How to detect paleoploidy?

Transcription

1 Genome duplications (polyploidy) / ancient genome duplications (paleopolyploidy) How to detect paleoploidy? e.g. a diploid cell undergoes failed meiosis, producing diploid gametes, which selffertilize to produce a tetraploid zygote.

2 Timing of duplication by trees (phylogenetic timing)

3 Phylogenetic timing of duplicates b

4 Paramecium genome duplications

5 Comparison of two scaffolds originating from a common ancestor at the recent WGD

6 Saccharomyces cerevisiae

7 Just before genome duplication

8 Just after genome duplication

9 More time after genome duplication

10 Unaligned view (removing gaps just like in cerev has occurred)

11

12

13 Saccharomyces cerevisiae

14 Problem reciprocal gene loss (extreme case); how to solve?

15 Problem reciprocal gene loss (extreme case); how to solve?

16 Just before genome duplication Outgroup!

17 Just after genome duplication Outgroup

18 Just after genome duplication Outgroup

19 More time after genome duplication Outgroup

20 Problem (extreme case); how to solve? Outgroup

21 Outgroup

22 Outgroup

23 Outgroup

24 Outgroup

25 Using other genomes Wong et al PNAS

26 Centromeres

27 Vertebrate genome duplication

28 Nature Apr 10. [Epub ahead of print] Ancestral polyploidy in seed plants and angiosperms. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, Depamphilis CW.

29 Teleosts S. serevisiae and close relatives Paramecium MOSS Flowering plants Vertebrates

30 Reconstructed map of genome duplications allows unprecedented mapping of evolutionary history of genes in genomes

31 Reconstructed map of genome duplications allows unprecedented mapping of evolutionary history of genes in genomes

32 Major fate is gene loss

33 In paramecium 3 or 4 genome duplications!

34 Massive gene loss

35 Correlation to (adaptive) radiation?

36 Correlation to (adaptive) radiation?

37 Explanations for adaptive radiation? Incompatibility at essential loci

38 Explanations for adaptive radiation? Regulatory innovations Plants

39 Acknowledgements John van Dam (Bioinformatics, UU) Like Fokkens (Bioinformatics, UU) Peer Bork (EMBL, Heidelberg) Martijn Huynen (CMBI, Nijmegen) Hans Bos (UMCU) Holger Rehmann (UMCU) Fried Swartkruis (UMCU) Geert Kops (UMCU)

40 How we use the WGD As a controlled experiment! How do ks / ka / expression diverge after duplication and how does this correlate with epigenetic modifications

41 A. thaliana s history Traces of (at least) 3 whole-genome duplications The latest (α or 3R) is the most wellannotated 3821 paralogous pairs Van de Peer et al. (2009), Trends in Plant Science

42 Fate of duplicated genes (paralogs) Loss Depends on scale of duplication and function of the gene (Maere et al., 2005) Subfunctionalization: e.g. divergence of expression paterns between paralogs Increases with evolutionary time Depends on mode/scale of duplication and function of the gene (Casneuf et al., 2006)

43 Fate of duplicated genes (paralogs) Loss Depends on scale of duplication and function of the gene (Maere et al., 2005) Subfunctionalization: e.g. divergence of expression paterns between paralogs Increases with evolutionary time Depends on mode/scale of duplication and function of the gene (Casneuf et al., 2006) Blanc G, Wolfe KH (2004), The Plant Cell

44 Fate of duplicated genes (paralogs) Why do expression patterns of paralogs diverge at different rates? It might be epigenetics Blanc G, Wolfe KH (2004), The Plant Cell.

45 Histones and their modifications Array of modifications: Acetylation Phosphorylation Methylation Ubiquitination And many more... Epigenetic marks Role: regulation Zhang Y, Reinberg D (2001), Genes & Development

46 H3K27me3 Regulation of expression: Repressive mark Gene-specific (unlike in animals) Tissue- or developmental stagespecific genes (at least) 16% of Arabidopsis genome ChIP-chip data for seedlings Zhang X et al. (2007), PLoS Biology

47 RESULTS

48 Paralogs from the latest Arabidopsis WGD (Bowers et al., 2003) Genes of the same age Genes with the H3K27me3 mark Union of ChIP-chip experiments (Zhang et al., 2003; Turck, unpublished) Significant overlap (p<1.0e-99) Datasets

49 Datasets Paralogs from the latest Arabidopsis WGD (Bowers et al., 2003) Genes with the H3K27me3 mark Possible situations: Both paralogs with mark One paralog with mark No paralogs with mark gene1 gene2 gene1 gene2 gene1 gene2

50 Rate of sequence divergence (Ks) Ks: number of synonymous substitutions per synonymous site (Often assumed not to be under evolutionary pressure) No H3K27me3: slower rate of sequence evolution Genes with H3K27me3 are tightly regulated and have lower average expression Sequences of genes with lower expression evolve faster Two sample Kolmogorov-Smirnov test: none is significantly different (p<2.2e-16), partial-both (p = 4.6e-05)

51 Expression divergence MAs from a wide range of experiments (TAIR)

52 Expression divergence MAs from a wide range of experiments (TAIR)

53 Expression divergence MAs from a wide range of experiments (TAIR)

54 Expression divergence MAs from a wide range of experiments (TAIR) Paralogs sharing mark status (0 or 2) have higher correlation Not significantly different Partial inches towards random distribution Different from both (p = 3.863e-07) and none (p = 4.44e-16)

55 Expression divergence

56 Expression divergence: TFs Paralogous pairs both keeping the mark have more similar expression patterns p-values both-partial: , both-none: