Insights from the Genome of the Major Coffee Insect Pest Worldwide: The Coffee Berry Borer

The Coffee Berry Borer (CBB, Hypothenemus hampei) brings major challenges for insect control due to its particular biology and genetics. Most of its life cycle occurs inside the coffee bean where an extreme inbreeding drives the mating behavior between the diploid females and their parahaploid male siblings. These CBB biological features make hard to implement effective control methods in field conditions. The availability of CBB whole genome assemblies open new opportunities to better understand the biology of the insect and its interaction with coffee plants. A hybrid de novo CBB genome assembly (~160 Mb) using FLX-454 and Illumina reads from both female and male individuals will be presented. Compared with our initial FLX-454-based assembly and other published CBB genome assembly, the new hybrid assembly has improved sequence contiguity. Transcriptomics data obtained from RNA-seq supported around 21,000 predicted genes in this assembly, which account for over 95% of genome completeness. We annotated different gene families of interest, including odorant receptors and odorant-binding proteins as well as G protein coupled receptors (GPCRs) as a prerequisite for exploring new methods of insect behavioral control or selection of safer insecticides. A reduction in genes related to olfactory functions was found comparable with other curculionid beetles. Genome sequence analyses revealed also a low content of repetitive DNA compared with other insect genomes. Only ~8% of the CBB genome consist of transposon elements and ~1% of tandem repeats. This low content of repetitive DNA sequences may represent an evolutionary adaptation to the extreme inbreeding in the CBB. Female and male-specific genome assemblies showed structural differences. This information along with the identification of several genes involved in sex determination mechanisms are essential to elucidate the sex-determination process in the insect.