Repeat-Rich Architecture and Gene Duplication Characterize the Expanded Genome of the Chestnut Gall Wasp

Dryocosmus kuriphilus, the chestnut gall wasp, is a globally invasive pest that reproduces by thelytokous parthenogenesis. Despite the absence of conventional sexual recombination, the species has spread widely and persists under diverse environmental conditions, but the genomic features associated with this capacity remain poorly understood. Here, a chromosome-level assembly of D. kuriphilus was compared with seven representative insect genomes, with emphasis on repetitive sequences, orthogroups, and gene-duplication patterns. The 2.28-Gb D. kuriphilus genome contained 79.7% repetitive sequences, including 62.3% transposable elements (TEs), most of which occurred in intergenic regions. OrthoFinder assigned 13,271 D. kuriphilus genes to multi-copy orthogroups, representing 61.5% of the protein-coding gene set. Independent MCScanX analysis classified genes into mutually exclusive dispersed, proximal, tandem, and segmental duplication modes, with segmental and dispersed representing the two largest duplicated-gene classes. D. kuriphilus contained substantially more segmental duplicates than the other species examined. Synonymous-substitution distributions revealed low- and high-Ks components representing different levels of synonymous divergence among duplicated genes, and genes in these components showed distinct functional profiles. Numerous local duplications were found near TEs and included genes involved in host recognition, nutrient utilisation, xenobiotic metabolism, and energy production. Compared with the closely related gall wasp Belonocnema kinseyi, D. kuriphilus has a broader reported distribution and host range and contains higher copy numbers in several gene families associated with chemosensation, detoxification, metabolism, and stress responses. Together, these findings show that the expanded D. kuriphilus genome is characterized by extensive repeat accumulation and increased gene copy number, whereas duplication at multiple scales increased and reshaped the functional gene repertoire. These genomic features identify candidate mechanisms that may contribute to genomic and ecological plasticity, although their adaptive significance requires expression, evolutionary, and functional validation.