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

Updated genome assembly and annotation of <em>Aphis glycines</em> biotype 4. <strong>Overview of files included in this release:</strong> <strong>Frozen release:</strong> Updated <em>A. glycines </em>biotype 4 genome assembly: Aphis_glycines_4.v2.1.scaffolds.fa.gz BRAKER2 gene models for updated <em>A. glycines </em>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 <strong>Unfiltered raw intermediate genome assemblies:</strong> 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 <strong>Mitochondrial and endosymbiont contigs extracted from the pilon polished quickmerge assembly: </strong> <em>A. glycines </em>biotype 4 mitochondrial genome: Aphis_glycines_4_Buchnera_v1.fa <em>A. glycines </em>biotype 4 <em>Buchnera aphidicola</em> contigs: Aphis_glycines_4_Buchnera_v1.fa <em>A. glycines </em>biotype 4 <em>Wolbachia</em> contigs: Aphis_glycines_4_Buchnera_v1.fa <strong>Other files:</strong> MUSCLE alignment of <em>A. glycines </em>v1, <em>A. glycines </em>biotype 4 v2.1 and <em>Drosophila melanogaster</em> 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