Additional File 1 of Brown Marmorated Stink Bug, Halyomorpha Halys (stål), Genome: Putative Underpinnings of Polyphagy, Insecticide Resistance Potential and Biology of a Top Worldwide Pest

Additional file 1: Main Supplementary Information text file, including Tables S1-S17 and Figures S1-S18. Table S1. Sequencing, assembly, annotation statistics and accession numbers. Table S2. OrthoDB v10 comparison of five species for ortholog presence and copy-number in Hemiptera-level orthogroups. Table S3. Scaffolds present in the H. halys assembly (accession GCA_000696795.1) that may originate from contaminant sources. Table S4. Counts of repetitive DNA elements encountered in the H. halys genome assembly. Table S5. H. halys predicted protein products associated with the RNAi pathway. Table S6. Positional information for the annotated homeobox genes. Table S7. Nuclear receptors of H. halys. Table S8. Listing of candidate Y-linked genes. Table S9. Number of genes identified as putative cuticle proteins per family in the genome of H. halys. Table S10. Number of genes identified as putative cuticle proteins per species in the genomes of several insect orders. Table S11. Clusters of genes coding for cuticle proteins in the genome of H. halys. Table S12. Odorant-binding protein genes and pseudogenes (Ψ) annotated in the genome of H. halys. Table S13. Primer sequences used to validate the HhalOBP gene annotations. Table S14. Correspondences between H. halys predicted protein identifiers and cathepsin labels. Table S15. A total of 64 salivary effector proteins were identified in the H. halys genome. Table S16. A select subset of 15 H. halys salivary effector proteins having variable expression levels between nymphal and adult stages (up- or down-regulation). Table S17. Gene expression data for H. halys glutathione S-transferase genes. Figure S1. Phylogenetic organization of the Hemiptera. Figure S2. Ortholog distributions among hemipterans. Figure S3. Genome assembly quality control. Figure S4. Hox and Iro-C cluster gene loci. Figure S5. Halyomorpha mannosidase expansion. Figure S6. Maximum likelihood phylogenetic tree of selected mannosidase proteins from three bacterial outgroups and three hemipteran species. Figure S7. Phylogenetic tree of the OR family. Figure S8. Phylogenetic tree of the GR family. Figure S9. Phylogenetic tree of the IR family. Figure S10. Heteropteran global opsin gene tree. Figure S11. Array of β-esterase genes. Figure S12. Distribution of transcription factor families across insect genomes. Figure S13. Nanos amino acid sequence alignments from different species. Figure S14. Location of pair-rule gene orthologs in the H. halys genome. Figure S15. H. halys odd-family genes. Figure S16. Alignment of Wnt family domain proteins. Figure S17. Engrailed and Invected are shared among diverse insects. Figure S18. Phylogenetic analysis of hemipteran genes named “NR2E1” reveals that they are orthologous to NR2E6.