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

<p>Updated genome assembly and annotation of <em>Aphis&nbsp;glycines</em> biotype 4.</p> <p><strong>Overview of files included in this release:</strong></p> <p><strong>Frozen release:</strong></p> <p>Updated <em>A. glycines </em>biotype 4 genome assembly: Aphis_glycines_4.v2.1.scaffolds.fa.gz&nbsp;</p> <p>BRAKER2 gene models for updated <em>A. glycines </em>biotype 4 genome assembly: Aphis_glycines_4.v2.1.scaffolds.fa.gff</p> <p>BRAKER2 protein sequences:&nbsp;Aphis_glycines_4.v2.1.scaffolds.fa.gff.aa.fa</p> <p>BRAKER2 nucleotide coding sequences:&nbsp;&nbsp;Aphis_glycines_4.v2.1.scaffolds.fa.gff.CDS.fa</p> <p><strong>Unfiltered raw intermediate genome assemblies:</strong></p> <p>Canu assembly of biotype 4 PacBio data from Wenger et. al. (2017):&nbsp;canu.fa.gz</p> <p>DBG2OLC hybrid assembly of selected biotype 4 MiSeq data and biotype 4 PacBio data from&nbsp;Wenger et. al. (2017):&nbsp;DBG2OLC.fa.gz</p> <p>Merged Canu and DBG2OLC assembly created with quickmerge:&nbsp;quickmerge.fa.gz</p> <p>Pilon polished (2 rounds) quickmerge assembly:&nbsp;quickmerge.pilon_r2.fa.gz</p> <p><strong>Mitochondrial and endosymbiont contigs extracted from the pilon polished quickmerge assembly:&nbsp;</strong></p> <p><em>A. glycines </em>biotype 4 mitochondrial genome:&nbsp;Aphis_glycines_4_Buchnera_v1.fa</p> <p><em>A. glycines </em>biotype 4&nbsp;<em>Buchnera aphidicola</em>&nbsp;contigs:&nbsp;Aphis_glycines_4_Buchnera_v1.fa</p> <p><em>A. glycines </em>biotype 4&nbsp;<em>Wolbachia</em> contigs:&nbsp;Aphis_glycines_4_Buchnera_v1.fa</p> <p><strong>Other files:</strong></p> <p>MUSCLE alignment of <em>A. glycines </em>v1, <em>A. glycines </em>biotype 4 v2.1 and <em>Drosophila&nbsp;melanogaster</em> R6.22 Osiris proteins in fasta format:&nbsp;D_mel_v1_v2_osiris.prots.muscle.fasta</p> <p>FastTree Maximum Likelihood phylogeny based on the MUSCLE alignment of Osiris genes in newick format:&nbsp;D_mel_v1_v2_osiris.prots.muscle.FastTree.nwk</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p>