1. Reconstructing Ancestral Vertebrate Genomes by in silico Palaeogenomics Hugues Roest Crollius Laboratoire Dyogen - CNRS Ecole Normale Supérieure Paris Bioinformatics Course Pasteur Institute Tunis, april 02 2007 NB: This version only contains a subset of the slides presented at the course

3. C AB AB C ancestor

4. 1995 1998 1996 1997 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 S. cerevisiae C. elegans D. melanogaster H. sapiens M. musculus P. troglodytes G. gallus C. familiaris A. taliana 100 gigabases T. nigroviridis T. rubripes R. norvegicus H. influenzae

5. Le séquençage des génomes de vertébrés

6. « Light » sequencing of mammal genomes (NHGRI/Broad) And also: Gorilla Macaque Pig …

7. Cephalochordates (Amphioxus) Urochordates (Ciona intestinalis) Hagfish (Myxiniformes) CRANIATES (-480 My) Mus musculus Homo sapiens Gallus gallus Tetraodon nigroviridis Takifugu rubripes Danio rerio Mammals Tetrapodes Coelacanthimorpha Birds Teleosteans Acipenseriforms (sturgeons,…) Percomorphs Cypriniforms Tetraodontiforms Chondrichthyes (cartilaginous fish) Osteichthyes (bony fish) 300 400 500 Paleozoic Cambrian Ordovician Silurian Devonian Carboniferous Permian 0 100 200 Mezozoic Cenozoic Triassic Jurassic Cretaceous Vertebrate evolution Gasterosteus aculeatus Million years ago Actinopterygians Sarcopterygians Amniotes

8. Duplication of the ancestral teleost genome? Amores et al. (1998) Science 282:1711-1714 Postlethwait et al. (2000) Genome Research 10:1890-1902 zebrafishmammals Christoffels et al. (2004) Mol. Biol. Evol.21:1146-1151 Fugu scaffolds

9. Common ancestor duplication Homo sapiensTetraodon nigroviridis whole genome duplication in teleosts diploidisation

10. Duplication Diploïdisation Whole Genome Duplication ~800 pairs of paralogs in Tetraodon

11. Example of Double Conserved Synteny between chicken and Tetraodon Gg.1 Tn.A Tn.B Gg.1 Tn.ATn.B Gg.1 Tetraodon chromosomes 12345678910111213141516171819 20 21 Gg.1 Whole Genome Duplication

12. 12345678910111213141516171819 20 21 Chromosomes de Tetraodon Gg.1 Both independent datasets (orthologs and paralogs) converge well. Whole Genome Duplication

13. Identification of DCS blocks Chicken chromosome PositionChromosome Tetraodon A Chromosome Tetraodon B 12201319 12221319 12241319 122519 122619 122719 12321319 123313 123419 123513 123713 123913 124013 124319 6835 orthologues Chicken / Tetraodon 4299 in 517 DCS = 8.3 genes per DCS This can be repeated between chicken and each of the 4 other fish genome

14. Identifying strict synteny blocks Gene loss block 1 block 2 blocks 3 Series of « ultra conserved » tetrapod syntenic blocks: same chromosome Same order Same orientation No insertion / deletion Each pair of genome is « scanned » for overlapping blocks

15. Independent validation with cytogenetic data Froenicke et al.,Genome Research 2006 16:306-310 > 80 Zoo-FISH comparison between mammals and human In silico method: 2n = 44 Fusion 10p - 12a not seen (but weak in cytogenetic data) Fusion 16q - 19q not seen; visible in cow and mouse but not strong enough. New fusion 5 + 19p (weak, disappears if no Oppossum) New fusion 2p + 9q (Strongly supported)

16. The 2R hypothesis Susumu Ohno 1928-2002 « It is likely that the first vertebrate to emerge on this earth [had a genome] which was probably derived from a primitive chordate by tetraploidization » S. Ohno et al. (1968) Heredity 59(1):169-187 « An ancient crossopterygian fish, which served as direct ancestor of mammals, already attained the characteristic DNA content [of mammals] by a second tetraploidisation before coming on land to live» S. Ohno et al. (1968) Heredity 59(1):169-187 « Yet it is our contention that either at the fish stage or at the amphibian stage, the mammalian ancestor went through at least one tetraploid evolution» S. Ohno. (1970) Evolution by Gene Duplication p. 102. Springer- Verlag Ed. New-York Inc.

17. Collaborators: O. Jaillon, J-M. Aury, J. Weissenbach et coll. Genoscope The Ensembl group www.ensembl.org M. Robinson Rechavi, R. Studer, Université de Lausanne Matthieu Muffato Hugues Roest Crollius http://www.biologie.ens.fr/dyogen