W186
The Genome of the Coffee Berry Borer, Hypothenemus hampei, the Major Insect Pest of Coffee Worldwide

Date: Sunday, January 12, 2014
Time: 4:20 PM
Room: Pacific Salon 4-5 (2nd Floor)
Pablo Benavides , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchiná, Colombia
Lucio Navarro , Purdue University, West Lafayette, IN
Flor Acevedo , Pennsylvania State University, State College, PA
Ricardo Acuña , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchiná, Colombia
David O'Brochta , University of Maryland, Rockville, MD
Stuart Jeffrey , Purdue University, West Lafayette, IN
Jonathan Nuñez , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchiná, Colombia
Erick Hernandez , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchiná, Colombia
William Giraldo , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchiná, Colombia
Marco A. Cristancho , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchiná, Colombia
Marcela Yepes , Cornell University, Geneva, NY
Herb Aldwinckle , Cornell University, Geneva, NY
Alvaro Gaitan , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchiná, Colombia
Coffee supports the livelihood of millions of families in producing countries, and enriches the life of millions of coffee consumers worldwide.  However, the most globally devastating insect pest of coffee: Hypothenemus hampei, the Coffee Berry Borer (CBB), threatens the sustainability of the coffee industry in the context of climate change, as increasing temperatures favor higher reproduction rates increasing rapidly insect populations.  CBB infests the coffee beans, and the damage caused by the insect during feeding makes the beans unmarketable impacting directly production and coffee quality.  Control measures are hard to implement since the insect spends most of its life cycle inside the coffee berry, and insecticide resistance has been reported.  Efforts to control this pest are underway at CENICAFE, the research branch of the Colombian National Coffee Growers Federation.  We have sequenced the genome and transcriptome of H. hampei using next generation sequencing platforms (454 Roche and Illumina) to develop innovative control strategies that help reduce the impact of climate over CBB population dynamics, while gaining an in depth understanding of the biological basis for this insect’s unique life history and habits, to use this knowledge to devise new strategies to control or eradicate this pest.  In collaboration with Purdue University, the genome of CBB was assembled using more than 6 million FLX-454 reads obtained from both CBB males and females. The assembly was built with Newbler including single reads from WGS libraries (9.2X average coverage), and pair-end reads of long insert libraries (8Kb and 20Kb).  The H. hampei genome assembly is 194 Mb, composed of 45,995 contigs (N50: 6.1Kb, ~165.6Mb total) and 9,932 scaffolds (N50: 437.7Kb). Although gene annotation is still in progress, initial analysis predicts ~20,500 genes, a similar number (~20,600) was obtained from whole transcriptome assembly (using RNA-seq), physical mapping using a CBB BAC library is on going. The identification of ubiquitous ultra-conserved and single-copy core genes was conducted, estimating a genome completeness of 95%.  Genes involved in CBB metabolism are related to enzyme families involved with arabinoxylans and other metabolism polysaccharides, which possibly had the same evolutive dynamic as mannanases, an enzyme recently described in CBB as a key compound in the quick worldwide dispersal and strong specialization of CBB over Coffea berries.  Putting together the biology of CBB, its genetics and the fact that the insect does outcross under field conditions, we are exploring control strategies to introduce deleterious genes in established CBB populations, as an autocidal genetic control strategy. Functional genomic strategies to characterize gene candidates have been developed in collaboration with University of Maryland.  We have demonstrated that the transposons Minos and piggyBacare effective transgene vectors in this species. We successfully obtained CBB transgenic individuals using transposon-based germ-line transformation to advance functional genomics studies for candidate CBB control genes.

**Research Co-sponsored by the Colombian National Coffee Growers Federation and the Colombian Ministry of Agriculture.