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. The draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface

“…While the A. glabripennis genome (female 981.42 ± 3.52 Mb, male 970.64 ± 3.69 Mb) is much larger than the four existing published beetle genomes (ranging from 163–208 Mb) [13–16], it is average-sized for the order Coleoptera (mean = 974 Mb) [17]. As in other draft genome assemblies, repetitive heterochromatin sequences could not be assembled, accounting for the differences between assembled sequence and genome sizes.…”

Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)

“…Draft genomes for both a male and female MPB are available, but the sequences are distributed across 8,188 and 6,520 scaffolds, respectively (Keeling et al, 2013), and only a few gene families have been annotated (Fraser, Bonnett, Keeling, & Huber, 2017). Research into MPB gene function is aided by comparisons with resources for related species (McKenna et al, 2016;Richards et al, 2008;Vega et al, 2015), and the MPB genome has considerable synteny with that of the red flour beetle (Tribolium castaneum Herbst) (Keeling et al, 2013). Synteny has been historically defined as any two genes located on a single chromosome, but has now shifted to mean orthologous genes located in the genomes of separate species and sharing common descent (Passarge, Horsthemke, & Farber, 1999).…”

A massive incorporation of microbial genes into the genome ofTetranychus urticae, a polyphagous arthropod herbivore

“…Animal biology is thought to preclude HGT owing to such major barriers as a separated germ cell line and nucleus. Although HGT detection can be confounded by assembly and annotation artefacts (Koutsovoulos et al, 2016;Ku & Martin, 2016), more and more sequenced animal genomes are showing clear signs of HGT (Andersson, 2005;Dunning Hotopp, 2011;Crisp et al, 2015;Vega et al, 2015;Benoit et al, 2016;McKenna et al, 2016). Recent analyses of genomes of species within the Hexapoda lineage uncovered a great number of HGTs from various microbial sources (Table 2), including bacterial endosymbionts (Dunning Hotopp et al, 2007;Nikoh et al, 2008; Aikawa et al, 2009;Doudoumis et al, 2012; genome screens that detect Wolbachia-specific HGT are not included in Table 2).…”