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.
Highlights
We have sequenced the genome of female coffee berry borers in an attempt to gain a better understanding of the basic biology of the insect
Two other Coleopteran genomes have been published to date: the red flour beetle, Tribolium castaneum[4] (Tenebrionidae), and the mountain pine beetle, Dendroctonus ponderosae[5], an insect in the same subfamily (Scolytinae) as the coffee berry borer
RepeatMasker analysis shows that only 2.7% of the assembled genome contains identifiable repeats and low complexity regions, which is very low for an arthropod genome, suggesting that repeated sequences may be underrepresented in the assembly
Summary
We have sequenced the genome of female coffee berry borers in an attempt to gain a better understanding of the basic biology of the insect. Two other Coleopteran genomes have been published to date: the red flour beetle, Tribolium castaneum[4] (Tenebrionidae), and the mountain pine beetle, Dendroctonus ponderosae[5], an insect in the same subfamily (Scolytinae) as the coffee berry borer. Analysis was focused on genes that could reveal important aspects of the insect’s biology, including some that might be useful in developing novel pest management strategies
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