Genome duplication in the Tetraodon nigroviridis genome reveals the early vertebrate karotype. What did our paleozoic ancestor genome look like?
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1 Genome duplication in the Tetraodon nigroviridis genome reveals the early vertebrate karotype What did our paleozoic ancestor genome look like?
2 64% of the genome is anchored to chromosomes 36% remains as independent sequences
3 Paléozoic Gnatostomata (jawed vertebrates) Osteichthyes (bony fishes) Chondrichthyes (cartilaginous fishes) Sarcopterygiens (lobe finned fish) Actinoptérygiens (ray finned fish) Tetrapodes Coelacanthimorpha Teleosts Acipenseriforms (sturgeons, ) 225 my Mammals Sauropsidae Percomorphs Otophysi Beloniforms Tetraodontiforms Cypriniforms Mézozoic Mus Homo musculus sapiens Gallus gallus Oryzias latipes Tetraodon nigroviridis Takifugu rubripes Danio rerio
4 Genome Duplication A powerful source of functional innovation (whole metabolic pathways) How do duplicate gene copies evolve (redundancy)? How does a genome duplication spread in a population? What impact does it have on the cell (cycle, regulation, nutrients)?
5 Following a genome duplication, all genes are in two copies important redundancy Most supernumerary gene copies are progressively eliminated diploid tetraploid diploid duplication diploidization If most copies are eliminated, what is there left to prove that a duplication took place?
6 Ancestral species speciation A orthologs B paralogs duplication B Species 1 Species 2 A and B derive from an ancestral gene by speciation: they are orthologs B appears by duplication of B: they are paralogs Signature? Signature?
7 Ancestral genome Duplication Deletions intra-chromosomal rearrangements Fusions and fissions Translocations Time (tenth of million years)
8 Identification of duplicate genes Tetraodon Takifugu n = 1078 Ks <=0.35 n = % Ks > 0.35 n = % n = 995 Ks <=0.35 n = % Ks > 0.35 n = %
9 Distribution of 748 duplicate genes in the Tetraodon genome
10 Common ancestor duplication diploidization Homo sapiens Tetraodon nigroviridis
11 Tetraodon genome: Synteny with the human genome Human genome: Synteny with the Tetraodon genome
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13 Gnatostomata (jawed vertebrates) Osteichthyes (bony vertebrates) Chondrichthyes (cartilaginous vertebrates) Sarcopterygiens (lobbed finned fishes) Actinoptérygiens (ray finned fishes) Tetrapods Coelacanthimorpha Teleosts Acipenseriforms (esturgeons, ) Mammals Sauropsidae Percomorphs Otophysi Beloniforms Tetraodontiforms Cypriniforms Mus musculus Homo sapiens Gallus gallus Oryza latipes Tetraodon nigroviridis Takifugu rubripes Danio rerio
14 Ancêtre commun Homo sapiens Tetraodon nigroviridis
15 The ancestral osteichthyes genome (bony vertebrates)
16 What are the intermediary steps in the evolution of the Tetraodon and the human genome?
17 Modeling the evolution of a duplicated Tetraodon chromosome Gene order is progressively rearranged over time along Tetraodon and human chromosomes (independently) The degree of rearrangement along a chromosome segment is thus a measure of elapsed time Modeling a few simple cases of chromosomal rearrangements in Tetraodon: 1) No rearrangement 2) a recent fusion between two chromosomes 3) an ancient fusion between two chromosomes 4) a fission (break) of a chromosome
18 A simple case: no interchromosomal rearrangement after the dulication Ancestral genome Homo sapiens Tetraodon nigroviridis
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20 Distribution of 6884 orthologs in their respective genomes Chromosomes Humain 22 X X Chromosomes Tetraodon chromosomes
21 Case 2) : recent fusion between two chromosomes Ancestral genome Homo sapiens Tetraodon nigroviridis
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23 Chromosomes Humain 22 X Chromosomes Tetraodon
24 Case 3) : ancient fusion between two chromosomes Ancestral genome Homo sapiens Tetraodon nigroviridis
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26 Human chromosomes 22 X Tetraodon chromosomes
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