A coffee berry borer (Hypothenemus hampei) genome assembly reveals a reduced chemosensory receptor gene repertoire and male-specific genome sequences

Abstract

Coffee berry borer—CBB (Hypothenemus hampei) is a globally important economic pest of coffee (Coffea spp.). Despite current insect control methods for managing CBB, development of future control strategies requires a better understanding of its biology and interaction with its host plant. Towards this objective, we performed de novo CBB genome and transcriptome sequencing, improved CBB genome assembly and predicted 18,765 protein-encoding genes. Using genome and transcriptome data, we annotated the genes associated with chemosensation and found a reduced gene repertoire composed by 67 odorant receptors (ORs), 62 gustatory receptors (GRs), 33 ionotropic receptors (IRs) and 29 odorant-binding proteins (OBPs). In silico transcript abundance analysis of these chemosensory genes revealed expression enrichment in CBB adults compared with larva. Detection of differentially expressed chemosensory genes between males and females is likely associated with differences in host-finding behavior between sexes. Additionally, we discovered male-specific genome content and identified candidate male-specific expressed genes on these scaffolds, suggesting that a Y-like chromosome may be involved in the CBB’s functional haplodiploid mechanism of sex determination.

Genome assembly of the southern pine beetle (Dendroctonus frontalisZimmerman) reveals the origins of gene content reduction inDendroctonus

“…We identified 39,588 transcripts from 13,354 putative gene loci in the SPB genome ( Table 1 ). A similar number of loci was identified in the recently improved assembly of D. ponderosae (Keeling et al 2022) and in the D. valens genome (14), whereas the genome of H. hampei and I. typographus contains a significantly higher number of genes (15–17). Among all mapped transcripts, 9,678 (72.5%) were functionally annotated with eggNOG-mapper v2 (46) (Table S6) .…”

“…This finding has been confirmed by the genome sequencing of the red turpentine beetle (RTB), D. valens (14). Intriguingly, two other sequenced bark beetle species, Ips typographus (European spruce bark beetle) (15), and Hypothenemus hampei (coffee berry borer) (16, 17) contained between19,000-23,000 genes. The more distantly related wood-boring species Anoplophora glabripennis (Asian Longhorned Beetle) and Agrilus planipennis (Emerald Ash Borer) shared a similarly high gene content (18).…”

Interacting pest control and pollination services in coffee systems

“…Perhaps because of fewer available fruits which combined with the aggregated nature of the broca beetle and the lack of predation from birds contributed to an increase in infestation. Second, broca use olfactory and visual cues to find hosts ( 49 ), perhaps at earlier stages of fruit development those fruits pollinated by bees with greater quality (size, color) might be more attractive to broca.…”