Additional file 1 of Comparative genomics reveal signatures of ecological specialization in the striped ambrosia beetle Trypodendron lineatum

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Additional file 1: Supplementary Table 1. Summary of beetle species included in comparative genomics and orthology analyses. For each species, taxonomic family, GenBank accession number, protein sequence source, and inclusion status in ortholog analysis are indicated. Annotated proteins were downloaded in April 2025. Supplementary Table S2. Genome assembly statistics, including contig number, total assembly length, contig length metrics (N50, N90), and number of contigs greater than specific length thresholds for each beetle species used in the study. Supplementary Table S3. Cumulative distribution of Annotation Edit Distance (AED) scores across iterative MAKER rounds for Trypodendron lineatum. Supplementary Table S4. BUSCO assessment of genome annotation completeness for Trypodendron lineatum and eight additional Coleoptera species using the insecta_odb10 dataset. Supplementary Table S5. Functional annotation of Trypodendron lineatum gene models using InterProScan. Supplementary Table S6. Functional annotation of Trypodendron lineatum gene models using EggNOGmapper. Supplementary Table S7. Best BLASTp hit in the T. lineatum MAKER proteome for each of the 140 chemoreceptor sequences from Biswas et al. 2024 (pseudogenes excluded). Supplementary Table S8. Statistics summarizing the ortholog group analysis. Supplementary Table S9. Comparison of assigned versus unassigned Trypodendron lineatum proteins by OrthoFinder, in terms of length, functional annotation coverage, and transposable element overlap. Supplementary Table S10. Summary of orthogroup assignment statistics for Trypodendron lineatum and related beetle species. Supplemenatry Table S11. Complete Gene Ontology (GO) enrichment results for the 228 Trypodendron lineatum-specific genes (73 orthogroups) across the three GO ontologies: Biological Process (BP), Molecular Function (MF), and Cellular Component (CC). Supplementary Table S12. Significantly enriched GO terms (weight01 p < 0.05) for the 228 Trypodendron lineatum-specific genes, tested with topGO using the weight01 algorithm and Fisher's exact test. BP = Biological Process, MF = Molecular Function, CC = Cellular Component. FDR_BH = Benjamini–Hochberg-adjusted p-value. Supplementary Table S13. Significantly enriched Pfam protein domains in Trypodendron lineatum-specific gene families (FDR < 0.05; Fisher's exact test, one-sided, with Benjamini–Hochberg correction). Supplementary Table S14. Results of gene family expansion and contraction analysis in Trypodendron lineatum and nine additional species using CAFE. Supplementary Table S15. Functional annotation of orthogroups associated with expanded and contracted gene families in Trypodendron lineatum.

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