Genome sequence of the banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and its symbionts

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> <./working_dir>