Myzus persicae clone O v2 frozen release Genome assembly: Myzus_persicae_O_v2.0.scaffolds.fa.gz BRAKER2 gene models: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3 List of gene models containing internal stop codons (removed from the protein and cds fasta files): Myzus_persicae_O_v2.0.scaffolds.braker2.bad_genes.lst BRAKER2 protein sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.LTPG.fa BRAKER2 coding sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.fa BRAKER2 coding sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.LTPG.fa De novo repeat library (ReapeatModeler merged with repbase insecta): Myzus_persicae_O_v2.0_repeat_lib.repeatmodeler_merged_repbase_insecta.fa RepeatMasker transposable element annotation using the M. persicae de novo repeat library: Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff.out RepeatMasker transposable element annotation using the M. persicae de novo repeat library (gff format): Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff Acyrthosiphon pisum clone JIC1 v1 frozen release Genome assembly: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.fa.gz BRAKER2 gene models: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff List of gene models containing internal stop codons (removed from the protein and cds fasta files): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.bad_genes.lst BRAKER2 protein sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.LTPG.fa BRAKER2 coding sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.fa BRAKER2 coding sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.LTPG.fa De novo repeat library (ReapeatModeler merged with repbase insecta): Acyrthosiphon_pisum_JIC1_repeat_lib.repeatmodeler_merged_repbase_insecta.fa RepeatMasker transposable element annotation using the A. pisum de novo repeat library: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.out RepeatMasker transposable element annotation using the A. pisum de novo repeat library (gff format): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff Rhodnius prolixus DNA zoo chromosome-scale genome assembly annotation R. prolixus chromosome-scale genome assembly was obtained here: https://www.dnazoo.org/assemblies/Rhodnius_prolixus. Genome assembly: Rhodnius_prolixus-3.0.3_HiC.fasta BRAKER2 gene models: Rhodnius_prolixus-3.0.3_HiC.braker2.gff BRAKER2 protein sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.LTPG.fa BRAKER2 coding sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.cds.fa Triatoma rubrofasciata chromosome-scale genome assembly annotation T. rubrofasciata chromosome-scale genome assembly was obtained here: http://dx.doi.org/10.5524/100614 Genome assembly: zhuichun_assembly.fasta BRAKER2 gene models: zhuichun_assembly.braker2.gff BRAKER2 protein sequences: zhuichun_assembly.braker2.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): zhuichun_assembly.braker2.gff.aa.LTPG.fa BRAKER2 coding sequences: zhuichun_assembly.braker2.gff.cds.fa Hemiptera orthogroups and species tree OrthoFinder was used to cluster proteomes of 14 Hemiptera into orthogroups for phylogenomic analysis. All proteomes were reduced to the longest transcript per gene. See here for full details: Species included, taxon IDs and data source: Mcer = Myzus cerasi v1.1 (https://bipaa.genouest.org/sp/myzus_cerasi/) MperO = Myzus persicae clone O v2 (This study) Dnox = Diuraphis noxia Thorpe et. al. gene predictions (https://bipaa.genouest.org/sp/diuraphis_noxia/) Apis = Acyrthosiphon pisum JIC1 v1 (This study) Pnig = Pentalonia nigronervosa (This study) Rmai = Rhopalosiphum maidis v0.1 (http://gigadb.org/dataset/100572) Rpad = Rhopalosiphum padi v1.0 (https://bipaa.genouest.org/sp/rhopalosiphum_padi/) Agly = Aphis glycines biotype 4 v2.1 (https://zenodo.org/record/3453468#.XnpL5JOgLRY) BtabMEAM1 = Bemissia tabacci MEAM1 v1.2 (http://www.whiteflygenomics.org/cgi-bin/bta/index.cgi) Trub = Triatoma rubrofasciata (This study) Rpro = Rhodnius prolixus (This study) Ofas = Oncopeltus fasciatus OGS v1.0 (https://i5k.nal.usda.gov/Oncopeltus_fasciatus) Sfuc = Sogatella furcifera v1 (http://dx.doi.org/10.5524/100255) Nlug = Nilaparvata lugens (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0521-0#Sec42) Files: Proteomes included in the analysis: proteomes.tar.gz Orthogroups: Orthogroups.txt Gene counts per orthogroup, per species: Orthogroups.GeneCount.csv Single copy conserved orthogroups used for species tree: SingleCopyOrthogroups.txt Species tree alignment: SpeciesTreeAlignment.fa r8s configuration file (includes time calibrations and OrthoFinder ML species tree with branch lengths): species_tree_rooted.r8s.nex r8s time calibrated species tree: r8s_tree.nwk

This work was funded by a BBSRC Future Leader Fellowship (BB/R01227X/1) awarded to TCM, the BBSRC Industrial Partnership Award (IPA) with Syngenta Ltd (BB/L002108/1 and BB/R009481/1) awarded to SAH, DS and CvO and BBSRC PhD fellowship of RW. Additional support was received from the BBSRC Institute Strategy Programme (BB/P012574/1) and the John Innes Foundation.