Afre.gff3Auanema freiburgense Genome

Auanema freiburgense chromosomal-scal genome assembly. The PacBio data was assembled using Canu (version 1.6), using a minimum read length (minReadLength) of 3kb and setting the corrected error rate (correctedErrorRate) to 0.030 as this resulted in the most contiguous assembly. The estimated genome size (genomeSize) was set to 55Mb. Bacterial contamination was identified and removed through BLASTn (version 2.7.1), alignments to a contaminant database that included 3,000 bacterial genomes downloaded from the European Nucleotide Archive (ENA) on March 30, 2018. The genome was polished first using Quiver with PacBio raw reads (version 0.3.1). Then the genome was further polished using Pilon with all available Illumina short reads. The assembled genome polished with Illumina reads was used as a reference genome to genotype all 100 RIAILs built using two A. freiburgensis strains (APS14 and APS7). A genetic linkage map was constructed with the genotyped lines using R/qtl and ASMap R packages. Scaffolds were anchored into the genetic map, producing a chromosomal assembly, where scaffolds were ordered into their respective position within each linkage group