Improved genome assembly and annotation of the soybean aphid (Aphis glycines Matsumura)

Updated genome assembly and annotation of Aphis glycines biotype 4.

Overview of files included in this release:

Frozen release:

Updated A. glycines biotype 4 genome assembly: Aphis_glycines_4.v2.1.scaffolds.fa.gz 

BRAKER2 gene models for updated A. glycines biotype 4 genome assembly: Aphis_glycines_4.v2.1.scaffolds.fa.gff

BRAKER2 protein sequences: Aphis_glycines_4.v2.1.scaffolds.fa.gff.aa.fa

BRAKER2 nucleotide coding sequences:  Aphis_glycines_4.v2.1.scaffolds.fa.gff.CDS.fa

Unfiltered raw intermediate genome assemblies:

Canu assembly of biotype 4 PacBio data from Wenger et. al. (2017): canu.fa.gz

DBG2OLC hybrid assembly of selected biotype 4 MiSeq data and biotype 4 PacBio data from Wenger et. al. (2017): DBG2OLC.fa.gz

Merged Canu and DBG2OLC assembly created with quickmerge: quickmerge.fa.gz

Pilon polished (2 rounds) quickmerge assembly: quickmerge.pilon_r2.fa.gz

Mitochondrial and endosymbiont contigs extracted from the pilon polished quickmerge assembly: 

A. glycines biotype 4 mitochondrial genome: Aphis_glycines_4_Buchnera_v1.fa

A. glycines biotype 4 Buchnera aphidicola contigs: Aphis_glycines_4_Buchnera_v1.fa

A. glycines biotype 4 Wolbachia contigs: Aphis_glycines_4_Buchnera_v1.fa

Other files:

MUSCLE alignment of A. glycines v1, A. glycines biotype 4 v2.1 and Drosophila melanogaster R6.22 Osiris proteins in fasta format: D_mel_v1_v2_osiris.prots.muscle.fasta

FastTree Maximum Likelihood phylogeny based on the MUSCLE alignment of Osiris genes in newick format: D_mel_v1_v2_osiris.prots.muscle.FastTree.nwk