Published April 24, 2020 | Version v1
Dataset Open

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

Authors/Creators

  • 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

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.

Files

Orthogroups.txt

Files (500.4 MB)

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Additional details

Funding

UK Research and Innovation
Evolutionary genomics of host range expansion in aphid crop pests BB/R01227X/1