About the Authors

Ariel D. Chipman

Affiliation The Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel

David E. K. Ferrier

Affiliation The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, St Andrews, Fife, United Kingdom

Carlo Brena

Affiliation Department of Zoology, University of Cambridge, Cambridge, United Kingdom

Jiaxin Qu

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Daniel S. T. Hughes

Current address: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Affiliation EMBL - European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom

Reinhard Schröder

Affiliation Institut für Biowissenschaften, Universität Rostock, Abt. Genetik, Rostock, Germany

Montserrat Torres-Oliva

Current address: Department of Developmental Biology, Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung Entwicklungsbiologie, GZMB, Göttingen, Germany

Affiliation Department of Zoology, University of Cambridge, Cambridge, United Kingdom

Nadia Znassi

Current address: Centre de Recherche de Biochimie Macromoléculaire, Bioinformatique Structurale et Modélisation Moléculaire, Montpellier, France

Affiliation Department of Zoology, University of Cambridge, Cambridge, United Kingdom

Huaiyang Jiang

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Francisca C. Almeida

Affiliations Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad Nacional de Tucumán, Facultad de Ciencias Naturales e Instituto Miguel Lillo, San Miguel de Tucumán, Argentina

Claudio R. Alonso

Affiliation School of Life Sciences, University of Sussex, Brighton, United Kingdom

Zivkos Apostolou

Affiliations Department of Zoology, University of Cambridge, Cambridge, United Kingdom, Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology - Hellas, Heraklion, Crete, Greece

Peshtewani Aqrawi

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Wallace Arthur

Affiliation Department of Zoology, National University of Ireland, Galway, Ireland

Jennifer C. J. Barna

Affiliation Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom

Kerstin P. Blankenburg

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Daniela Brites

Affiliations Evolutionsbiologie, Zoologisches Institut, Universität Basel, Basel, Switzerland, Swiss Tropical and Public Health Institute, Basel, Switzerland

Salvador Capella-Gutiérrez

Affiliation Centre for Genomic Regulation, Barcelona, Barcelona, Spain

Marcus Coyle

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Peter K. Dearden

Affiliation Gravida and Genetics Otago, Biochemistry Department, University of Otago, Dunedin, New Zealand

Louis Du Pasquier

Affiliation Evolutionsbiologie, Zoologisches Institut, Universität Basel, Basel, Switzerland

Elizabeth J. Duncan

Affiliation Gravida and Genetics Otago, Biochemistry Department, University of Otago, Dunedin, New Zealand

Dieter Ebert

Affiliation Evolutionsbiologie, Zoologisches Institut, Universität Basel, Basel, Switzerland

Cornelius Eibner

Current address: Department of Genetics, Friedrich Schiller University, Germany

Affiliation Department of Zoology, National University of Ireland, Galway, Ireland

Galina Erikson

Affiliations Razavi Newman Center for Bioinformatics, Salk Institute, La Jolla, California, United States of America, Scripps Translational Science Institute, La Jolla, California, United States of America

Peter D. Evans

Affiliation The Babraham Institute, Cambridge, United Kingdom

Cassandra G. Extavour

Affiliation Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America

Liezl Francisco

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Toni Gabaldón

Affiliations Centre for Genomic Regulation, Barcelona, Barcelona, Spain, Universitat Pompeu Fabra (UPF), Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

William J. Gillis

Affiliation Department of Biochemistry and Cell Biology, Center for Developmental Genetics, Stony Brook University, Stony Brook, New York, United States of America

Elizabeth A. Goodwin-Horn

Affiliation Department of Biology, Hendrix College, Conway, Arkansas, United States of America

Jack E. Green

Affiliation Department of Zoology, University of Cambridge, Cambridge, United Kingdom

Sam Griffiths-Jones

Affiliation Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom

Cornelis J. P. Grimmelikhuijzen

Affiliation Center for Functional and Comparative Insect Genomics, University of Copenhagen, Copenhagen, Denmark

Sai Gubbala

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Roderic Guigó

Affiliations Universitat Pompeu Fabra (UPF), Barcelona, Spain, Center for Genomic Regulation, Barcelona, Spain

Yi Han

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Frank Hauser

Affiliation Center for Functional and Comparative Insect Genomics, University of Copenhagen, Copenhagen, Denmark

Paul Havlak

Affiliation Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America

Luke Hayden

Affiliation Department of Zoology, National University of Ireland, Galway, Ireland

Sophie Helbing

Affiliation Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany

Michael Holder

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Jerome H. L. Hui

Affiliation School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China

Julia P. Hunn

Affiliation Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands

Vera S. Hunnekuhl

Affiliation Department of Zoology, University of Cambridge, Cambridge, United Kingdom

LaRonda Jackson

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Mehwish Javaid

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Shalini N. Jhangiani

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Francis M. Jiggins

Affiliation Department of Genetics, University of Cambridge, Cambridge, United Kingdom

Tamsin E. Jones

Affiliation Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America

Tobias S. Kaiser

Affiliation Max F. Perutz Laboratories, University of Vienna, Vienna, Austria

Divya Kalra

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Nathan J. Kenny

Affiliation School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China

Viktoriya Korchina

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Christie L. Kovar

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

F. Bernhard Kraus

Affiliations Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, Department of Laboratory Medicine, University Hospital Halle (Saale), Halle (Saale), Germany

François Lapraz

Affiliation Department of Genetics, Evolution and Environment, University College London, London, United Kingdom

Sandra L. Lee

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Jie Lv

Affiliation Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America

Christigale Mandapat

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Gerard Manning

Current address: Genentech, Inc., South San Francisco, California, United States of America

Affiliation Razavi Newman Center for Bioinformatics, Salk Institute, La Jolla, California, United States of America

Marco Mariotti

Affiliations Universitat Pompeu Fabra (UPF), Barcelona, Spain, Center for Genomic Regulation, Barcelona, Spain

Robert Mata

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Tittu Mathew

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Tobias Neumann

Affiliations Max F. Perutz Laboratories, University of Vienna, Vienna, Austria, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria

Irene Newsham

Current address: M.D. Anderson Cancer Center, Houston, Texas, United States of America

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Dinh N. Ngo

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Maria Ninova

Affiliation Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom

Geoffrey Okwuonu

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Fiona Ongeri

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

William J. Palmer

Affiliation Department of Genetics, University of Cambridge, Cambridge, United Kingdom

Shobha Patil

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Pedro Patraquim

Affiliation School of Life Sciences, University of Sussex, Brighton, United Kingdom

Christopher Pham

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Ling-Ling Pu

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Nicholas H. Putman

Affiliation Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America

Catherine Rabouille

Affiliation Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, The Netherlands

Olivia Mendivil Ramos

Current address: Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, United States of America

Affiliation The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, St Andrews, Fife, United Kingdom

Adelaide C. Rhodes

Affiliation Harte Research Institute, Texas A&M University Corpus Christi, Corpus Christi, Texas, United States of America

Helen E. Robertson

Affiliation Department of Genetics, Evolution and Environment, University College London, London, United Kingdom

Hugh M. Robertson

Affiliation Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America

Matthew Ronshaugen

Affiliation Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom

Julio Rozas

Affiliation Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain

Nehad Saada

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Alejandro Sánchez-Gracia

Affiliation Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain

Steven E. Scherer

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Andrew M. Schurko

Affiliation Department of Biology, Hendrix College, Conway, Arkansas, United States of America

Kenneth W. Siggens

Affiliation Department of Zoology, University of Cambridge, Cambridge, United Kingdom

DeNard Simmons

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Anna Stief

Affiliations Department of Zoology, University of Cambridge, Cambridge, United Kingdom, Institute for Biochemistry and Biology, University Potsdam, Potsdam-Golm, Germany

Eckart Stolle

Affiliation Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany

Maximilian J. Telford

Affiliation Department of Genetics, Evolution and Environment, University College London, London, United Kingdom

Kristin Tessmar-Raible

Affiliations Max F. Perutz Laboratories, University of Vienna, Vienna, Austria, Research Platform “Marine Rhythms of Life”, Vienna, Austria

Rebecca Thornton

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Maurijn van der Zee

Affiliation Institute of Biology, Leiden University, Leiden, The Netherlands

Arndt von Haeseler

Affiliations Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria, Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria

James M. Williams

Affiliation Department of Biology, Hendrix College, Conway, Arkansas, United States of America

Judith H. Willis

Affiliation Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America

Yuanqing Wu

Current address: Institute for Applied Cancer Science, MD Anderson Cancer Center, Houston, Texas, United States of America

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Xiaoyan Zou

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Daniel Lawson

Affiliation EMBL - European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom

Donna M. Muzny

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Kim C. Worley

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Richard A. Gibbs

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Michael Akam

Affiliation Department of Zoology, University of Cambridge, Cambridge, United Kingdom

Stephen Richards

stephenr@bcm.edu

Affiliation Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

The author(s) have made the following declarations about their contributions: Conceived and designed the experiments: MA SR. Performed the experiments: CB SES SNJ NS LLP SP XZ SG KPB SLL IN YW VK GO RM CP LF DS DNN PA MC LJ CM TM MJ RT CLK MH MJ FO YH JQ SR KCW HJ DSTH DL DK DMM MA RAG. Analyzed the data: HJ SR KCW DSTH DL CB TG SCG NHP PH JL MTO NZ JCJB DSTH DL DEKF OMR VSH KWS AS ZA RS JEG PP CRA WA LH CE PKD EJD LDP DE DB PDE CGE TEJ CJPG FH JHLH NJK FMJ WJP GM GE MM RG ACR MJT FL HER MR SGJ MN JR ASG FCA HMR ES FBK SH TSK TN AVH KTR MVDZ CR JPH JHW AMS EAGH JMW WJG ADC. Contributed reagents/materials/analysis tools: RAG MA DMM CB DSTH DL MTO NZ JCJB DSTH DL TG SCG NHP PH JL DK. Wrote the paper: ADC DEKF RS MA SR. Project management and senior authors: ADC DEKF RS MA SR. Sequencing PI: RAG. Centipede PI: MA. Specimen identification and preparation: CB. Sequencing operations manager: DMM. Sequencing project management: SES SNJ. Library: NS L-LP SP XZ SG KPB SLL IN YW. 454 sequencing: VK GO RM CP LF DS DNN PA MC LJ CM TM MJ RT CLK MH. Illumina sequencing: MJ FO YH. Assembly: JQ SR KCW. Automated annotation: HJ SR KCW DSTH DL. Submissions: DK. PhyloDB: TG SC-G. Chromosomal synteny conservation: NHP PH JL. Manual annotation: organization: MT-O NZ JCJB DSTH DL. Homeobox genes: DEKF OMR VSH KWS AS ZA. FGF signaling: RS. Sex chromosomes: JEG. Hox mRNA: PP CRA. wnt signaling: WA LH RS CE. Conserved gene clusters and methylation: PKD EJD. Dscam: LDP DE DB. Biogenic amine receptors: PDE. Germline genes: CGE TEJ. Neuropeptides and receptors: CJPG FH. Juvenile hormone systems: JHLH NJK. Immunity: FMJ WJP. Kinome: GM GE. Selenoproteins: MM RG. Mitochondria: ACR MJT FL HER. MiRNAs: MR SG-J MN. Chemosensory genes: JR AS-G FCA HMR. Repetitive elements: ES FBK SH. Light perception and circadian clock: TSK TN AVH KT-R. Innexins and TGF beta: MVDZ CR JPH. Cuticular proteins: JHW. Meiosis genes: AMS EAG-H JMW. Developmental transcription factors: WJG ADC VH JEG CB ZA.