Reconstructing the History of Large-scale Genomic Changes. Jian Ma

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1 Reconstructing the History of Large-scale Genomic Changes Jian Ma

2 The Human Genome: the blueprint of our body Initial sequencing and analysis of the human genome International Human Genome Sequencing Consortium* Nature 2001 * A partial list of authors appears on the opposite page. Af liations are listed at the end of the paper.... The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence. Finishing the euchromatic sequence of the human genome International Human Genome Sequencing Consortium* * A list of authors and their affiliations appears in the Supplementary Information Nature 2004 Phase 2: Interpret the genetic code, i.e. How the Human Genome works? GTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAATACTAGCTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAA CAACCATAGGATGATAATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATATATAAATGGAAAAGCTGCATAACCACTTTAACTAATACTTTCAACATTTTCAG TTTGTATTACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAATTGTTAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCTGAGTTCAATTCTAGCG CAAAGGAATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGGATTTTGTTGCTAGATCGCCTGGTAGAGTCAATCTAATTGGTGAACATATTGATTATTGTGACT TCTCGGTTTTACCTTTAGCTATTGATTTTGATATGCTTTGCGCCGTCAAAGTTTTGAACGATGAGATTTCAAGTCTTAAAGCTATATCAGAGGGCTAAGCATGTGTATTCTGAATCTTTAAGAGTCTTGAAGGCTGTGAAATTA ATGACTACAGCGAGCTTTACTGCCGACGAAGACTTTTTCAAGCAATTTGGTGCCTTGATGAACGAGTCTCAAGCTTCTTGCGATAAACTTTACGAATGTTCTTGTCCAGAGATTGACAAAATTTGTTCCATTGCTTTGTCAAAT GGATCATATGGTTCCCGTTTGACCGGAGCTGGCTGGGGTGGTTGTACTGTTCACTTGGTTCCAGGGGGCCCAAATGGCAACATAGAAAAGGTAAAAGAAGCCCTTGCCAATGAGTTCTACAAGGTCAAGTACCCTAAGATCACT GATGCTGAGCTAGAAAATGCTATCATCGTCTCTAAACCAGCATTGGGCAGCTGTCTATATGAATTAGTCAAGTATACTTCTTTTTTTTACTTTGTTCAGAACAACTTCTCATTTTTTTCTACTCATAACTTTAGCATCACAAAA TACGCAATAATAACGAGTAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGC TTTCAACCGCTGCGTTTTGGATACCTATTCTTGACATGATATGACTACCATTTTGTTATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAG...TTGCGAAGTTCTTGGCAAGTTGCCAACTGACGAGATGCAGTAAC ACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGCTTTCAACCGCTGCGTTTTGGATAC CTATTCTTGACATGATATGACTACCATTTTGTTATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAGTCATTTGCGAAGTTCTTGGCAAGTTGCCAACTGACGAGATGCAGTTTCCTACGCATAATAAGAATAGGAGG GAATATCAAGCCAGACAATCTATCATTACATTTAAGCGGCTCTTCAAAAAGATTGAACTCTCGCCAACTTATGGAATCTTCCAATGAGACCTTTGCGCCAAATAATGTGGATTTGGAAAAAGAGTATAAGTCATCTCAGAGTAA TATAACTACCGAAGTTTATGAGGCATCGAGCTTTGAAGAAAAAGTAAGCTCAGAAAAACCTCAATACAGCTCATTCTGGAAGAAAATCTATTATGAATATGTGGTCGTTGACAAATCAATCTTGGGTGTTTCTATTCTGGATTC ATTTATGTACAACCAGGACTTGAAGCCCGTCGAAAAAGAAAGGCGGGTTTGGTCCTGGTACAATTATTGTTACTTCTGGCTTGCTGAATGTTTCAATATCAACACTTGGCAAATTGCAGCTACAGGTCTACAACTGGGTCTAAA TTGGTGGCAGTGTTGGATAACAATTTGGATTGGGTACGGTTTCGTTGGTGCTTTTGTTGTTTTGGCCTCTAGAGTTGGATCTGCTTATCATTTGTCATTCCCTATATCATCTAGAGCATCATTCGGTATTTTCTTCTCTTTATG GCCCGTTATTAACAGAGTCGTCATGGCCATCGTTTGGTATAGTGTCCAAGCTTATATTGCGGCAACTCCCGTATCATTAATGCTGAAATCTATCTTTGGAAAAGATTTACAATGATTGTACGTGGGGCAGTTGACGTCTTATCA TATGTCAAAGTCATTTGCGAAGTTCTTGGCAAGTTGCCAACTGACGAGATGCAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCACAA 2

3 Sequence conservation implies function chr2 (q31.1) 21 p14 2p q34 q35 chr2: DLX1 DLX UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative Genomics Vertebrate Multiz Alignment & PhastCons Conservation (28 Species) Vertebrate Cons Chimp Rhesus Bushbaby Tree_shrew Mouse Rat Guinea_Pig Shrew Hedgehog Dog Cat Horse Cow Armadillo Elephant Tenrec Opossum Platypus Lizard Chicken Zebrafish Tetraodon Fugu Stickleback Medaka DLX1 Gaps Human Chimp Rhesus Bushbaby Tree_shrew Mouse Rat Guinea_Pig Shrew Hedgehog Dog Cat Horse Cow Armadillo Elephant Tenrec Opossum Platypus Lizard Chicken Zebrafish Tetraodon Fugu Stickleback Medaka UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative Genomics K P R T I Y S S L Q L Q A L N Vertebrate Multiz Alignment & PhastCons Conservation (28 Species) 1 A A A C C C A G G A C G A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C G A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C G A T T T A T T C C A G C T T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C G A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A T A A A C C C A G G A C G A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C A A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C A A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C C C C C C T A G G A C A A T T T A T T C C A G T T T G C A G C T G G A C G C T T T G A A T A A A C C C A G G A C G A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C A A G C C C A G G A C A A T C T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C G A T T T A C T C C A G T T T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C G A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C G A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C G A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C G A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C A A T T T A T T C C A G T T T G C A G T T G C A G G C T T T G A A C A A A C C T A G G A C G A T T T A T T C C A G T T T G C A G C T G C A G G C T T T G A A T A A A C C C A G G A C T A T T T A T T C C A G T C T G C A G T T G C A G G C T T T G A A C A A A C C C A G G A C T A T A T A T T C C A G T T T G C A G T T G C A G G C A T T G A A C A A G C C G C G C A C C A T C T A C T C C A G C C T C C A G C T C C A G G C C T T G A A C A A A C C C A G G A C T A T T T A T T C C A G T T T G C A G C T G C A G G C T C T G A A C A A G C C C C G G A C C A T A T A C T C C A G T C T C C A G C T G C A G G C T C T G A A C A A A C C C A G G A C T A T C T A T T C C A G T T T A C A G C T C C A G G C C C T G A A C A A A C C A A G G A C T A T C T A T T C A A G T T T A C A A C T C C A A G C C C T G A A C A A A C C A A G G A C T A T C T A T T C C A G T T T A C A A C T T C A A G C T C T A A A C A A A C C A A G G A C T A T A T A T T C C A G T T T A C A G C T T C A G G C T C T G A A C 3

4 Chromosomal differences between human and mouse Human Mouse 4

5 Mammalian evolution Hominini ancestor Human Chimpanzee Orangutan Hominidae ancestor Macaque Catarrhini ancestor Primates Baboon Colobus monkey Owl monkey Primate ancestor Marmoset Dusky titi Mouse lemur Euarchontoglires ancestor Galago Mouse Boreoeutherian ancestor Rabbit Eutherian ancestor Cow Bat Shrew Mammalian ancestor Laurasiatheria Dog Glires Rat Hedgehog Armadillo Xenarthra Elephant Te nrec Afrotheria Monodelphis Platypus 5

6 Reconstruction provides additional dimension for Comparative Genomics NM_ boreoeutherian euarc primate ape human boreoeutherian euarc primate ape human TransMap RefSeq Genes A V G W V I F A G C C G T G G G C T G G G T C A T C T T T G C G C C G T G G G C T G G G T C A T C T T T G C G C T G T G G G C T G G G T C C T C T T T G C G C T G T G G G C T G A G T C C T C T T T G C G C T G T G G G C T G A G T C C T C T T T G C A V G W V I F A A V G W V I F A A V G W V L F A A V G V L F A A V G * V L F A ACYL3: a gene lost in humans and chimps Zhu et al., PLoS Comp Bio

7 Base-level ancestral reconstruction In the multiple alignment for sequences from different species, we often see gaps in it. human chimp macaque mouse rat dog cow ATCAGC------GGCGAT ATCAGC------GGCGAT ATCAGCCGGATCGGCGAT ATCAGCCGGATCGGCGAT ATCAGCCGGATCGGCGAT ATCAGCCGGATCGGCGAT ATCAGCCGGATCGGCGAT 7

8 Base-level ancestral reconstruction Substitutions (point mutations) Small insertions and deletions (indels) ARMADILLO TGCTACTAATAT-----T-TAGTA-CATAGAG-CC-CAGGGGTGCTGCTGAAA GTCTTAAAATGCACA MOUSELEMUR ATCACAG-TTGGGGGATGCCACTGGCCT-----C-AAGTG-GGTAGAG-AA-CAGGGAGGCTGAAAACC ACCCTGCAGAGCACG ORANGUTAN GTCACGATTTGGGAGATGCTTCTGGCTC-----G-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCAACAGTGCACA COW GCCTCTCTTT CTGCCCTGCAGGC-TAGAA-TGTATCA-CT-TAGATGTTCCAA ATCAGAAAGTGTTCA HORSE GTCACAATTTAGGAAGTGCCACTGGCCT-----C-TAGAG-GGTAGAA-GA-CAGGGATGCTAATAATCATCCCACGTCATCCTACAGTGCTCA CAT GTCACAGTTTAGGGGGTACTACTGGCAT-----C-TATCG-GGTGGAG-GA-TAGGGATACTGATAATC ATTCTACAGTGCACA DOG GTCACAATTTGGGGGATACTACTGGCAT-----C-TAATG-GGTAGAG-GA-CAGGGATACTGATAATT GCTTTACAGTGCACA HEDGEHOG GTCATAGTTT----GATTATATGGGCTT-----CTTAGTA-GACAAAGAAA-AAGATGTTCTGGTAGTC ATTCTGCTTTCCATA MOUSE GTCACAGTTTGGAGGATGTTACTGACAT-----C-TAGAG-AGTAGAC-TT-TAAAGATACTGATAGTC ACCCCATTGTGCAC- RAT GTCACAATTTGGAGGATGTTACTGGCAT-----C-TAGAG-AGTAGAC-TT-TAAGGACACTGATAATC ATACTATGCTGCAC- RABBIT ATCACAATTTGGGGAACACCACTGGCAT-----C-TCGGGTAGCAGGC----CAGGCATGCTGGTAATT ATACTACAGTGCACA LEMUR ATCACAA-TTGGGGG-TGCCACGGTCCT-----C-CAGTG-GGTAGAG-AA-CAGGGAGGCTGATAACC ACCCTGCAGTGCACA VERVET GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAG-AAACAGGGATGCTTATAATC ATCCTACAGTGCACA MACAQUE GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAG-AAACAGGAATGCTTATAATC ATCCTACAGTGCACA BABOON GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAA-AAACAGGGATGCTTATAATC ATCCTACAGTGCACA GORILLA GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGTGGGGATGCTTATACTC ATCCTACAGTGCACA CHIMP GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCTACAGTGCACA HUMAN GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCTACAGTGCACA Blanchette et al., Genome Res

9 Base-level ancestral reconstruction Substitutions (point mutations) Small insertions and deletions (indels) ARMADILLO TGCTACTAATAT-----T-TAGTA-CATAGAG-CC-CAGGGGTGCTGCTGAAA GTCTTAAAATGCACA MOUSELEMUR ATCACAG-TTGGGGGATGCCACTGGCCT-----C-AAGTG-GGTAGAG-AA-CAGGGAGGCTGAAAACC ACCCTGCAGAGCACG ORANGUTAN GTCACGATTTGGGAGATGCTTCTGGCTC-----G-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCAACAGTGCACA COW GCCTCTCTTT CTGCCCTGCAGGC-TAGAA-TGTATCA-CT-TAGATGTTCCAA ATCAGAAAGTGTTCA HORSE GTCACAATTTAGGAAGTGCCACTGGCCT-----C-TAGAG-GGTAGAA-GA-CAGGGATGCTAATAATCATCCCACGTCATCCTACAGTGCTCA CAT GTCACAGTTTAGGGGGTACTACTGGCAT-----C-TATCG-GGTGGAG-GA-TAGGGATACTGATAATC ATTCTACAGTGCACA DOG GTCACAATTTGGGGGATACTACTGGCAT-----C-TAATG-GGTAGAG-GA-CAGGGATACTGATAATT GCTTTACAGTGCACA HEDGEHOG GTCATAGTTT----GATTATATGGGCTT-----CTTAGTA-GACAAAGAAA-AAGATGTTCTGGTAGTC ATTCTGCTTTCCATA MOUSE GTCACAGTTTGGAGGATGTTACTGACAT-----C-TAGAG-AGTAGAC-TT-TAAAGATACTGATAGTC ACCCCATTGTGCAC- RAT GTCACAATTTGGAGGATGTTACTGGCAT-----C-TAGAG-AGTAGAC-TT-TAAGGACACTGATAATC ATACTATGCTGCAC- RABBIT ATCACAATTTGGGGAACACCACTGGCAT-----C-TCGGGTAGCAGGC----CAGGCATGCTGGTAATT ATACTACAGTGCACA LEMUR ATCACAA-TTGGGGG-TGCCACGGTCCT-----C-CAGTG-GGTAGAG-AA-CAGGGAGGCTGATAACC ACCCTGCAGTGCACA VERVET GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAG-AAACAGGGATGCTTATAATC ATCCTACAGTGCACA MACAQUE GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAG-AAACAGGAATGCTTATAATC ATCCTACAGTGCACA BABOON GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAA-AAACAGGGATGCTTATAATC ATCCTACAGTGCACA GORILLA GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGTGGGGATGCTTATACTC ATCCTACAGTGCACA CHIMP GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCTACAGTGCACA HUMAN GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCTACAGTGCACA Blanchette et al., Genome Res

10 Base-level ancestral reconstruction Substitutions (point mutations) Small insertions and deletions (indels) ARMADILLO TGCTACTAATAT-----T-TAGTA-CATAGAG-CC-CAGGGGTGCTGCTGAAA GTCTTAAAATGCACA MOUSELEMUR ATCACAG-TTGGGGGATGCCACTGGCCT-----C-AAGTG-GGTAGAG-AA-CAGGGAGGCTGAAAACC ACCCTGCAGAGCACG ORANGUTAN GTCACGATTTGGGAGATGCTTCTGGCTC-----G-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCAACAGTGCACA COW GCCTCTCTTT CTGCCCTGCAGGC-TAGAA-TGTATCA-CT-TAGATGTTCCAA ATCAGAAAGTGTTCA HORSE GTCACAATTTAGGAAGTGCCACTGGCCT-----C-TAGAG-GGTAGAA-GA-CAGGGATGCTAATAATCATCCCACGTCATCCTACAGTGCTCA CAT GTCACAGTTTAGGGGGTACTACTGGCAT-----C-TATCG-GGTGGAG-GA-TAGGGATACTGATAATC ATTCTACAGTGCACA DOG GTCACAATTTGGGGGATACTACTGGCAT-----C-TAATG-GGTAGAG-GA-CAGGGATACTGATAATT GCTTTACAGTGCACA HEDGEHOG GTCATAGTTT----GATTATATGGGCTT-----CTTAGTA-GACAAAGAAA-AAGATGTTCTGGTAGTC ATTCTGCTTTCCATA MOUSE GTCACAGTTTGGAGGATGTTACTGACAT-----C-TAGAG-AGTAGAC-TT-TAAAGATACTGATAGTC ACCCCATTGTGCAC- RAT GTCACAATTTGGAGGATGTTACTGGCAT-----C-TAGAG-AGTAGAC-TT-TAAGGACACTGATAATC ATACTATGCTGCAC- RABBIT ATCACAATTTGGGGAACACCACTGGCAT-----C-TCGGGTAGCAGGC----CAGGCATGCTGGTAATT ATACTACAGTGCACA LEMUR ATCACAA-TTGGGGG-TGCCACGGTCCT-----C-CAGTG-GGTAGAG-AA-CAGGGAGGCTGATAACC ACCCTGCAGTGCACA VERVET GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAG-AAACAGGGATGCTTATAATC ATCCTACAGTGCACA MACAQUE GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAG-AAACAGGAATGCTTATAATC ATCCTACAGTGCACA BABOON GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAA-AAACAGGGATGCTTATAATC ATCCTACAGTGCACA GORILLA GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGTGGGGATGCTTATACTC ATCCTACAGTGCACA CHIMP GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCTACAGTGCACA HUMAN GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCTACAGTGCACA NNNNNNNNNNNNNNNNNNNNNNNNNNNN-----N-NNNNN-NNNNNNN-NN-NNNNNNNNNNNNNNNNN NNNNNNNNNNNNNN Blanchette et al., Genome Res

11 Base-level ancestral reconstruction Substitutions (point mutations) Small insertions and deletions (indels) ARMADILLO TGCTACTAATAT-----T-TAGTA-CATAGAG-CC-CAGGGGTGCTGCTGAAA GTCTTAAAATGCACA MOUSELEMUR ATCACAG-TTGGGGGATGCCACTGGCCT-----C-AAGTG-GGTAGAG-AA-CAGGGAGGCTGAAAACC ACCCTGCAGAGCACG ORANGUTAN GTCACGATTTGGGAGATGCTTCTGGCTC-----G-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCAACAGTGCACA COW GCCTCTCTTT CTGCCCTGCAGGC-TAGAA-TGTATCA-CT-TAGATGTTCCAA ATCAGAAAGTGTTCA HORSE GTCACAATTTAGGAAGTGCCACTGGCCT-----C-TAGAG-GGTAGAA-GA-CAGGGATGCTAATAATCATCCCACGTCATCCTACAGTGCTCA CAT GTCACAGTTTAGGGGGTACTACTGGCAT-----C-TATCG-GGTGGAG-GA-TAGGGATACTGATAATC ATTCTACAGTGCACA DOG GTCACAATTTGGGGGATACTACTGGCAT-----C-TAATG-GGTAGAG-GA-CAGGGATACTGATAATT GCTTTACAGTGCACA HEDGEHOG GTCATAGTTT----GATTATATGGGCTT-----CTTAGTA-GACAAAGAAA-AAGATGTTCTGGTAGTC ATTCTGCTTTCCATA MOUSE GTCACAGTTTGGAGGATGTTACTGACAT-----C-TAGAG-AGTAGAC-TT-TAAAGATACTGATAGTC ACCCCATTGTGCAC- RAT GTCACAATTTGGAGGATGTTACTGGCAT-----C-TAGAG-AGTAGAC-TT-TAAGGACACTGATAATC ATACTATGCTGCAC- RABBIT ATCACAATTTGGGGAACACCACTGGCAT-----C-TCGGGTAGCAGGC----CAGGCATGCTGGTAATT ATACTACAGTGCACA LEMUR ATCACAA-TTGGGGG-TGCCACGGTCCT-----C-CAGTG-GGTAGAG-AA-CAGGGAGGCTGATAACC ACCCTGCAGTGCACA VERVET GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAG-AAACAGGGATGCTTATAATC ATCCTACAGTGCACA MACAQUE GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAG-AAACAGGAATGCTTATAATC ATCCTACAGTGCACA BABOON GTCAGAATTTGGGGGATGCTTCTGGCTC-----T-ACTTG-GGTAGAA-AAACAGGGATGCTTATAATC ATCCTACAGTGCACA GORILLA GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGTGGGGATGCTTATACTC ATCCTACAGTGCACA CHIMP GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCTACAGTGCACA HUMAN GTCACGATTTGGGGGATGCTTCTGGCTC-----A-ACTTG-GGTAGAG-AAGCGGGGATGCTTATAATC ATCCTACAGTGCACA NNNNNNNNNNNNNNNNNNNNNNNNNNNN-----N-NNNNN-NNNNNNN-NN-NNNNNNNNNNNNNNNNN NNNNNNNNNNNNNN GTCACAATTTGGGGGATGCTACTGGCAT-----C-TAGTG-GGTAGAG-AA-CAGGGATGCTGATAATC ATCCTACAGTGCAC Blanchette et al., Genome Res

12 rrangements. Each green or red rectangle is a chromo- mammalian genome evolution. ates what the chromosomes look like before and after mathematical Large-scale model structural of chromosome genomic evolution, changesa chrom g of numbers (or permutation), and a genome as a set o gested where that separates Robertsonian chromosomes. translocation Numbers also on played a chromo an volution. e.g. a single base, a gene, or larger piece of DNA seque of + chromosome or, which indicate evolution, thearelative chromosome orientation can be of the rep-gutation), rearrangements and a genome discussed as a set in the of these previous strings, section e.g. ca inversion me omosomes. ersion: 1 2 Numbers on a chromosome could 6 7 (In be bioinf any alled ene, or reversal); larger piece Translocation: of DNA sequence Numbers may 6 e2the 3 4relative orientation Fission: 1 2of 3the 4 5 genomic 67 content scussed form composite in the previous operations. section For can example, be interpreted as by two overlapping translocation inversions (reciprocal, robertsonian) followed by a fission: (In bioinformatics literature, ocation: Fusion: Overlapping or 9

13 rates chromosomes Numbers 6 7 8, where on a chromosome separates chro cou base, Large-scale a gene, genomic or larger structural content, piecegenomic of e.g. DNA a single sequence. changes base, Num a ge been h indicate suggested the have relative that signs, Robertsonian orientation either + translocation orof, the which genomic indicate also play con ments enome discussed evolution. The in the chromosome previous section rearrangements can be inter dis l 4model 5 67 of chromosome the following: evolution, Inversion: 6 7 (In a chromosome bioinformatics can 67 bl ); (or Translocation: permutation), 1 and 2 3 afusion 4 genome 5 67 as a 17 set of 6 these string inversion is also called reversal); Translo 5. rates chromosomes. Numbers on a chromosome could b Fission: Fission: 7. Overla 1 base, a gene, or larger piece of DNA sequence. Number ite operations. nested For example, operations1 form 2 3 4composite can operat be tra h indicate the relative orientation of the genomic conten rlapping inversions to followed by 7 aby fission: two overlapping i ments discussed in the previous section can be interpre (In bioinformatics liter ); Translocation: fission Fus Synteny blocks Fission: Overlapp ite operations. For example, can be transf tent that signed permutations Identifying thecan genomic represent content has alway that s rlapping inversions followed by a fission:

14 Partition the genomes into synteny blocks human chr13 (q12.13-q13.3) p13 p q q34 dog rat mouse chr13: Level 1 Level 2 Level 3 Level 4 Level 5 Level 6 Level 1 Level 2 Level 3 Level 4 Level 5 Level 6 Level 1 Level 2 Level 3 Level 4 Level 5 Level Dog (May 2005/canFam2) Alignment Net Rat (Nov. 2004/rn4) Alignment Net Mouse (July 2007/mm9) Alignment Net (A) human dog rat mouse (B) 11

15 Duplications and other structural changes Transposition Duplication (A) tandem duplication (B) segmental duplication 12

16 Operation-based ancestral reconstruction The parsimony problem: Given a set of present day genomes, find the evolutionary history for them with the minimum number of operations Pair-wise case: Hannenhalli-Pevzner theory for inversions A = , B = d(a,b) = 7 Median Problem A = d(m,a) + d(m,b) + d(m,c) B = M = C =

17 Adjacency-based ancestral reconstruction human chr13 (q21.1) q human: opossum dog rat mouse rhesus chr13: Level 1 Level 2 Level 3 Level 4 Level 5 Level 6 Level 1 Level 2 Level 3 Level 4 Level 5 Level 6 Level 1 Level 2 Level 3 Level 4 Level 5 Level 6 Level 1 Level 2 Level 3 Level 4 Level 5 Level 6 Level 1 Level 2 Level 3 Level 4 Level 5 Level Opossum (Jan. 2006/monDom4) Alignment Net Dog (May 2005/canFam2) Alignment Net Rat (Nov. 2004/rn4) Alignment Net Mouse (July 2007/mm9) Alignment Net Rhesus (Jan. 2006/rheMac2) Alignment Net (B) How to determine the ancestral orders? opossum: dog: rat: mouse: rhesus:

18 1-2 3 Adjacency-based ancestral reconstruction opossum dog mouse rat rhesus human

19 1-2 3 Adjacency-based ancestral reconstruction opossum dog mouse rat rhesus human

20 Fitch s algorithm human {A} {A G T} {A G} chimp {G} Goal: to infer minimum character changes in a specified tree topology {A} mouse {T} dog {A} The algorithm works sequentially, in two stages. For each position, in a bottom-up fashion, it first determines a set M π of candidate nucleotides at each node π in the tree according to the following rule: if π is a leaf, M π just contains its nucleotide character; otherwise, if π has children τ and ϕ, thenm π equals to M τ M ϕ or M τ M ϕ depending on whether M τ and M ϕ are disjoint or not. I.e., if M τ M ϕ 0 then M π M τ M ϕ else M π M τ M ϕ where X denotes the number of items in the set X. Then, in a top-down fashion, it assigns a character b π from M π to π according to the following rule: Let ρ be the parent of π; ifthecharacterb ρ assigned to ρ belongs to M π, then, b π = b ρ. Otherwise, set b π to be any character in M π. Although character assignment in this second stage may not be unique, any assignment gives an evolutionary history with the minimum number of substitution events. 16

21 Generalize the algorithm to track all the synteny blocks In our case, we deal with sequences of signed integers, rather than characters of nucleotides or amino acids, and instead of keeping track of letters at a particular sequence position, we track the synteny blocks for each of the immediately adjacent positions. Based on this logic, for a certain ancestor, we can infer what would be the most parsimonious neighbors of each synteny block in it. Finally, we connect the synteny blocks in the ancestor based on possible neighboring relationships into chromosomes. 17

22 The algorithm predecessor p g (i) is defined as the signed block that immediately precedes i successor s g (i) of i is defined analogously; e. For instance, let have the chromosome Thus, for any genome g, we associate with each block i two sets of signed blocks, denoted P g (i) and S g (i), giving potential predecessors and successors of i relative to chromosomes of g. If g is a modern genome, P g (i) ={p g (i)} and S g (i) ={s g (i)}, foreachi. If g does not contain i, then both sets are empty. GET-PREDECESSOR-SUCCESSOR(π) 1 if t is non-leaf node 2 then GET-PREDECESSOR-SUCCESSOR(τ) 3 GET-PREDECESSOR-SUCCESSOR(ϕ) 4 for i N to N (i 0) 5 do if P τ (i) P ϕ (i) 0 6 then P π (i) P τ (i) P ϕ (i) 7 else P π (i) P τ (i) P ϕ (i) 8 if S τ (i) S ϕ (i) 0 9 then S π (i) S τ (i) S ϕ (i) 10 else S π (i) S τ (i) S ϕ (i) 18

23 Reconstructing the Boreoeutherian common ancestor CAR 2 CAR CAR 1 CAR p 8p 8p 21q 3 5 CAR 6 15q 14q CAR 5 6 CAR 7 X 22q 12 22q CAR 12 CAR 15 8q CAR 10 2q CAR CAR 11 7 CAR CAR 13 2 CAR q 19q CAR q CAR CAR 9 11 CAR 22 7 CAR 8 10 CAR q 22q22q CAR 16 13q CAR Ma et al., Genome Res

24 Structural genomic variation between human individuals Variation Rearrangement type Size range a Single base-pair changes Small insertions/deletions Single nucleotide polymorphisms, point mutations Binary insertion/deletion events of short sequences (majority <10 bp in size) 1 bp 1 50 bp Short tandem repeats Microsatellites and other simple repeats bp Fine-scale structural variation Deletions, duplications, tandem repeats, inversions 50 bp to 5 kb Retroelement insertions SINEs, LINEs, LTRs, ERVs b 300 bp to 10 kb Intermediate-scale structural variation Large-scale structural variation Chromosomal variation Deletions, duplications, tandem repeats, inversions Deletions, duplications, large tandem repeats, inversions Euchromatic variants, large cytogenetically visible deletions, duplications, translocations, inversions, and aneuploidy 5 kb to 50 kb 50 kb to 5 Mb 5 Mb to entire chromosomes Sharp et al. Annu. Rev. Genomics Hum. Genet

25 Comparing Venter s Genome with the reference genome from public HGP a Assembly 1 Assembly 2 Matched b Assembly 1 Mismatch Assembly 2 c Assembly 1 Assembly 2 Unmatched d e f Assembly 1 Assembly 2 Assembly 1 Assembly 2 Assembly 1 Assembly 2 Copyunmatched Inversion Gap Khaja et al. Nature Genetics X Y Green bars -- unmatched Red bars -- copy-unmatched 21

26 Robertsonian translocation can cause Down syndrome Down syndrome is a chromosomal disorder which causes physical and intellectual delays in development and occurs when there are 3 chromosome 21's, resulting in 47 total chromosomes instead of the normal

27 ', * #*(&(+(& % * ** '" & ', ($', &-,,$(' individuals. Roughly 75 cancer genomes have been sequenced to some extent and published; researchers expect to have several hundred completed sequences by the end of the year. The efforts are certainly creating bigger hay stacks. Comparing the gene sequence of any tumour to that of a normal cell reveals dozens of single-letter changes, or point mutations, along with repeated, deleted, swapped or inverted sequences (see Genomes at a glance ). The difficulty, says Bert Vogelstein, a cancer researcher at the similar they might look clinically, most tumours seem to differ geneti cally. This stymies efforts to distinguish the mutations that cause and accelerate cancers the drivers from the accidental by-products of a cancer s growth and thwarted ETV6-ITPR2 fusion gene in the breast DNA-repair mechanisms the passengers. Researchers can look for mutations that pop up cancer PD3668a (Stephens et al. Nature again and again, or they can identify key path Figure 14: Fusion genes in cancer genomes. (A) CACNA2D4-WDR43 ways that are mutated at different points. But fusion gene identified in the NCI2009) ',* #*(&(+(& % H2171 cancer cell line. The 5 portion of are theproviding CACNA2D4 gene is amplified. A rearrangement breaks * ** '" &lung ', the projects more questions than ()0 '-& * # '" 23 answers. you take The the fewsequence obvious muta the gene in exon 36, fusing it into intron 3 of Once WDR43. at the breakpoint creates an almost (A) ur a ed in amat the ocitrate omoting And at least Agios Pharhusetts is he process. covery, ask cer genome will probably Cancer is another group of genetic diseases associated with massive amount of structural genomic changes ional mutahanged only es isocitrate ing enzyme were plenty 13,000 genes Nobody impor scu, a om hns re, to Chromosomal aberrations in cancer (B)

28 Summary Structural genomic changes can happen: 1) between different species 2) between different individuals in the same population 3) in disease genomes As the genomic data grows exponentially, the idea of ancestral genome reconstruction is an elegant way to organize a large number of related species, creating a vertical map so that we can navigate the genomes and trace the history from past to present. 24