title: Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei.
abstract: The coffee berry borer, Hypothenemus hampei, is the most economically important insect pest of coffee worldwide. We present an analysis of the draft genome of the coffee berry borer, the third genome for a Coleopteran species. The genome size is ca. 163 Mb with 19,222 predicted protein-coding genes. Analysis was focused on genes involved in primary digestion as well as gene families involved in detoxification of plant defense molecules and insecticides, such as carboxylesterases, cytochrome P450, gluthathione S-transferases, ATP-binding cassette transporters, and a gene that confers resistance to the insecticide dieldrin. A broad range of enzymes capable of degrading complex polysaccharides were identified. We also evaluated the pathogen defense system and found homologs to antimicrobial genes reported in the Drosophila genome. Ten cases of horizontal gene transfer were identified with evidence for expression, integration into the H. hampei genome, and phylogenetic evidence that the sequences are more closely related to bacterial rather than eukaryotic genes. The draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.
authors.affiliation: Sustainable Perennial Crops Laboratory, U. S. Department of Agriculture, Agricultural Research Service, Bldg. 001, Beltsville, Maryland 20705 USA.
authors.forename: Fernando E
authors.initials: FE
authors.lastname: Vega
authors.affiliation: NYU Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016 USA.
authors.forename: Stuart M
authors.initials: SM
authors.lastname: Brown
authors.affiliation: NYU Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016 USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Chen
authors.affiliation: NYU Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York 10016 USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Shen
authors.affiliation: Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal-Jeddah, Saudi Arabia.
authors.forename: Mridul B
authors.initials: MB
authors.lastname: Nair
authors.affiliation: Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA.
authors.forename: Javier A
authors.initials: JA
authors.lastname: Ceja-Navarro
authors.affiliation: Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA.
authors.forename: Eoin L
authors.initials: EL
authors.lastname: Brodie
authors.affiliation: El Colegio de la Frontera Sur (ECOSUR), Carretera Antiguo Aeropuerto Km. 2.5, Tapachula, 30700 Chiapas, México.
authors.forename: Francisco
authors.initials: F
authors.lastname: Infante
authors.affiliation: Crop Bioprotection Research Unit, U. S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, Illinois 61604 USA.
authors.forename: Patrick F
authors.initials: PF
authors.lastname: Dowd
authors.affiliation: Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal-Jeddah, Saudi Arabia.
authors.forename: Arnab
authors.initials: A
authors.lastname: Pain
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics / Q000378:metabolism; D000818:Animals; D002110:Caffeine / Q000493:pharmacokinetics; D043182:Carboxylesterase / Q000235:genetics / Q000378:metabolism; D040503:Coffea; D018556:Crops, Agricultural; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics / Q000378:metabolism; D004798:Enzymes / Q000235:genetics / Q000378:metabolism; D005260:Female; D022761:Gene Transfer, Horizontal; D049750:Genome, Insect; D008658:Inactivation, Metabolic; D019476:Insect Proteins / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family; D010802:Phylogeny; D022661:RNA, Untranslated; D048889:Weevils / Q000187:drug effects / Q000235:genetics* / Q000502:physiology
chemical_list: D018528:ATP-Binding Cassette Transporters; D004798:Enzymes; D019476:Insect Proteins; D022661:RNA, Untranslated; D002110:Caffeine; D003577:Cytochrome P-450 Enzyme System; D043182:Carboxylesterase