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Renoz F, Parisot N, Baa-Puyoulet P, Gerlin L, Fakhour S, Charles H, Hance T, Calevro F. PacBio Hi-Fi genome assembly of Sipha maydis, a model for the study of multipartite mutualism in insects. Sci Data 2024; 11:450. [PMID: 38704391 PMCID: PMC11069519 DOI: 10.1038/s41597-024-03297-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
Dependence on multiple nutritional endosymbionts has evolved repeatedly in insects feeding on unbalanced diets. However, reference genomes for species hosting multi-symbiotic nutritional systems are lacking, even though they are essential for deciphering the processes governing cooperative life between insects and anatomically integrated symbionts. The cereal aphid Sipha maydis is a promising model for addressing these issues, as it has evolved a nutritional dependence on two bacterial endosymbionts that complement each other. In this study, we used PacBio High fidelity (HiFi) long-read sequencing to generate a highly contiguous genome assembly of S. maydis with a length of 410 Mb, 3,570 contigs with a contig N50 length of 187 kb, and BUSCO completeness of 95.5%. We identified 117 Mb of repetitive sequences, accounting for 29% of the genome assembly, and predicted 24,453 protein-coding genes, of which 2,541 were predicted enzymes included in an integrated metabolic network with the two aphid-associated endosymbionts. These resources provide valuable genetic and metabolic information for understanding the evolution and functioning of multi-symbiotic systems in insects.
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Affiliation(s)
- François Renoz
- Biodiversity Research Centre, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, 1348, Belgium.
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR203, Villeurbanne, F-69621, France.
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan.
| | - Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR203, Villeurbanne, F-69621, France.
| | | | - Léo Gerlin
- Univ Lyon, INRAE, INSA Lyon, BF2I, UMR203, Villeurbanne, F-69621, France
| | - Samir Fakhour
- Biodiversity Research Centre, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, 1348, Belgium
- Department of Plant Protection, National Institute for Agricultural Research (INRA), Béni-Mellal, 23000, Morocco
| | - Hubert Charles
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR203, Villeurbanne, F-69621, France
| | - Thierry Hance
- Biodiversity Research Centre, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, 1348, Belgium
| | - Federica Calevro
- Univ Lyon, INRAE, INSA Lyon, BF2I, UMR203, Villeurbanne, F-69621, France.
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2
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Parisot N, Vargas-Chávez C, Goubert C, Baa-Puyoulet P, Balmand S, Beranger L, Blanc C, Bonnamour A, Boulesteix M, Burlet N, Calevro F, Callaerts P, Chancy T, Charles H, Colella S, Da Silva Barbosa A, Dell'Aglio E, Di Genova A, Febvay G, Gabaldón T, Galvão Ferrarini M, Gerber A, Gillet B, Hubley R, Hughes S, Jacquin-Joly E, Maire J, Marcet-Houben M, Masson F, Meslin C, Montagné N, Moya A, Ribeiro de Vasconcelos AT, Richard G, Rosen J, Sagot MF, Smit AFA, Storer JM, Vincent-Monegat C, Vallier A, Vigneron A, Zaidman-Rémy A, Zamoum W, Vieira C, Rebollo R, Latorre A, Heddi A. The transposable element-rich genome of the cereal pest Sitophilus oryzae. BMC Biol 2021; 19:241. [PMID: 34749730 PMCID: PMC8576890 DOI: 10.1186/s12915-021-01158-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. RESULTS We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis. CONCLUSIONS Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.
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Affiliation(s)
- Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Carlos Vargas-Chávez
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Present Address: Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Clément Goubert
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, New York, 14853, USA
- Present Address: Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Séverine Balmand
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Louis Beranger
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Caroline Blanc
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aymeric Bonnamour
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Matthieu Boulesteix
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Federica Calevro
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Patrick Callaerts
- Department of Human Genetics, Laboratory of Behavioral and Developmental Genetics, KU Leuven, University of Leuven, B-3000, Leuven, Belgium
| | - Théo Chancy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | - Stefano Colella
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, INRAE, SupAgro, Univ Montpellier, Montpellier, France
| | - André Da Silva Barbosa
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Elisa Dell'Aglio
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Alex Di Genova
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
- Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Gérard Febvay
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Toni Gabaldón
- Life Sciences, Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Mechanisms of Disease, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Institut Catalan de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Alexandra Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | | | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Justin Maire
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Florent Masson
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain
| | | | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653, Le Rheu, France
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | | | | | | | - Agnès Vallier
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aurélien Vigneron
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Department of Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, 55128, Mainz, Germany
| | - Anna Zaidman-Rémy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Waël Zamoum
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France.
- ERABLE European Team, INRIA, Rhône-Alpes, France.
| | - Rita Rebollo
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain.
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain.
| | - Abdelaziz Heddi
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
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3
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Oeyen JP, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen MJM, Childers C, Cridge AG, Dearden P, Dinh H, Doddapaneni HV, Dolan A, Donath A, Dowling D, Dugan S, Duncan E, Elpidina EN, Friedrich M, Geuverink E, Gibson JD, Grath S, Grimmelikhuijzen CJP, Große-Wilde E, Gudobba C, Han Y, Hansson BS, Hauser F, Hughes DST, Ioannidis P, Jacquin-Joly E, Jennings EC, Jones JW, Klasberg S, Lee SL, Lesný P, Lovegrove M, Martin S, Martynov AG, Mayer C, Montagné N, Moris VC, Munoz-Torres M, Murali SC, Muzny DM, Oppert B, Parisot N, Pauli T, Peters RS, Petersen M, Pick C, Persyn E, Podsiadlowski L, Poelchau MF, Provataris P, Qu J, Reijnders MJMF, von Reumont BM, Rosendale AJ, Simao FA, Skelly J, Sotiropoulos AG, Stahl AL, Sumitani M, Szuter EM, Tidswell O, Tsitlakidis E, Vedder L, Waterhouse RM, Werren JH, Wilbrandt J, Worley KC, Yamamoto DS, van de Zande L, Zdobnov EM, Ziesmann T, Gibbs RA, Richards S, Hatakeyama M, Misof B, Niehuis O. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. Genome Biol Evol 2021; 12:1099-1188. [PMID: 32442304 PMCID: PMC7455281 DOI: 10.1093/gbe/evaa106] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.
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Affiliation(s)
- Jan Philip Oeyen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Lead Contact
| | | | | | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | | | - Anja Buttstedt
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Germany
| | - Federica Calevro
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Elizabeth I Cash
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University.,Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Hubert Charles
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | | | - Andrew G Cridge
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Peter Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Daniel Dowling
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Elizabeth Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Biology, Georgia Southern University, Statesboro.,Department of Entomology, Purdue University, West Lafayette
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | | | - Ewald Große-Wilde
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague (CULS), Praha 6-Suchdol, Czech Republic
| | - Cameron Gudobba
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Bill S Hansson
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Frank Hauser
- Department of Biology, University of Copenhagen, Denmark
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Emmanuelle Jacquin-Joly
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Versailles, France
| | | | - Jeffery W Jones
- Department of Biological Sciences, Oakland University, Rochester
| | - Steffen Klasberg
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Peter Lesný
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | - Mackenzie Lovegrove
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Sebastian Martin
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | | | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Nicolas Montagné
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Victoria C Moris
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Monica Munoz-Torres
- Berkeley Bioinformatics Open-source Projects (BBOP), Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Shwetha Canchi Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, Kansas
| | - Nicolas Parisot
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Thomas Pauli
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Ralph S Peters
- Arthropoda Department, Center for Taxonomy and Evolutionary Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Emma Persyn
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Panagiotis Provataris
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Maarten J M F Reijnders
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Björn Marcus von Reumont
- Institute for Insect Biotechnology, University of Gießen, Germany.,Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | | | - Felipe A Simao
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - John Skelly
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | | | - Aaron L Stahl
- Department of Biological Sciences, University of Cincinnati.,Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida
| | - Megumi Sumitani
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Owashi, Tsukuba, Japan
| | - Elise M Szuter
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University
| | - Olivia Tidswell
- Biochemistry Department, University of Otago, Dunedin, New Zealand.,Zoology Department, University of Cambridge, United Kingdom
| | | | - Lucia Vedder
- Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Jeanne Wilbrandt
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Daisuke S Yamamoto
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Yakushiji, Shimotsuke, Japan
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Tanja Ziesmann
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Masatsugu Hatakeyama
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, NARO, Owashi, Tsukuba, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
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4
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Renoz F, Foray V, Ambroise J, Baa-Puyoulet P, Bearzatto B, Mendez GL, Grigorescu AS, Mahillon J, Mardulyn P, Gala JL, Calevro F, Hance T. At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica. Front Cell Infect Microbiol 2021; 11:660007. [PMID: 34268133 PMCID: PMC8275996 DOI: 10.3389/fcimb.2021.660007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/14/2021] [Indexed: 01/10/2023] Open
Abstract
Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and mobile elements, suggesting that these three pathogenic strains are in the early stages of the adaptation to their host. Compared to their intracellular mutualistic relatives, the three strains harbor a greater diversity of genes coding for virulence factors and metabolic pathways, suggesting that they are likely adapted to infect new hosts and are a potential source of metabolic innovation for insects. The presence in their genomes of secondary metabolism gene clusters associated with the production of antimicrobial compounds and phytotoxins supports the hypothesis that S. symbiotia symbionts evolved from plant-associated strains and that plants may serve as intermediate hosts. Mutualistic associations between insects and bacteria are the result of independent transitions to endosymbiosis initiated by the acquisition of environmental progenitors. In this context, the genomes of free-living S. symbiotica strains provide a rare opportunity to study the inventory of genes held by bacterial associates of insects that are at the gateway to a host-dependent lifestyle.
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Affiliation(s)
- François Renoz
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Vincent Foray
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
- Institut de Recherche sur la Biologie de l’insecte, UMR 7261, CNRS, Université de Tours, Tours, France
| | - Jérôme Ambroise
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | | | - Bertrand Bearzatto
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | - Gipsi Lima Mendez
- Louvain Institute of Biomolecular Science and Technology (LIBST), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Luc Gala
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2i, UMR203, F-69621, Villeurbanne, France
| | - Thierry Hance
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
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5
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Rispe C, Legeai F, Nabity PD, Fernández R, Arora AK, Baa-Puyoulet P, Banfill CR, Bao L, Barberà M, Bouallègue M, Bretaudeau A, Brisson JA, Calevro F, Capy P, Catrice O, Chertemps T, Couture C, Delière L, Douglas AE, Dufault-Thompson K, Escuer P, Feng H, Forneck A, Gabaldón T, Guigó R, Hilliou F, Hinojosa-Alvarez S, Hsiao YM, Hudaverdian S, Jacquin-Joly E, James EB, Johnston S, Joubard B, Le Goff G, Le Trionnaire G, Librado P, Liu S, Lombaert E, Lu HL, Maïbèche M, Makni M, Marcet-Houben M, Martínez-Torres D, Meslin C, Montagné N, Moran NA, Papura D, Parisot N, Rahbé Y, Lopes MR, Ripoll-Cladellas A, Robin S, Roques C, Roux P, Rozas J, Sánchez-Gracia A, Sánchez-Herrero JF, Santesmasses D, Scatoni I, Serre RF, Tang M, Tian W, Umina PA, van Munster M, Vincent-Monégat C, Wemmer J, Wilson ACC, Zhang Y, Zhao C, Zhao J, Zhao S, Zhou X, Delmotte F, Tagu D. Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. BMC Biol 2020; 18:123. [PMID: 32917281 PMCID: PMC7488435 DOI: 10.1186/s12915-020-00864-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
| | - Fabrice Legeai
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France.
| | - Paul D Nabity
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Rosa Fernández
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Present address: Institute of Evolutionary Biology (CSIC-UPF), Passeig marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Arinder K Arora
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Celeste R Banfill
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | | | - Miquel Barberà
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980, Paterna, València, Spain
| | - Maryem Bouallègue
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092, Tunis, Tunisia
| | - Anthony Bretaudeau
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | | | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Olivier Catrice
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Thomas Chertemps
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Carole Couture
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Laurent Delière
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Keith Dufault-Thompson
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Paula Escuer
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Honglin Feng
- Department of Biology, University of Miami, Coral Gables, USA.,Current affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, USA
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Frédérique Hilliou
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Silvia Hinojosa-Alvarez
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Yi-Min Hsiao
- Institute of Biotechnology and Department of Entomology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan.,Present affiliation: Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sylvie Hudaverdian
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | | | - Edward B James
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | | | - Gaëlle Le Goff
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Gaël Le Trionnaire
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | - Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Shanlin Liu
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, Guangdong Province, People's Republic of China.,BGI-Shenzhen, Shenzhen, 518083, Guangdong Province, People's Republic of China.,Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Eric Lombaert
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Hsiao-Ling Lu
- Department of Post-Modern Agriculture, MingDao University, Changhua, Taiwan
| | - Martine Maïbèche
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Mohamed Makni
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092, Tunis, Tunisia
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - David Martínez-Torres
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980, Paterna, València, Spain
| | - Camille Meslin
- INRAE, Institute of Ecology and Environmental Sciences, Versailles, France
| | - Nicolas Montagné
- Sorbonne Université, Institute of Ecology and Environmental Sciences, Paris, France
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Daciana Papura
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Yvan Rahbé
- Univ Lyon, INRAE, INSA-Lyon, CNRS, UCBL, UMR5240 MAP, F-69622, Villeurbanne, France
| | | | - Aida Ripoll-Cladellas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stéphanie Robin
- BIPAA IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | - Céline Roques
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326, Castanet-Tolosan Cedex, France
| | - Pascale Roux
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Jose F Sánchez-Herrero
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Rémy-Félix Serre
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326, Castanet-Tolosan Cedex, France
| | - Ming Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Wenhua Tian
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Paul A Umina
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Manuella van Munster
- BGPI, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Joshua Wemmer
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Alex C C Wilson
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Chaoyang Zhao
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Jing Zhao
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, Guangdong Province, People's Republic of China.,BGI-Shenzhen, Shenzhen, 518083, Guangdong Province, People's Republic of China
| | - Serena Zhao
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | | | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France.
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6
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Rispe C, Legeai F, Nabity PD, Fernández R, Arora AK, Baa-Puyoulet P, Banfill CR, Bao L, Barberà M, Bouallègue M, Bretaudeau A, Brisson JA, Calevro F, Capy P, Catrice O, Chertemps T, Couture C, Delière L, Douglas AE, Dufault-Thompson K, Escuer P, Feng H, Forneck A, Gabaldón T, Guigó R, Hilliou F, Hinojosa-Alvarez S, Hsiao YM, Hudaverdian S, Jacquin-Joly E, James EB, Johnston S, Joubard B, Le Goff G, Le Trionnaire G, Librado P, Liu S, Lombaert E, Lu HL, Maïbèche M, Makni M, Marcet-Houben M, Martínez-Torres D, Meslin C, Montagné N, Moran NA, Papura D, Parisot N, Rahbé Y, Lopes MR, Ripoll-Cladellas A, Robin S, Roques C, Roux P, Rozas J, Sánchez-Gracia A, Sánchez-Herrero JF, Santesmasses D, Scatoni I, Serre RF, Tang M, Tian W, Umina PA, van Munster M, Vincent-Monégat C, Wemmer J, Wilson ACC, Zhang Y, Zhao C, Zhao J, Zhao S, Zhou X, Delmotte F, Tagu D. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. BMC Biol 2020; 18:90. [PMID: 32698880 PMCID: PMC7376646 DOI: 10.1186/s12915-020-00820-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/22/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture. RESULTS Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world. CONCLUSIONS The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.
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Affiliation(s)
| | - Fabrice Legeai
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Paul D. Nabity
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Rosa Fernández
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
- Present address: Institute of Evolutionary Biology (CSIC-UPF), Passeig marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Arinder K. Arora
- Department of Entomology, Cornell University, Ithaca, NY 14853 USA
| | | | | | | | - Miquel Barberà
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València Spain
| | - Maryem Bouallègue
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092 Tunis, Tunisia
| | - Anthony Bretaudeau
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | | | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Olivier Catrice
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Thomas Chertemps
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Carole Couture
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Laurent Delière
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Angela E. Douglas
- Department of Entomology, Cornell University, Ithaca, NY 14853 USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Keith Dufault-Thompson
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI USA
| | - Paula Escuer
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Honglin Feng
- Department of Biology, University of Miami, Coral Gables, USA
- Current affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, USA
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Frédérique Hilliou
- Université Côte d’Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Silvia Hinojosa-Alvarez
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Yi-min Hsiao
- Institute of Biotechnology and Department of Entomology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Present affiliation: Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sylvie Hudaverdian
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | | | - Edward B. James
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843 USA
| | | | - Gaëlle Le Goff
- Université Côte d’Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Gaël Le Trionnaire
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Pablo Librado
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Shanlin Liu
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Eric Lombaert
- Université Côte d’Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Hsiao-ling Lu
- Department of Post-Modern Agriculture, MingDao University, Changhua, Taiwan
| | - Martine Maïbèche
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Mohamed Makni
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092 Tunis, Tunisia
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - David Martínez-Torres
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València Spain
| | - Camille Meslin
- INRAE, Institute of Ecology and Environmental Sciences, Versailles, France
| | - Nicolas Montagné
- Sorbonne Université, Institute of Ecology and Environmental Sciences, Paris, France
| | - Nancy A. Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Daciana Papura
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Yvan Rahbé
- Univ Lyon, INRAE, INSA-Lyon, CNRS, UCBL, UMR5240 MAP, F-69622 Villeurbanne, France
| | | | - Aida Ripoll-Cladellas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stéphanie Robin
- BIPAA IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Céline Roques
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Pascale Roux
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Jose F. Sánchez-Herrero
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | | | - Rémy-Félix Serre
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Ming Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Wenhua Tian
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Paul A. Umina
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Manuella van Munster
- BGPI, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Joshua Wemmer
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Alex C. C. Wilson
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI USA
| | - Chaoyang Zhao
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Jing Zhao
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
| | - Serena Zhao
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | | | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
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7
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Consuegra J, Grenier T, Baa-Puyoulet P, Rahioui I, Akherraz H, Gervais H, Parisot N, da Silva P, Charles H, Calevro F, Leulier F. Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth. PLoS Biol 2020; 18:e3000681. [PMID: 32196485 PMCID: PMC7112240 DOI: 10.1371/journal.pbio.3000681] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 04/01/2020] [Accepted: 03/04/2020] [Indexed: 01/14/2023] Open
Abstract
The interplay between nutrition and the microbial communities colonizing the gastrointestinal tract (i.e., gut microbiota) determines juvenile growth trajectory. Nutritional deficiencies trigger developmental delays, and an immature gut microbiota is a hallmark of pathologies related to childhood undernutrition. However, how host-associated bacteria modulate the impact of nutrition on juvenile growth remains elusive. Here, using gnotobiotic Drosophila melanogaster larvae independently associated with Acetobacter pomorumWJL (ApWJL) and Lactobacillus plantarumNC8 (LpNC8), 2 model Drosophila-associated bacteria, we performed a large-scale, systematic nutritional screen based on larval growth in 40 different and precisely controlled nutritional environments. We combined these results with genome-based metabolic network reconstruction to define the biosynthetic capacities of Drosophila germ-free (GF) larvae and its 2 bacterial partners. We first established that ApWJL and LpNC8 differentially fulfill the nutritional requirements of the ex-GF larvae and parsed such difference down to individual amino acids, vitamins, other micronutrients, and trace metals. We found that Drosophila-associated bacteria not only fortify the host’s diet with essential nutrients but, in specific instances, functionally compensate for host auxotrophies by either providing a metabolic intermediate or nutrient derivative to the host or by uptaking, concentrating, and delivering contaminant traces of micronutrients. Our systematic work reveals that beyond the molecular dialogue engaged between the host and its bacterial partners, Drosophila and its associated bacteria establish an integrated nutritional network relying on nutrient provision and utilization. A study of gnotobiotic fruit flies shows that the animal is involved in an integrated nutritional network with its facultative commensal bacteria, centered around the utilization and sharing of nutrients.
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Affiliation(s)
- Jessika Consuegra
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
| | - Théodore Grenier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
| | - Patrice Baa-Puyoulet
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - Isabelle Rahioui
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - Houssam Akherraz
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
| | - Hugo Gervais
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
| | - Nicolas Parisot
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - Pedro da Silva
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - Hubert Charles
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - Federica Calevro
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR0203, Villeurbanne, France
| | - François Leulier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
- * E-mail:
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8
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Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang CC, Chao H, Chen MJM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao YM, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol 2019. [PMID: 30935422 DOI: 10.1101/201731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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Affiliation(s)
- Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK.
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Deniz Erezyilmaz
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
- Present address: Department of Physiology, Anatomy and Genetics and Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, OX1 3SR, UK
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA, 02481, USA
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
- Present address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, SupAgro, University of Montpellier, Montpellier, France
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Robert M Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
- Present address: Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Present address: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present address: Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - Elizabeth J Duncan
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Barbara M I Vreede
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | | | - Chloé S Berger
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Chun-Che Chang
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mei-Ju M Chen
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Yen-Ta Chen
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Ariel D Chipman
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Andrew G Cridge
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Antonin J J Crumière
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Peter K Dearden
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: School of Life Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Neta Ginzburg
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter Heger
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Yi-Min Hsiao
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Tamsin E Jones
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Stefan Koelzer
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Megan Leask
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chien-Yueh Lee
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Mackenzie R Lovegrove
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Hsiao-Ling Lu
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yong Lu
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Patricia J Moore
- Department of Entomology, University of Georgia, 120 Cedar St., Athens, GA, 30602, USA
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Subba R Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter N Refki
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
- Present address: Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Rose Richter
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: Earthworks Institute, 185 Caroline Street, Rochester, NY, 14620, USA
| | - Rolando Rivera-Pomar
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Siegfried Roth
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Lena Sachs
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - M Emília Santos
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Essia Sghaier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jayendra N Shukla
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Present address: Department of Biotechnology, Central University of Rajasthan (CURAJ), NH-8, Bandarsindri, Ajmer, 305801, India
| | - Richard J Stancliffe
- Argelander-Institut für Astronomie, Universität Bonn, Auf dem Hügel 71, 53121, Bonn, Germany
- Present address: E. A. Milne Centre for Astrophysics, Department of Physics and Mathematics, University of Hull, Hull, HU6 7RX, UK
| | - Olivia Tidswell
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- Present address: Department of Zoology, University of Cambridge, Cambridge, CB2 3DT, UK
| | - Lucila Traverso
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Maurijn van der Zee
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Séverine Viala
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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9
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Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang CC, Chao H, Chen MJM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao YM, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol 2019; 20:64. [PMID: 30935422 PMCID: PMC6444547 DOI: 10.1186/s13059-019-1660-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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Affiliation(s)
- Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK.
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Deniz Erezyilmaz
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
- Present address: Department of Physiology, Anatomy and Genetics and Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, OX1 3SR, UK
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA, 02481, USA
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
- Present address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, SupAgro, University of Montpellier, Montpellier, France
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Robert M Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
- Present address: Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Present address: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present address: Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - Elizabeth J Duncan
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Barbara M I Vreede
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | | | - Chloé S Berger
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Chun-Che Chang
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mei-Ju M Chen
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Yen-Ta Chen
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Ariel D Chipman
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Andrew G Cridge
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Antonin J J Crumière
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Peter K Dearden
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: School of Life Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Neta Ginzburg
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter Heger
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Yi-Min Hsiao
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Tamsin E Jones
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Stefan Koelzer
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Megan Leask
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chien-Yueh Lee
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Mackenzie R Lovegrove
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Hsiao-Ling Lu
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yong Lu
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Patricia J Moore
- Department of Entomology, University of Georgia, 120 Cedar St., Athens, GA, 30602, USA
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Subba R Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter N Refki
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
- Present address: Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Rose Richter
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: Earthworks Institute, 185 Caroline Street, Rochester, NY, 14620, USA
| | - Rolando Rivera-Pomar
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Siegfried Roth
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Lena Sachs
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - M Emília Santos
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Essia Sghaier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jayendra N Shukla
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Present address: Department of Biotechnology, Central University of Rajasthan (CURAJ), NH-8, Bandarsindri, Ajmer, 305801, India
| | - Richard J Stancliffe
- Argelander-Institut für Astronomie, Universität Bonn, Auf dem Hügel 71, 53121, Bonn, Germany
- Present address: E. A. Milne Centre for Astrophysics, Department of Physics and Mathematics, University of Hull, Hull, HU6 7RX, UK
| | - Olivia Tidswell
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- Present address: Department of Zoology, University of Cambridge, Cambridge, CB2 3DT, UK
| | - Lucila Traverso
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Maurijn van der Zee
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Séverine Viala
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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10
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Colella S, Parisot N, Simonet P, Gaget K, Duport G, Baa-Puyoulet P, Rahbé Y, Charles H, Febvay G, Callaerts P, Calevro F. Bacteriocyte Reprogramming to Cope With Nutritional Stress in a Phloem Sap Feeding Hemipteran, the Pea Aphid Acyrthosiphon pisum. Front Physiol 2018; 9:1498. [PMID: 30410449 PMCID: PMC6209921 DOI: 10.3389/fphys.2018.01498] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/04/2018] [Indexed: 11/13/2022] Open
Abstract
Nutritional symbioses play a central role in the ability of insects to thrive on unbalanced diets and in ensuring their evolutionary success. A genomic model for nutritional symbiosis comprises the hemipteran Acyrthosiphon pisum, and the gamma-3-proteobacterium, Buchnera aphidicola, with genomes encoding highly integrated metabolic pathways. A. pisum feeds exclusively on plant phloem sap, a nutritionally unbalanced diet highly variable in composition, thus raising the question of how this symbiotic system responds to nutritional stress. We addressed this by combining transcriptomic, phenotypic and life history trait analyses to determine the organismal impact of deprivation of tyrosine and phenylalanine. These two aromatic amino acids are essential for aphid development, are synthesized in a metabolic pathway for which the aphid host and the endosymbiont are interdependent, and their concentration can be highly variable in plant phloem sap. We found that this nutritional challenge does not have major phenotypic effects on the pea aphid, except for a limited weight reduction and a 2-day delay in onset of nymph laying. Transcriptomic analyses through aphid development showed a prominent response in bacteriocytes (the core symbiotic tissue which houses the symbionts), but not in gut, thus highlighting the role of bacteriocytes as major modulators of this homeostasis. This response does not involve a direct regulation of tyrosine and phenylalanine biosynthetic pathway and transporter genes. Instead, we observed an extensive transcriptional reprogramming of the bacteriocyte with a rapid down-regulation of genes encoding sugar transporters and genes required for sugar metabolism. Consistently, we observed continued overexpression of the A. pisum homolog of RRAD, a small GTPase implicated in repressing aerobic glycolysis. In addition, we found increased transcription of genes involved in proliferation, cell size control and signaling. We experimentally confirmed the significance of these gene expression changes detecting an increase in bacteriocyte number and cell size in vivo under tyrosine and phenylalanine depletion. Our results support a central role of bacteriocytes in the aphid response to amino acid deprivation: their transcriptional and cellular responses fine-tune host physiology providing the host insect with an effective way to cope with the challenges posed by the variability in composition of phloem sap.
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Affiliation(s)
- Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Pierre Simonet
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Karen Gaget
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Gabrielle Duport
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | | | - Yvan Rahbé
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Patrick Callaerts
- Laboratory of Behavioral and Developmental Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
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11
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Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DRG, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson ACC, van Oosterhout C, Swarbreck D, Hogenhout SA. Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biol 2017; 18:63. [PMID: 28376841 PMCID: PMC5381131 DOI: 10.1186/s13059-017-1202-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 03/29/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Thomas C Mathers
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Yazhou Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | | | - Fabrice Legeai
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Sam T Mugford
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Patrice Baa-Puyoulet
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Anthony Bretaudeau
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | | | - Stefano Colella
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France.,Present Address: INRA, UMR1342 IRD-CIRAD-INRA-SupAgro-Université de Montpellier, Laboratoire des Symbioses Tropicales et Méditéranéennes, Campus International de Baillarguet, TA-A82/J, F-34398, Montpellier cedex 5, France
| | - Olivier Collin
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Derrien
- CNRS, UMR 6290, Institut de Génétique et Developpement de Rennes, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000, Rennes, France
| | - Honglin Feng
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Toni Gabaldón
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Anna Jordan
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Irene Julca
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Graeme J Kettles
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Rothamsted Research, Harpenden, Hertforshire, ALF5 2JQ, UK
| | - Krissana Kowitwanich
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: J. R. Simplot Company, Boise, ID, USA
| | - Dominique Lavenier
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Paolo Lenzi
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Alson H. Smith Jr. Agriculture and Extension Center, Virginia Tech, Winchester, 22602, VA, USA
| | - Sara Lopez-Gomollon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Present address: Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Damian Loska
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Daniel Mapleson
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Florian Maumus
- The International Aphid Genomics Consortium, Miami, USA.,Unité de Recherche Génomique-Info (URGI), INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Simon Moxon
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Daniel R G Price
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL 33146, USA.,Present address: Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Akiko Sugio
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Manuella van Munster
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Marilyne Uzest
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Darren Waite
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Georg Jander
- The International Aphid Genomics Consortium, Miami, USA.,Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Denis Tagu
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Alex C C Wilson
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Cock van Oosterhout
- The International Aphid Genomics Consortium, Miami, USA.,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Saskia A Hogenhout
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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12
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Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DRG, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson ACC, van Oosterhout C, Swarbreck D, Hogenhout SA. Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biol 2017; 18:27. [PMID: 28190401 PMCID: PMC5304397 DOI: 10.1186/s13059-016-1145-3] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/22/2016] [Indexed: 12/04/2022] Open
Abstract
Background The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. Results To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. Conclusions Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1145-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas C Mathers
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Yazhou Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | | | - Fabrice Legeai
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Sam T Mugford
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Patrice Baa-Puyoulet
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Anthony Bretaudeau
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | | | - Stefano Colella
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France.,Present Address: INRA, UMR1342 IRD-CIRAD-INRA-SupAgro-Université de Montpellier, Laboratoire des Symbioses Tropicales et Méditéranéennes, Campus International de Baillarguet, TA-A82/J, F-34398, Montpellier cedex 5, France
| | - Olivier Collin
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Derrien
- CNRS, UMR 6290, Institut de Génétique et Developpement de Rennes, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000, Rennes, France
| | - Honglin Feng
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Toni Gabaldón
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Anna Jordan
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Irene Julca
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Graeme J Kettles
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Rothamsted Research, Harpenden, Hertforshire, ALF5 2JQ, UK
| | - Krissana Kowitwanich
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: J. R. Simplot Company, Boise, ID, USA
| | - Dominique Lavenier
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Paolo Lenzi
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Alson H. Smith Jr. Agriculture and Extension Center, Virginia Tech, Winchester, 22602, VA, USA
| | - Sara Lopez-Gomollon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Present address: Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Damian Loska
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Daniel Mapleson
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Florian Maumus
- The International Aphid Genomics Consortium, Miami, USA.,Unité de Recherche Génomique-Info (URGI), INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Simon Moxon
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Daniel R G Price
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.,Present address: Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Akiko Sugio
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Manuella van Munster
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Marilyne Uzest
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Darren Waite
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Georg Jander
- The International Aphid Genomics Consortium, Miami, USA.,Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Denis Tagu
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Alex C C Wilson
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Cock van Oosterhout
- The International Aphid Genomics Consortium, Miami, USA.,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Saskia A Hogenhout
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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13
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Baa-Puyoulet P, Parisot N, Febvay G, Huerta-Cepas J, Vellozo AF, Gabaldón T, Calevro F, Charles H, Colella S. ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. Database (Oxford) 2016; 2016:baw081. [PMID: 27242037 PMCID: PMC5630938 DOI: 10.1093/database/baw081] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/25/2016] [Indexed: 01/25/2023]
Abstract
Arthropods interact with humans at different levels with highly beneficial roles (e.g. as pollinators), as well as with a negative impact for example as vectors of human or animal diseases, or as agricultural pests. Several arthropod genomes are available at present and many others will be sequenced in the near future in the context of the i5K initiative, offering opportunities for reconstructing, modelling and comparing their metabolic networks. In-depth analysis of these genomic data through metabolism reconstruction is expected to contribute to a better understanding of the biology of arthropods, thereby allowing the development of new strategies to control harmful species. In this context, we present here ArthropodaCyc, a dedicated BioCyc collection of databases using the Cyc annotation database system (CycADS), allowing researchers to perform reliable metabolism comparisons of fully sequenced arthropods genomes. Since the annotation quality is a key factor when performing such global genome comparisons, all proteins from the genomes included in the ArthropodaCyc database were re-annotated using several annotation tools and orthology information. All functional/domain annotation results and their sources were integrated in the databases for user access. Currently, ArthropodaCyc offers a centralized repository of metabolic pathways, protein sequence domains, Gene Ontology annotations as well as evolutionary information for 28 arthropod species. Such database collection allows metabolism analysis both with integrated tools and through extraction of data in formats suitable for systems biology studies. Database URL:http://arthropodacyc.cycadsys.org/
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Affiliation(s)
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Jaime Huerta-Cepas
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Augusto F Vellozo
- Univ Lyon, Univ Lyon1, CNRS, LBBE, UMR5558, F-69622, Villeurbanne, France
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
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14
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Rabatel A, Febvay G, Gaget K, Duport G, Baa-Puyoulet P, Sapountzis P, Bendridi N, Rey M, Rahbé Y, Charles H, Calevro F, Colella S. Tyrosine pathway regulation is host-mediated in the pea aphid symbiosis during late embryonic and early larval development. BMC Genomics 2013; 14:235. [PMID: 23575215 PMCID: PMC3660198 DOI: 10.1186/1471-2164-14-235] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 03/14/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Nutritional symbioses play a central role in insects' adaptation to specialized diets and in their evolutionary success. The obligatory symbiosis between the pea aphid, Acyrthosiphon pisum, and the bacterium, Buchnera aphidicola, is no exception as it enables this important agricultural pest insect to develop on a diet exclusively based on plant phloem sap. The symbiotic bacteria provide the host with essential amino acids lacking in its diet but necessary for the rapid embryonic growth seen in the parthenogenetic viviparous reproduction of aphids. The aphid furnishes, in exchange, non-essential amino acids and other important metabolites. Understanding the regulations acting on this integrated metabolic system during the development of this insect is essential in elucidating aphid biology. RESULTS We used a microarray-based approach to analyse gene expression in the late embryonic and the early larval stages of the pea aphid, characterizing, for the first time, the transcriptional profiles in these developmental phases. Our analyses allowed us to identify key genes in the phenylalanine, tyrosine and dopamine pathways and we identified ACYPI004243, one of the four genes encoding for the aspartate transaminase (E.C. 2.6.1.1), as specifically regulated during development. Indeed, the tyrosine biosynthetic pathway is crucial for the symbiotic metabolism as it is shared between the two partners, all the precursors being produced by B. aphidicola. Our microarray data are supported by HPLC amino acid analyses demonstrating an accumulation of tyrosine at the same developmental stages, with an up-regulation of the tyrosine biosynthetic genes. Tyrosine is also essential for the synthesis of cuticular proteins and it is an important precursor for cuticle maturation: together with the up-regulation of tyrosine biosynthesis, we observed an up-regulation of cuticular genes expression. We were also able to identify some amino acid transporter genes which are essential for the switch over to the late embryonic stages in pea aphid development. CONCLUSIONS Our data show that, in the development of A. pisum, a specific host gene set regulates the biosynthetic pathways of amino acids, demonstrating how the regulation of gene expression enables an insect to control the production of metabolites crucial for its own development and symbiotic metabolism.
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Affiliation(s)
- Andréane Rabatel
- Insa-Lyon, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
| | - Gérard Febvay
- Inra, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
| | - Karen Gaget
- Inra, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
| | - Gabrielle Duport
- Inra, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
| | - Patrice Baa-Puyoulet
- Inra, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
| | - Panagiotis Sapountzis
- Inra, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
| | - Nadia Bendridi
- Insa-Lyon, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
| | - Marjolaine Rey
- Inra, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
| | - Yvan Rahbé
- Inra, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
- Inria Rhône-Alpes, Bamboo, Monbonnot Saint-Martin, F-38330, France
| | - Hubert Charles
- Insa-Lyon, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
- Inria Rhône-Alpes, Bamboo, Monbonnot Saint-Martin, F-38330, France
| | - Federica Calevro
- Insa-Lyon, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
| | - Stefano Colella
- Inra, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, F-69621, France
- Université de Lyon, Lyon, F-69000, France
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15
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Vellozo AF, Véron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldón T, Sagot MF, Charles H, Colella S. CycADS: an annotation database system to ease the development and update of BioCyc databases. Database (Oxford) 2011; 2011:bar008. [PMID: 21474551 PMCID: PMC3072769 DOI: 10.1093/database/bar008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In recent years, genomes from an increasing number of organisms have been sequenced, but their annotation remains a time-consuming process. The BioCyc databases offer a framework for the integrated analysis of metabolic networks. The Pathway tool software suite allows the automated construction of a database starting from an annotated genome, but it requires prior integration of all annotations into a specific summary file or into a GenBank file. To allow the easy creation and update of a BioCyc database starting from the multiple genome annotation resources available over time, we have developed an ad hoc data management system that we called Cyc Annotation Database System (CycADS). CycADS is centred on a specific database model and on a set of Java programs to import, filter and export relevant information. Data from GenBank and other annotation sources (including for example: KAAS, PRIAM, Blast2GO and PhylomeDB) are collected into a database to be subsequently filtered and extracted to generate a complete annotation file. This file is then used to build an enriched BioCyc database using the PathoLogic program of Pathway Tools. The CycADS pipeline for annotation management was used to build the AcypiCyc database for the pea aphid (Acyrthosiphon pisum) whose genome was recently sequenced. The AcypiCyc database webpage includes also, for comparative analyses, two other metabolic reconstruction BioCyc databases generated using CycADS: TricaCyc for Tribolium castaneum and DromeCyc for Drosophila melanogaster. Linked to its flexible design, CycADS offers a powerful software tool for the generation and regular updating of enriched BioCyc databases. The CycADS system is particularly suited for metabolic gene annotation and network reconstruction in newly sequenced genomes. Because of the uniform annotation used for metabolic network reconstruction, CycADS is particularly useful for comparative analysis of the metabolism of different organisms. Database URL:http://www.cycadsys.org
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Affiliation(s)
- Augusto F Vellozo
- UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INRA, INSA-Lyon, Université de Lyon, 20 av. A. Einstein, F-69621 Villeurbanne, France.
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