Genome Evolution Greg Lang, Department of Biological Sciences

Transcription

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

2 Gene number varies between species Saccharomyces cerevisiae Species Gene # 6,294 Neurospora crassa 10,082 Drosophila melanogaster Caenorhabditis elegans 13,600 19,000 Question: Where do new genes come from? Homo sapiens 20,251 Takifugu rubripes 22-29,000 Arabadopsis thaliana 27,400 Oryza sativa 32-50,000 Populus trichocarpa 45,555

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

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 I C F 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 W F G P 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 P L G C H E Y M C S Q Y Q 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 V V III VI IV VII II VIII I (c) (d) V III VI IV VII II VIII I Question: Why is red/ green colorblindness much more common in males? 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 Gilad et al. PLoS Biol Jan;2(1):E5. Trichromatic vision in howler monkeys

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

9 Genomes rearrange during evolution Human Genome Mouse Genome Question: How many chromosome does a chimpanzee have? Lisa Stubbs, Oak Ridge National Laboratory

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 Philadelphia Chromosome Bcr-Abl Wikimedia Commons

13 Genome rearrangements as a genetic barrier

14 Engineering evolution to study speciation in yeast S. cerevisiae S. cerevisiae - translocation 90.3% 60.4% 88.8% 0.6% 20.0% 88.9% Question: Why might account for the rest of the species barrier? S. mikatae Delneri et al. Nature Mar 6;422(6927):68-72.

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

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

17 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

18 Whole genome duplications are common in plants Plant Genome Duplication Database

19 Genome rearrangements as a genetic barrier

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

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

22 Evidence for a whole-genome duplication in yeast Copy 1 Pre-duplication Copy 2 Kellis et al. Nature Apr 8;428(6983):

23 Fates of duplicated genes Dosage Subfunctionalization Neofunctionalization

24 Subfunctionalization following WGD Pre-duplication Enzyme Regulator GAL1 mrna GAL1 mrna GAL1 + galactose GAL1 Post-duplication Regulator GAL3 mrna GAL3 + galactose GAL3 mrna GAL3 Enzyme GAL1 Conant and Wolfe. Mol Systems Bio galactose GAL1 GAL1mRNA

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

26 Increase in metabolic flux following WGD HXT Glucose HXK2 HXK1 GLK1 EML2 Glucose-6-phosphate PGI1 Fructose-6-phosphate Question: Why do yeast want to make alcohol? PFK1 PFK2 Glycolysis Fructose-1-6-bisphosphate FBA1 TDH1 Glyceraldehyde-3- phosphate TDH2 TDH3 TPI1 DHAP 3-Phospho-Dglyceroyl-phosphate PGK1 3-Phosphoglycerate GPM2 GPM3 GPM1 2-Phosphoglycerate Ethanol EN01 ENO2 Phosphoenolpyruvate ADH2 ADH1 ADH3 CDC19 PYK2 Pyruvate PDC1 PDC1 PDC1 Fermentation Acetaldehyde ADH5 ADH4 Respiration Conant and Wolfe. Mol Syst Biol. 2007;3:129.

27 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