RECONSTRUCTING ANCESTRAL GENOMES TO UNDERSTAND MAJOR TRANSITIONS Jordi Paps Public @JordiPaps Public Animals Public THE ORIGIN OF THE ANIMAL KINGDOM Public Public Where? Animals Origins Public Adl et al 2012 Opisthokonta Animal Origins Animals Choanoflagellata Fungi Public Opisthokonta Animal Origins Animals Choanoflagellata Filasterea Corallochytrium Ichthyosporea Fungi Public Choanoflagellata Animal Origins Nicole King Public Origin of Multicellular Animals Individual choanoflagellate Choano- flagellates OTHER EUKARYOTES Sponges Animals Collar cell (choanocyte) Other animals • Morphological and molecular evidence points to choanoflagellates as the closest living relatives to animals Public Animal Origins Filasterea (Capsaspora) Ichthyosporea (Sphaeroforma) Iñaki Ruiz-Trillo Public When? 560 Mya Ediacaran biota 2,000 Mya Oldest eukaryote fossils 4,000 Mya Origin of life Public Ediacaran biota • Ediacaran biota (560 million years ago) composed by multicellular organisms. Strong debate about their nature: animals or not? 1.5 cm 0.4 cm (a) Mawsonites spriggi (b) Spriggina floundersi Public Public When? 542 Mya Cambrian explosion 560 Mya Ediacaran biota 2,000 Mya Oldest eukaryote fossils 4,000 Mya Origin of life Public The Cambrian explosion (535 to 525 Mya): sudden fossil appearance of all the major groups of extant groups animals Burgess shale Public When? Animal Origins 833–650 Ma Dos Reis et al 2015 Public Public Ecology Triggers Public Environment Triggers Public Genome Triggers •Gene regulation (TFs,and signalling pathways) •Cell adhesion •Cell type specialization •Cell cycle •Immunity Public HOW TO MAKE A BABY? Public Genome How to make a baby… Public Genome Development converts info from 1D (DNA) to 4D space ATGTATCTATA… time Public Genome Genome •Gene regulation (TFs,and signalling pathways) •Cell adhesion •Cell type specialization •Cell cycle •Immunity Public Differential gene expression space time Public Signalling pathways: cell communication Genome Ligand Public Signalling pathways: Wnt Genome Public Nucleus Transcription Factor myoD Other muscle-specific genes DNA Embryonic precursor cell OFF OFF mRNA OFF MyoD protein Myoblast (transcription (determined) factor) mRNA mRNA mRNA mRNA Myosin, other muscle proteins, MyoD Another and cell cycle– Part of a muscle fiber transcription blocking proteins (fully differentiated cell) factor Public Nucleus Transcription Factor myoD Other muscle-specific genes DNA Embryonic precursor cell OFF OFF mRNA OFF MyoD protein Myoblast (transcription (determined) factor) mRNA mRNA mRNA mRNA Myosin, other muscle proteins, MyoD Another and cell cycle– Part of a muscle fiber transcription blocking proteins (fully differentiated cell) factor Public Nucleus Master regulatory gene myoD Other muscle-specific genes DNA Embryonic precursor cell OFF OFF mRNA OFF MyoD protein Myoblast (transcription (determined) factor) ON ON ON mRNA mRNA mRNA mRNA Myosin, other muscle proteins MyoD Another Part of a muscle fiber transcription (fully differentiated cell) factor Public Genome Transcription Factors (TFs): Hox genes Public Genome Transcription Factors (TFs): Hox genes Learn genetics http://learn.genetics.utah.edu/c ontent/basics/hoxgenes/ Public Genome Genome •Gene regulation (TFs,and signalling pathways) •Cell adhesion •Cell type specialization •Cell cycle •Immunity Public Cell adhesion Public Genome Triggers •Gene regulation (TFs,and signalling pathways) •Cell adhesion •Cell type specialization •Cell cycle •Immunity Public Cell types space time Public Genome Triggers •Gene regulation (TFs,and signalling pathways) •Cell adhesion •Cell type specialization •Cell cycle •Immunity Public Cell cycle space time Public Programmed cell death: apoptosis Interdigital tissue 1 mm Public Genome Triggers •Gene regulation (TFs,and signalling pathways) •Cell adhesion •Cell type specialization •Cell cycle •Immunity Public Public Public Genomic Novelties Old vs New New Animals genes Choanoflagellata Fungi Public Old vs New Nicole King Genomic Tinkering Animals Iñaki Ruiz-Trillo Animal genes Choanoflagellata Animal genes Animal Filasterea genes Corallochytrium Ichthyosporea Fungi Public Old vs new Old vs New ? Public COMPARE GENOMES TO PROFILE THE ROLE OF NOVELTY IN ANIMAL ORIGINS Peter WH Holland Public THE PIPELINE Public Pipeline Complete genomes Define groups of homologous genes Map genes distribution Public Pipeline Complete genomes Public Eukaryotes Pipeline 62 Genomes 13 metazoan phyla 10 outgroups Public Adl et al 2012 Animals Origins 62 Genomes 13 metazoan phyla 10 outgroup lineages Public Animal root: spongctenophorifera Pipeline Public Pipeline Complete genomes Define groups of homologous genes Public Pipeline Homology assignment Speed Accuracy Orthology/Paralogy Phylostratigraphy +++ + None one spp query (assumes one-to-one) one-way BLAST Reciprocal Best BLAST ++ ++ BLAST e-value (i.e. Inparanoid) All spp vs all Gene trees Two-way BLAST RBB/RBD/RBH… Reciprocal BLAST + HMM + +++ BLAST e-value (i.e. OrthoMCL) All spp vs all Gene trees Two-way BLAST MCL Public MCLMarkov(MarkovClusteringCLuster) Pipeline •1,500,000 genes in the 62 genomes •2,000,000,000,000 one vs one comparisons •268,440 homology groups (HG) Public Pipeline Why no orthology/paralogy? Assymetric evolution Public Public Ferguson et al 2014 Pipeline Homeobox Superfamily Class ANTP Subclass HOXL Family Hox1 •All human genome: 9,415 homology groups •All fruit fly genome: 7,681 homology clusters Public Zhong and Holland 2011 Pipeline Complete genomes Define groups of homologous genes Map genes distribution Public Phylogenetically-Aware Parsing Script L C A Public Types of gene groups Ancestral HG Novel HG L L C C A A ? Novel Core HG L C A Public Limitations Pipeline •Based on protein-coding genes, neglecting the role of non-coding genes (e.g., non-coding RNAs), transposable elements, and regulatory elements (e.g., enhancer, promoters, etc.). •Based on BLAST, ignoring gene fusions and fissions, alternative splicing, etc. Limited to the detection power of the algorithm. •Robust taxon sampling, but still far from complete. Public THE GENOME OF THE FIRST ANIMAL Public Animal results Clade Ancestral Holozoa Metazoa Deuterostomia (12 species) Ecdysozoa (12) Lophotrochozoa (12) Metazoa 6331 Cnidaria (3) Placozoa (1) Ctenophora (2) Porifera (2) Choanoflagellata (2) Filasterea (1) Ichthyosporea (2) Holomycota (4) Apusozoa (1) Outgroups (8) Public Animal results Public 6331 homology groups in the first animal Animal results •Gene regulation nucleic acid binding (PC00171) hydrolase (PC00121) •Metabolism transferase (PC00220) oxidoreductase (PC00176) transporter (PC00227) enzyme modulator (PC00095) transcription factor (PC00218) receptor (PC00197) 17% cytoskeletal protein (PC00085) 3% 3% signaling molecule (PC00207) 3% ligase (PC00142) 4% calcium-binding protein (PC00060) 14% transfer/carrier protein (PC00219) 4% membrane traffic protein (PC00150) 5% extracellular matrix protein (PC00102) 6% 9% lyase (PC00144) isomerase (PC00135) 7% 8% 7% chaperone (PC00072) cell adhesion molecule (PC00069) defense/immunity protein (PC00090) •60% of modern human cell junction protein (PC00070) transmembrane receptor regulatory/adaptor and fruit fly genes descend protein (PC00226) from these homology structural protein (PC00211) storage protein (PC00210) groups. viral protein (PC00237) Public Animal results Clade Ancestral Holozoa Metazoa Deuterostomia (12 species) Bilateria 9337 Planulozoa Ecdysozoa (12) 8433 Eumetazoa 4910 Lophotrochozoa (12) Metazoa 6331 Cnidaria (3) Node 2 4883 Placozoa (1) Ctenophora (2) Node 1 Porifera (2) 4182 Choanoflagellata (2) Holozoa 3878 Filasterea (1) Ichthyosporea (2) Holomycota (4) Apusozoa (1) Outgroups (8) Public Evolution of Ancestral HG Animal results 20 Animals 18 16 14 12 10 8 6 4 2 0 nucleic acid hydrolase transferase oxidoreductase transporter enzyme transcription receptor cytoskeletal signaling binding (PC00121) (PC00220) (PC00176) (PC00227) modulator factor (PC00218) (PC00197) protein molecule (PC00171) (PC00095) (PC00085) (PC00207) Opisthokonta Holozoa Node 1 Node 2 Metazoa Eumetazoa Planulozoa Bilateria Drosophila melanogaster Homo sapiens Public A GENOMIC EXPLOSION OF NOVELTY Public Animal results Clade Ancestral Holozoa Metazoa Novel Deuterostomia (12 species) Bilateria 9337 1580 Planulozoa 8433 Ecdysozoa (12) 1201 Eumetazoa 4910 494 Metazoa Lophotrochozoa (12) 6331 1189 Node 2 Cnidaria (3) 4883 399 Placozoa (1) Node 1 Ctenophora (2) 4182 Porifera (2) 340 Holozoa Choanoflagellata (2) 3878 389 Filasterea (1) Ichthyosporea (2) Holomycota (4) Apusozoa (1) Outgroups (8) Public Animal results % Novelty Animals Public 90 Number of hits in Novel HG Animal results 80 per GO category 70 60 50 40 Protein Class GO number Class GO number hits Protein of 30 20 10 0 nucleic acid transcription signaling receptor transporter hydrolase enzyme oxidoreductase chaperone extracellular structural binding factor molecule (PC00197) (PC00227) (PC00121) modulator (PC00176) (PC00072) matrix protein protein (PC00171) (PC00218) (PC00207) (PC00095) (PC00102) (PC00211) Holozoa Node 1 (Filasterea + Node 2) Node 2 (Choanoflagellata + Metazoa) Metazoa Eumetazoa Planulozoa Bilateria Public 25 ESSENTIAL NEW ANIMAL HOMOLOGY GROUPS Public Animal results Clade Ancestral Holozoa Metazoa Novel Bilateria Deuterostomia (12 species) Novel 9337 essential 1580 Planulozoa 0 8433 1201 Ecdysozoa (12) Eumetazoa 1 4910 494 Metazoa 3 Lophotrochozoa (12) 6331 1189 Node 2 25 4883 Cnidaria (3) 399 Node 1 4 Placozoa (1) 4182 Ctenophora (2) 340 Porifera (2) Holozoa 4 3878 Choanoflagellata