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

Zaide Montes-Ortiz; Daniel Powell; Heiko Vogel; Christer Löfstedt; Martin N Andersson

doi:10.1186/s12864-026-13049-3

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

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

Zaide Montes-Ortiz, Daniel Powell, Heiko Vogel, Christer Löfstedt and Martin N Andersson

BMC Genomics, Vol.27(1), pp.1-15

2026

DOI: https://doi.org/10.1186/s12864-026-13049-3

PMID: 42298395

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Abstract

Coleoptera

Curculionidae

Scolytinae

Symbiosis

genome annotation

gene family evolution

Immune gene contraction

detoxification

Background Beetles (Coleoptera) display exceptional dietary diversity and occupy a wide range of ecological niches, often involving close associations with plants and microbes. Ambrosia beetles (Curculionidae; Scolytinae and Platypodinae) exemplify ecological specialization by cultivating mutualistic fungi within galleries excavated in their host trees’ xylem, with the fungi serving as their main food source. The striped ambrosia beetle Trypodendron lineatum is a pest of conifers, relying on its nutritional mutualist Phialophoropsis ferruginea for survival. This fungiculture-based lifestyle provides a system for exploring how specialized mutualism is reflected at the genomic level. Hence, we performed a comparative genomics analysis between T. lineatum and nine other beetle species with different ecological specializations. We hypothesized that fungiculture is associated with specific genomic adaptations, including changes in gene family composition related to nutrition, 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. Annotation generated 14,830 high-quality gene predictions, most of which were supported by transcript evidence or functional domains. Comparative orthology analysis across ten beetle species identified 13,896 orthogroups, with T.lineatum having 78 species-specific orthogroups comprising 238 genes. Gene family evolution analyses revealed 33 families with significant size changes in T. lineatum, 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, which may reflect the fungus-based, rather than plant-based, diet of T. lineatum, and reduced reliance on broad-spectrum immune defenses. In contrast, expansions in the THAP and CD80-like immunoglobulin domain families indicate diversification of genes involved in genomic regulation and immune recognition. Conclusions Our results suggest that the genome of T. lineatum is characterized by low repeat content and compact gene architecture. The observed contractions in key gene families involved in plant digestion, detoxification, and immunity may 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 gene families.

Details

Title: Comparative genomics reveal signatures of ecological specialization in the striped ambrosia beetle Trypodendron lineatum
Authors: Zaide Montes-Ortiz (Corresponding Author) - Lund University
Daniel Powell - University of the Sunshine Coast
Heiko Vogel - Max Planck Institute for Chemical Ecology
Christer Löfstedt - Lund University
Martin N Andersson - Lund University
Publication details: BMC Genomics, Vol.27(1), pp.1-15
Publisher: BioMed Central Ltd.
Date published: 2026
DOI: 10.1186/s12864-026-13049-3
ISSN: 1471-2164
PMID: 42298395
Copyright note: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Data Availability: The datasets supporting the conclusions of this study are included in this article and its Additional files.
Grant note: The study was funded by the Swedish Research Council FORMAS (grant #2018–01444 to M.N.A), the Max Planck Society (to H.V.), and the Max Planck Center next Generation Insect Chemical Ecology (nGICE, to C.L. and M.N.A).
Organisation Unit: Centre for Bioinnovation
Language: English
Record Identifier: 991245799502621
Output Type: Journal article

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