Supplementary data for: Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

<strong><em>Myzus persicae </em>clone O v2 frozen release</strong> 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 <em>De novo </em>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 <em>M. persicae de novo</em> repeat library: Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff.out RepeatMasker transposable element annotation using the <em>M. persicae</em> <em>de novo r</em>epeat library (gff format): Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff <strong><em>Acyrthosiphon pisum</em> clone JIC1 v1 frozen release</strong> 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 <em>De novo </em>repeat library (ReapeatModeler merged with repbase insecta): Acyrthosiphon_pisum_JIC1_repeat_lib.repeatmodeler_merged_repbase_insecta.fa RepeatMasker transposable element annotation using the <em>A. pisum</em> <em>de novo</em> repeat library: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.out RepeatMasker transposable element annotation using the <em>A. pisum de novo</em> repeat library (gff format): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff <strong><em>Rhodnius prolixus</em> DNA zoo chromosome-scale genome assembly annotation</strong> <em>R. prolixus </em>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 <strong><em>Triatoma rubrofasciata</em> chromosome-scale genome assembly annotation</strong> <em>T. rubrofasciata </em>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 <strong>Hemiptera orthogroups and species tree</strong> 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