The chromosome level genome of the Blueberry Stem Gall Wasp, Hemadas nubilipennis (Hymenoptera: Ormyridae) on lowbush blueberry (Vaccinium angustifolium) reveals repeat-driven expansion

Abstract

Gall-inducing insects are important models for studying plant-feeding lifestyle evolution, but genomic resources remain scarce. We present the first chromosome-level genome for the blueberry stem gall wasp (Hemadas nubilipennis), a native North American species now reaching outbreak densities on cultivated highbush blueberries. The 1.08 Gb genome (N50=218 Mb) is the second largest in Chalcidoidea, with size variation driven by transposable element proliferation (R²=0.96). Gene-body methylation is conserved and correlates with gene density. Mitochondrial COI sequences reveal 4.3–5.4% divergence among geographically separated populations, suggesting a cryptic species complex. We also assemble a near-complete Wolbachia genome (Supergroup A) encoding parthenogenesis-linked effectors. These resources establish foundations for population genomics, taxonomic revision, and applied management, while providing insights into genome architecture, epigenetics, and symbiont interactions, offering essential tools for distinguishing cryptic species and understanding this emergent pest’s biology.