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

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