Comparative genomics reveal signatures of ecological specialization in the striped ambrosia beetle Trypodendron lineatum

Background Beetles (Coleoptera) exhibit remarkable dietary versatility, which may drive genomic innovations. Ambrosia beetles (Curculionidae: Scolytinae) have evolved specific feeding habits and intricate relationships with symbiotic fungi. The striped ambrosia beetle Trypodendron lineatum is a pest of conifers, relying on its obligate nutritional mutualist Phialophoropsis ferruginea for survival. The beetles cultivate the fungi inside their galleries in the tree’s xylem, with the fungi serving as their sole food source. We hypothesize that this lifestyle is associated with genomic signatures that may reflect important adaptations. Hence, we performed a comparative genomic analysis between T. lineatum and nine other beetle species, including related scolytine bark beetles, to uncover genomic signatures of this specialization, focusing on gene families involved in e.g. digestion, detoxification, and immunity. Results The small genome of T. lineatum (74.4–83.6 Mb) exhibits comparatively low levels of repetitive DNA (19.9%), including a reduced proportion of transposable elements, and unusually short introns. Annotation generated 14,830 high-quality gene predictions, most of which were supported by transcript evidence or functional domains. Comparative orthology analysis identified 13,896 orthogroups, with T. lineatum showing 78 species-specific orthogroups and a set of gene family changes which may reflect its ecological specializations. Thirty-three T. lineatum gene families showed significant size changes, including 16 expansions and 17 contractions. Notably, gene families associated with digestion, detoxification, and immunity were contracted. These included glycoside hydrolase 28, cytochrome P450, serpin, and trypsin families, suggesting reduced reliance on plant-based digestion and broad-spectrum immune defenses. In contrast, expansions in the THAP domain and CD80-like immunoglobulin domain families indicate selective retention and diversification of genes involved in genomic regulation and immune recognition. Conclusions Our results suggests that the genome of T. lineatum is streamlined, characterized by a low repeat content and compact gene architecture. The observed contractions in key gene families involved in plant digestion, detoxification, and immunity likely represent genomic signatures of its obligate mutualistic specialization and narrow ecological niche. Our findings provide the first insights into the genomic adaptations of fungus-farming ambrosia beetles, suggesting that co-evolved insect-microbe mutualisms may lead to reductions in a variety of insect gene families.