1. Bioinformatis and Evolutionary Genomics Genome Duplications

2. Genome duplications / polyploidy Polyploid plants are very common and can arise spontaneously in nature by several mechanisms, including meiotic or mitotic failures, and fusion of unreduced (2n) or gametesPolyploid plants are very common and can arise spontaneously in nature by several mechanisms, including meiotic or mitotic failures, and fusion of unreduced (2n) or gametes

3. Gene duplication: trees

4. Gene duplication: blast These are all duplicates but we do not know the order in which they aroseThese are all duplicates but we do not know the order in which they arose

5. Segmental duplication

6. Whole Genome duplication Synonym: PolyploidySynonym: Polyploidy Proposed by Ohno (1970) to be a possible major force in genome evolutionProposed by Ohno (1970) to be a possible major force in genome evolution Result of errors in meiosis (not in bacteria?)Result of errors in meiosis (not in bacteria?) Synonym: PolyploidySynonym: Polyploidy Proposed by Ohno (1970) to be a possible major force in genome evolutionProposed by Ohno (1970) to be a possible major force in genome evolution Result of errors in meiosis (not in bacteria?)Result of errors in meiosis (not in bacteria?)

7. Vertebrate genome duplication

8. Fish: whole genome duplication in teleost fish

9. Saccharomyces cerevisiae Absence of triplicate regionsAbsence of triplicate regions Limited portion of the genome mapped (50%); other genomes neededLimited portion of the genome mapped (50%); other genomes needed Absence of triplicate regionsAbsence of triplicate regions Limited portion of the genome mapped (50%); other genomes neededLimited portion of the genome mapped (50%); other genomes needed

10. GénolevuresGénolevures Gene family size in S. cerevisiae is generally conserved in other speciesGene family size in S. cerevisiae is generally conserved in other species Observation of small duplicated segments from strict & pairwise comparisonsObservation of small duplicated segments from strict & pairwise comparisons Gene family size in S. cerevisiae is generally conserved in other speciesGene family size in S. cerevisiae is generally conserved in other species Observation of small duplicated segments from strict & pairwise comparisonsObservation of small duplicated segments from strict & pairwise comparisons

11. Génolevures part deux Wong et al. 2002 PNAS

12. CentromeresCentromeres

13. Unique amount of fungal genomes 727Mya 235Mya 125Mya 600Mya

14. Paramecium genome duplications

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

16. Representation of the successive duplications of the Paramecium genome. BRH: best reciprocal hits

17. Percentage identity between paralogous proteins, and comparisons with inter- species distances. Orange: human - mouse Brown: human - fish Pink: Paramecium - Tetrahymena thermophila

20. Plant genome duplications

22. Detection of genome duplicationsDetection of genome duplications –Trees –Ks/Similarity “bumps” –Synteny, indirect synteny (comparative genomics), BRH/BBH vs normal blast Effect of WGDEffect of WGD –Most duplicates are lost –Nevertheless thought to be important (origin of flowering plants, origin of vertebrates etc.) Detection of genome duplicationsDetection of genome duplications –Trees –Ks/Similarity “bumps” –Synteny, indirect synteny (comparative genomics), BRH/BBH vs normal blast Effect of WGDEffect of WGD –Most duplicates are lost –Nevertheless thought to be important (origin of flowering plants, origin of vertebrates etc.)