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. We find the draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.
- Authors:
-
- U.S. Department of Agriculture, Beltsville, MD (United States). Sustainable Perennial Crops Laboratory
- New York Univ. School of Medicine, New York, NY (United States)
- King Abdullah University of Science and Technology, Thuwal-Jeddah (Saudi Arabia)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Colegio de la Frontera Sur (ECOSUR), Tapachula, Chiapas (Mexico)
- U.S. Department of Agriculture, Peoria, IL (United States). Agricultural Research Service, National Center for Agricultural Utilization Research
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1256057
- Grant/Contract Number:
- AC02-05CH11231; AC02-05CH1121231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 5; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Vega, Fernando E., Brown, Stuart M., Chen, Hao, Shen, Eric, Nair, Mridul B., Ceja-Navarro, Javier A., Brodie, Eoin L., Infante, Francisco, Dowd, Patrick F., and Pain, Arnab. Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei. United States: N. p., 2015.
Web. doi:10.1038/srep12525.
Vega, Fernando E., Brown, Stuart M., Chen, Hao, Shen, Eric, Nair, Mridul B., Ceja-Navarro, Javier A., Brodie, Eoin L., Infante, Francisco, Dowd, Patrick F., & Pain, Arnab. Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei. United States. https://doi.org/10.1038/srep12525
Vega, Fernando E., Brown, Stuart M., Chen, Hao, Shen, Eric, Nair, Mridul B., Ceja-Navarro, Javier A., Brodie, Eoin L., Infante, Francisco, Dowd, Patrick F., and Pain, Arnab. Fri .
"Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei". United States. https://doi.org/10.1038/srep12525. https://www.osti.gov/servlets/purl/1256057.
@article{osti_1256057,
title = {Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei},
author = {Vega, Fernando E. and Brown, Stuart M. and Chen, Hao and Shen, Eric and Nair, Mridul B. and Ceja-Navarro, Javier A. and Brodie, Eoin L. and Infante, Francisco and Dowd, Patrick F. and Pain, Arnab},
abstractNote = {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. We find the draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.},
doi = {10.1038/srep12525},
journal = {Scientific Reports},
number = ,
volume = 5,
place = {United States},
year = {Fri Jul 31 00:00:00 EDT 2015},
month = {Fri Jul 31 00:00:00 EDT 2015}
}
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journal, January 2012
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Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
journal, January 2008
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Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest
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- Genome Biology, Vol. 14, Issue 3
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
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A Cytochrome P450 Conserved in Insects Is Involved in Cuticle Formation
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- Sztal, Tamar; Chung, Henry; Berger, Silke
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The coffee berry borer: the centenary of a biological invasion in Brazil
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- Brazilian Journal of Biology, Vol. 74, Issue 3 suppl 1
Increasing Coffee Berry Borer (Coleoptera: Curculionidae: Scolytinae) Female Density in Artificial Diet Decreases Fecundity
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