Genome Evolution Greg Lang, Department of Biological Sciences

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1 Genome Evolution Greg Lang, Department of Biological Sciences BioS 010: Bioscience in the 21st Century

2 Mechanisms of genome evolution Gene Duplication Genome Rearrangement Whole Genome Duplication

3 Gene number varies between species Species Saccharomyces cerevisiae Neurospora crassa Drosophila melanogaster Caenorhabditis elegans Homo sapiens Takifugu rubripes Arabadopsis thaliana Oryza sativa Populus trichocarpa Gene # 6,294 10,082 13,600 19,000 20, ,000 27, ,000 45,555

4 Fates of duplicated genes Dosage Subfunctionalization Neofunctionalization

5 Human opsin genes and trichromatic vision (a) In Out A P A V Q S T E T K S V T T S 348 A E Q Q E 240 D Q S D A 330 A P M S G N A T K F L T III C 140 A R VIII P K L E Q VI R V K R V F T N H II V V IV K K I N Q T G K Y V V A N C T K R T VII M F M L F Y V T V N L P I E N E K E Q G H V L T L L L I Y A L M L V G M I A G Q L V R T E C C M I A L N W S C Y I Y F V M I P I N F W T P N F L D A V I A L F A V I V V E V L G G M V I F I L A I L M F G F M I S T L L I V L W I K G F F A G F P V Y M F F G F A A P L A V Y A T A A C H F I C L V A P A V L P Y P F A T T T L E G T M L G C F V M S I Q F S T Y L M N F A I I Y A V G F F T W Y L S F I P W F G P E G P H T G Y F Y R S V N E I Y H F P T T D A E G I D Y 200 N Q E G S C P L G H E Y M C S Q Y Q V V III VI IV VII II VIII I P A E F P S R V V G T K N S F P V Y F N P G E T G N M 20 1 Terakita. Genome Biol. 2005;6(3):213.

6 Duplication of opsin genes in old-world primates Dulai et al. Genome Res Jul;9(7):

7 Trichromatic vision in howler monkeys Gilad et al. PLoS Biol Jan;2(1):E5.

8 Mechanisms of genome evolution Gene Duplication Genome Rearrangement Whole Genome Duplication

9 Genomes rearrange during evolution Mouse Genome Human Genome U.S. Department of Energy Human Genome Program:

10 The missing human chromosome Human 23 Chromosomes Chimpanzee 24 Chromosomes Gorilla 24 Chromosomes Orangutan 24 Chromosomes

11 Human Chromosome 2 arose through fusion Human Human Chromosome 2 Chimpanzee Gorilla Orangutan Yunis and Prakash. Science Mar 19;215(4539):

12 Genome rearrangement in cancer Bcr-Abl Philadelphia Chromosome Wikimedia Commons

13 Genome rearrangements as a genetic barrier

14 Engineering evolution to study speciation in yeast Delneri et al. Nature Mar 6;422(6927):68-72.

15 Engineering evolution to study speciation in yeast S. cerevisiae 90.3% 0.6% 88.9% S. mikatae Delneri et al. Nature Mar 6;422(6927):68-72.

16 Engineering evolution to study speciation in yeast S. cerevisiae S. cerevisiae - translocation 90.3% 88.8% 0.6% 88.9% S. mikatae Delneri et al. Nature Mar 6;422(6927):68-72.

17 Engineering evolution to study speciation in yeast S. cerevisiae S. cerevisiae - translocation 90.3% 60.4% 88.8% 0.6% 20.0% 88.9% S. mikatae Delneri et al. Nature Mar 6;422(6927):68-72.

18 Mechanisms of genome evolution Gene Duplication Genome Rearrangement Whole Genome Duplication

19 Evidence of two WGDs in vertebrate Hox clusters Swalla. Heredity Sep;97(3):

20 Gene number varies between species Species Saccharomyces cerevisiae Neurospora crassa Drosophila melanogaster Caenorhabditis elegans Homo sapiens Takifugu rubripes Arabadopsis thaliana Oryza sativa Populus trichocarpa Gene # 6,294 10,082 13,600 19,000 20, ,000 27, ,000 45,555

21 Genome rearrangements as a genetic barrier

22 Evidence for a whole-genome duplication in yeast Kellis et al. Nature Apr 8;428(6983):

23 Evidence for a whole-genome duplication in yeast Kellis et al. Nature Apr 8;428(6983):

24 Analysis of the whole-genome duplication in yeast Kellis et al. Nature Apr 8;428(6983):

25 Fates of duplicated genes Dosage Subfunctionalization Neofunctionalization

26 Subfunctionalization following WGD Hittinger and Carroll. Nature Oct 11;449(7163):

27 Increase in metabolic flux following WGD HXT## Key WGD duplications Glucose transport by numerous WGD duplicates in all proteins see table I post-wgd species WGD duplicates in S. cerevisiae, Glucose but not all post-wgd species Other duplications HXK2 HXK1 GLK1 EMI2 Glucose-6-phosphate PGI1 Ethanol Ethanol Fructose-6-phosphate ADH2 ADH1 ADH3 Glycolysis Fructose-1-6-bisphosphate Glyceraldehyde-3- phosphate TDH2 TDH1 TDH3 PFK1 3-Phospho-Dglyceroyl-phosphate PFK2 FBA1 DHAP TPI1 PDC5 ADH5 Acetaldehyde ALD6 Acetate PDC6 ACS1 ADH4 Acetaldehyde ALD5 ALD4 Acetate PGK1 3-Phosphoglycerate GPM1 Fermentation PDC1 ACS2 Acetyl-CoA GPM2 GPM3 2-Phosphoglycerate ENO1 ENO2 Phosphoenolpyruvate PDH complex Lipoamide LDP1 YPL017C Dihydrolipoamide LAT1 CDC19 PYK2 S-ADLA Pyruvate Respiration PDB1 Pyruvate PDA1 CoA PYC1 PYC2 Acetyl-CoA Cytosol Mitochondrion Oxaloacetic acid Malate FUM1 Fumarate SDH1 SDH2 SDH3 Oxaloacetic acid MDH2 CIT3 CIT1 YJL045W YMR118C CIT2 Cytosol Citrate ACO1 Isocitrate IDH2 SDH4 YLR164W IDH1 Succinate 2-Oxoglutarate LSC1 KGD1 LSC2 Succinyl-CoA KGD2 Succinyl-lipoate Conant and Wolfe. Mol Syst Biol. 2007;3:129.

28 Mechanisms of genome evolution Gene Duplication Dosage Subfunctionalization Neofunctionalization Genome Rearrangement Human Chromosome 2 Philadelphia Chromosome Species barriers Whole Genome Duplication Twice in vertebrates 100 MYA in yeast lineage