Genome sequence of the banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and its symbionts
- 1. John Innes Centre
- 2. International Institute of Tropical Agriculture
Description
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>
Notes
Files
Orthogroups.txt
Files
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Additional details
Funding
- Evolutionary genomics of host range expansion in aphid crop pests BB/R01227X/1
- UK Research and Innovation