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Title: Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei

Author
item Vega, Fernando
item BROWN, STUART - New York University School Of Medicine
item CHEN, HAO - New York University School Of Medicine
item SHEN, ERIC - New York University School Of Medicine
item NAIR, MRIDUL - King Abdullah University Of Science And Technology
item CEJA-NAVARRO, JAVIER - Department Of Energy
item BRODIE, EOIN - Department Of Energy
item INFANTE, FRANCISCO - Ecosur
item Dowd, Patrick
item PAIN, ARNAB - King Abdullah University Of Science And Technology

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/29/2015
Publication Date: 7/31/2015
Citation: Vega, F.E., Brown, S.M., Chen, H., Shen, E., Nair, M.B., Ceja-Navarro, J.A., Brodie, E.L., Infante, F., Dowd, P.F., Pain, A. 2015. Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei. Scientific Reports. 5:12525.

Interpretive Summary: The coffee berry borer, Hypothenemus hampei, is the most devastating pest of coffee throughout the world and causes millions of dollars in losses each year. Increased knowledge on the basic biology of the coffee berry borer can result in new insights on how to control this insect, thereby reducing losses and increasing yields. In this paper we report on the genome of the coffee berry borer and on specific genes involving plant digestion as well as detoxification of plant chemicals and insecticides. In addition, we present evidence for movement of bacterial genes to the coffee berry borer (horizontal gene transfer). Our findings have important implications for understanding the basic biology of this major pest and provides novel avenues for its control. This information will be of use to coffee scientists, entomologists, microbiologists, and the coffee industry.

Technical Abstract: The coffee berry borer, Hypothenemus hampei, is the most economically important insect pest of coffee worldwide, causing millions of dollars in yearly losses to coffee growers. We present the third genomic analysis for a Coleopteran species, a draft genome of female coffee berry borers. The genome size was ca. 163 Mb with 19,222 predicted genes. Analysis was focused on genes involved in primary digestion as well as the detoxification of plant allelochemicals including caffeine. Gene families involved in detoxification of plant defense molecules and insecticides, such as the carboxyl/cholinesterase gene family (CCE), the cytochromes p450 gene family (CYPs), the gluthathione S-transferases gene family (GSTs), the ATP-binding cassette transporter gene superfamily (ABC), and a gene (Rdl) that confers resistance to the insecticide dieldrin were examined in detail. We also evaluated the pathogen defense system and found homologs to antimicrobial genes reported in the Drosophila genome and detected antimicrobial peptide paralogous expansion. 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 strategies for control of this pest.