssembler Reconstructs ancestral gene order by joining duplicated blocks with overlapping gene content Uses ‘breakpoint median’ as objective function Similar to algorithms used in sequence assembly Blanc, Hokamp, Wolfe (2003) Genome Res. 13, 137-144.

29. PHYTOME integrating plant genome maps, sequences and phylogenies From www.plantgdb.org

30. Outline Ancient genome duplication –How can we reconstruct genomic history? Computational challenges Role of different classes of gene duplication in genome evolution

31. Gene duplications in a chromosomal context Turnover within gene families can be high –Rate of duplication= 0.002/gene*MY –Half-life=23MY Three modes of duplication –Tandem –Transpositional –Segmental How does the mode of origin affect the molecular and functional divergence of duplicate genes?

32. Gene family turnover Lynch and Conery (2000) Science 290, 1151

33. Importance of tandem and transpositional duplications ~10% of genes are in tandem arrays 85% of dispersed duplications are not in blocks Duplicates on the same chromosome are 20% more common than expected by chance Duplicates on the same chromosome are 86% as distant as would be expected by chance

35. Aux/IAA and ARF sister families Importance in Arabidopsis

36. Diversification of the Aux/ IAA gene family David Remington and Jason Reed

38. Diversification of ARF gene family

39. Chromosome 2-4 complex: 242 duplicated gene pairs

40. Substitutions in coding sequences silent substitutions (K s ) only alter the codon, not the resulting amino acid replacement substitutions (K a ) alter the amino acid K a and K s are standardized by the numbers of synonymous and nonsynonymous sites

41. Ratio of K a to K s K a /K s < 1selective constraint K a /K s = 1pure neutrality K a /K s > 1 positive selection

42. How have these ancient segmental duplicates diverged? 1.What is the variation in K a and K s among simultaneously duplicated pairs? 2.Do the K a /K s ratios suggest positive selection? 3.Do the members of each duplicated pair evolve at the same rate?

43. coefficient of variation = 0.67 coefficient of variation = 0.53

44. Relationship between K a and K s r 2 =0.558, p<0.001

45. Relative rate test O (outgroup)AB d1 d2 d3 compare the fit of a model in which d2 = d3 with one in which they are allowed to vary

46. Relative rate tests 105 gene pairs could be evaluated against an outgroup >30 showed significantly unequal rates of evolution no evident chromosomal or regional biases Distance measureSignificant pairs protein15 KaKa 29 KsKs 9

47. Are paralogs different than orthologs? Homologous genes are either –Paralogs that diverged through duplication –Orthologs that diverged though speciation Paralogs must coexist in the same genome – do they diverge differently as a result? Comparison to 212 Arabidopsis-Brassica orthologs by Tiffin and Hahn (2002) JME 54, 746. –For all pairs, K a /K s < 1 –K a /K s unimodal around 0.14 (as opposed to 0.20) –CV Ks /CV Ka is appx. 2

48. Conclusions A network of synteny due to duplication and gene loss makes deep comparative mapping difficult But phylogenetically-informed methods should allow us to go much deeper than at present Only by going deep will we be able to understand the varied roles of different kinds of duplication events in the diversification of gene families

49. Acknowledgements Arabidopsis genome evolution –Daniel Brown –Steven Tanksley Comparative mapping –Peter Calabrese –Sugata Chakravarty –Luke Huan Evolution of duplicated genes –Liqing Zhang –Brandon Gaut –David Remington –Jason Reed Support –USDA –NSF

51. Conservation of gene orientation parallel convergent divergent

52. Formulating the problem in terms of graph traversal nodes are matches edges are unidirectional edges have associated distances The putative duplicated blocks consist of the paths through the graph that traverse edges with short distances

53. Statistical framework Null model of duplications –Single-gene duplication/random transposition –Leads to uniformly distributed dots Null distribution for –The edge distance between nearest neighbors –The number of serially connected short edges Observed edge distances and path lengths analytically compared to null expectation Can be approximated by a permutation test

54. Only a fraction of the genes are (still?) duplicated Chr2 segment 1183 genes Chr4 segment 1168 genes 326 duplicates (~28%)

55. 271 (83%) pairwise duplications

56. Tandem substitutions correlation between K a and K s disappears when tandem substitutions are excluded could be due to –doublet mutations –compensatory substitutions

57. At2g18750 AT4g31000 49.5 calmodulin-binding protein49.62 beta-expansin AT4g28250 At2g20750 49.63 NADH-ubiquinone oxireductase At2g20800 AT4g28220 56.1 unknown transmembrane At2g23810 AT4g30430 tobacco 1698547 0.13 0.16 0.37 rice 8118436 Hemerocallis 3551953 p<0.0001 p<0.05 p<0.0001 p<0.01 0.30 0.10 0.22 0.14 0.160.29 0.22 0.12 0.70 potato 5734586