Pentalonia nigronervosa v1 frozen release Genome assembly: Pentalonia_nigronervosa.v1.scaffolds.fa.gz BRAKER2 gene models: Pentalonia_nigronervosa.v1.scaffolds.gff BRAKER2 protein sequences: Pentalonia_nigronervosa.v1.scaffolds.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Pentalonia_nigronervosa.v1.scaffolds.gff.aa.LTPG.fa BRAKER2 coding sequences: Pentalonia_nigronervosa.v1.scaffolds.gff.cds.fa InterProScan functional annotation: Pentalonia_nigronervosa.v1.scaffolds.gff.aa.LTPG.interproscan.tsv Pentalonia nigronervosa v1 mitochondrial genome: Pentalonia_nigronervosa.v1.mt_genome.fa Buchnera aphidicola (BPn) scaffolds: Buchnera_aphidicola_BPn.scaffolds.fa Wolbachia (WolPenNig) scaffolds: Wolbachia_WolPenNig.scaffolds.fa Myzus cerasi v1.2 frozen release Genome assembly: Myzus_cerasi.v1.2.scaffolds.fa BRAKER2 gene models: Myzus_cerasi.v1.2.scaffolds.gff BRAKER2 protein sequences: Myzus_cerasi.v1.2.scaffolds.gff.aa.fa BRAKER2 protein sequences (longest transcript per gene only): Myzus_cerasi.v1.2.scaffolds.gff.aa.LTPG.fa BRAKER2 coding sequences: Myzus_cerasi.v1.2.scaffolds.gff.cds.fa Aphid orthogroups and species tree 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: Orthogroups_for_concatenated_alignment.txt Species tree alignment: SpeciesTreeAlignment.fa Rooted species tree: SpeciesTree_rooted.nwk Bash script to run k-mer based assembly deduplication pipeline File: disco_filter_dups.v1.1.sh This script will parse a discovar de novo assembly and remove scaffolds likely to be haplotigs based on their k-mer content and a self alignment of the assembly (see manuscript for details). The input discovar assembly needs to have white space in scaffold IDs replaced with "_" before running. Illumina reads should be unzipped before running. Usage: sh disco_filter_dups.sh <./path_to_assembly> <./path_to_r1> <./path_to_r2> <homozyzgous_lower_cov> <homozyzgous_upper_cov> <nucmer_id_cutoff> <nucmer_cov_cutoff> <assembly_output_prefix> <threads> <./working_dir>

TCM is funded by a BBSRC Future Leader Fellowship (BB/R01227X/1). The described work was supported by a CEPAMs grant (17.03.2) to SH, a Bill and Melinda Gates Foundation grant (OPP1087428) awarded to LT, the BBSRC Institute Strategy Program (BB/P012574/1) award to the John Innes Centre, and the John Innes Foundation. This research was supported in part by the NBI Computing Infrastructure for Science Group, which provides technical support and maintenance to the John Innes Centre's high-performance computing cluster and storage systems.