Genome Biology (Jan 2020)
Gene content evolution in the arthropods
- Gregg W. C. Thomas,
- Elias Dohmen,
- Daniel S. T. Hughes,
- Shwetha C. Murali,
- Monica Poelchau,
- Karl Glastad,
- Clare A. Anstead,
- Nadia A. Ayoub,
- Phillip Batterham,
- Michelle Bellair,
- Greta J. Binford,
- Hsu Chao,
- Yolanda H. Chen,
- Christopher Childers,
- Huyen Dinh,
- Harsha Vardhan Doddapaneni,
- Jian J. Duan,
- Shannon Dugan,
- Lauren A. Esposito,
- Markus Friedrich,
- Jessica Garb,
- Robin B. Gasser,
- Michael A. D. Goodisman,
- Dawn E. Gundersen-Rindal,
- Yi Han,
- Alfred M. Handler,
- Masatsugu Hatakeyama,
- Lars Hering,
- Wayne B. Hunter,
- Panagiotis Ioannidis,
- Joy C. Jayaseelan,
- Divya Kalra,
- Abderrahman Khila,
- Pasi K. Korhonen,
- Carol Eunmi Lee,
- Sandra L. Lee,
- Yiyuan Li,
- Amelia R. I. Lindsey,
- Georg Mayer,
- Alistair P. McGregor,
- Duane D. McKenna,
- Bernhard Misof,
- Mala Munidasa,
- Monica Munoz-Torres,
- Donna M. Muzny,
- Oliver Niehuis,
- Nkechinyere Osuji-Lacy,
- Subba R. Palli,
- Kristen A. Panfilio,
- Matthias Pechmann,
- Trent Perry,
- Ralph S. Peters,
- Helen C. Poynton,
- Nikola-Michael Prpic,
- Jiaxin Qu,
- Dorith Rotenberg,
- Coby Schal,
- Sean D. Schoville,
- Erin D. Scully,
- Evette Skinner,
- Daniel B. Sloan,
- Richard Stouthamer,
- Michael R. Strand,
- Nikolaus U. Szucsich,
- Asela Wijeratne,
- Neil D. Young,
- Eduardo E. Zattara,
- Joshua B. Benoit,
- Evgeny M. Zdobnov,
- Michael E. Pfrender,
- Kevin J. Hackett,
- John H. Werren,
- Kim C. Worley,
- Richard A. Gibbs,
- Ariel D. Chipman,
- Robert M. Waterhouse,
- Erich Bornberg-Bauer,
- Matthew W. Hahn,
- Stephen Richards
Affiliations
- Gregg W. C. Thomas
- Department of Biology and Department of Computer Science, Indiana University
- Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münsterss
- Daniel S. T. Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Shwetha C. Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Monica Poelchau
- National Agricultural Library, USDA
- Karl Glastad
- School of Biological Sciences, Georgia Institute of Technology
- Clare A. Anstead
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne
- Nadia A. Ayoub
- Department of Biology, Washington and Lee University
- Phillip Batterham
- School of BioSciences Science Faculty, The University of Melbourne
- Michelle Bellair
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Greta J. Binford
- Department of Biology, Lewis & Clark College
- Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Yolanda H. Chen
- Department of Plant and Soil Sciences, University of Vermont
- Christopher Childers
- National Agricultural Library, USDA
- Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Jian J. Duan
- Beneficial Insects Introduction Research Unit, United States Department of Agriculture, Agricultural Research Service
- Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Lauren A. Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences
- Markus Friedrich
- Department of Biological Sciences, Wayne State University
- Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell
- Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne
- Michael A. D. Goodisman
- School of Biological Sciences, Georgia Institute of Technology
- Dawn E. Gundersen-Rindal
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory
- Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Alfred M. Handler
- USDA-ARS, Center for Medical, Agricultural, and Veterinary Entomology
- Masatsugu Hatakeyama
- Division of Insect Sciences, National Institute of Agrobiological Sciences
- Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel
- Wayne B. Hunter
- USDA ARS, U. S. Horticultural Research Laboratory
- Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva
- Joy C. Jayaseelan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Divya Kalra
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Abderrahman Khila
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1
- Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne
- Carol Eunmi Lee
- Department of Integrative Biology, University of Wisconsin
- Sandra L. Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Yiyuan Li
- Department of Biological Sciences, University of Notre Dame, 109B Galvin Life Sciences
- Amelia R. I. Lindsey
- Department of Entomology, University of California Riverside
- Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel
- Alistair P. McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University
- Duane D. McKenna
- Department of Biological Sciences, University of Memphis
- Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig
- Mala Munidasa
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Monica Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
- Donna M. Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Oliver Niehuis
- Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University of Freiburg
- Nkechinyere Osuji-Lacy
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Subba R. Palli
- Department of Entomology, University of Kentucky
- Kristen A. Panfilio
- School of Life Sciences, University of Warwick, Gibbet Hill Campus
- Matthias Pechmann
- Cologne Biocenter, Zoological Institute, Department of Developmental Biology, University of Cologne
- Trent Perry
- School of BioSciences Science Faculty, The University of Melbourne
- Ralph S. Peters
- Centre of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig
- Helen C. Poynton
- School for the Environment, University of Massachusetts Boston
- Nikola-Michael Prpic
- Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, Georg-August-Universität Göttingen
- Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Dorith Rotenberg
- Department of Entomology and Plant Pathology, North Carolina State University
- Coby Schal
- Department of Entomology and W.M. Keck Center for Behavioral Biology, North Carolina State University
- Sean D. Schoville
- Department of Entomology, University of Wisconsin-Madison
- Erin D. Scully
- Stored Product Insect and Engineering Research Unit, USDA-ARS Center for Grain and Animal Health Research
- Evette Skinner
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Daniel B. Sloan
- Department of Biology, Colorado State University
- Richard Stouthamer
- Department of Entomology, University of California Riverside
- Michael R. Strand
- Department of Entomology, University of Georgia
- Nikolaus U. Szucsich
- Present Address: Arkansas Biosciences Institute, Arkansas State University
- Asela Wijeratne
- Department of Biological Sciences, University of Memphis
- Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne
- Eduardo E. Zattara
- INIBIOMA, Univ. Nacional del Comahue – CONICET
- Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati
- Evgeny M. Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva
- Michael E. Pfrender
- Department of Biological Sciences, University of Notre Dame, 109B Galvin Life Sciences
- Kevin J. Hackett
- Crop Production and Protection, U.S. Department of Agriculture-Agricultural Research Service
- John H. Werren
- Department of Biology, University of Rochester
- Kim C. Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Richard A. Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- Ariel D. Chipman
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem
- Robert M. Waterhouse
- Department of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne
- Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münsterss
- Matthew W. Hahn
- Department of Biology and Department of Computer Science, Indiana University
- Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine
- DOI
- https://doi.org/10.1186/s13059-019-1925-7
- Journal volume & issue
-
Vol. 21,
no. 1
pp. 1 – 14
Abstract
Abstract Background Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Results Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. Conclusions These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.
Keywords
