Afre-v5_Repeats.gffAuanema 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弗赖堡奥内马线虫（Auanema freiburgense）染色体级基因组组装。本研究采用PacBio测序数据，使用Canu（版本1.6）进行组装，设置最小读取长度（minReadLength）为3kb，并将校正错误率（correctedErrorRate）设为0.030，该参数组合可得到最具连续性的组装结果。预估基因组大小（genomeSize）设定为55Mb。通过BLASTn（版本2.7.1）比对至污染数据库（该数据库包含2018年3月30日从欧洲核苷酸档案馆（European Nucleotide Archive, ENA）下载的3000个细菌基因组），完成细菌污染的鉴定与去除。基因组组装首先使用Quiver（版本0.3.1）结合PacBio原始reads进行第一轮抛光；随后使用Pilon结合所有可用的Illumina短读数据进行第二轮抛光。以经Illumina数据抛光后的组装基因组作为参考基因组，对由两株弗赖堡奥内马线虫（APS14与APS7）构建的全部100个高级互交重组近交系（RIAILs）进行基因分型。使用R/qtl与ASMap这两款R语言包，对完成基因分型的株系构建遗传连锁图谱。将支架序列（scaffolds）锚定至该遗传连锁图谱，最终完成染色体级组装：即将支架序列按照各自在每个连锁群内的位置进行排序。