gDNA resequencing of Glycine max landrace 'PI 603408'
High quality, high molecular weight intact DNA was isolated from ~50 mg of lyophilized seedling leaf tissue from five PI 603408 plants using a Dneasy mini plant kit according to manufacturers recommendations (Qiagen). Library construction and sequencing were performed by Global Biologics, Inc. (Columbia, MO, USA). Briefly, gDNA was fragmented to 100-300 bps and two replicate Illumina gDNA resequencing libraries (100-300 bp insert) were prepared and sequenced using 2 entire lanes on a HISeq 2000 (2x100 bp, paired end). A total of 679,467,503 reads were collected. FASTQ files were imported into CLC genomics workbench (version 9, Qiagen), and each lane was separately mapped (due to memory limitations) to the Williams 82 reference genome W82.a2.v1 ((Schmutz et al. 2010) using the following settings: Mismatch cost of 2, insertion cost=3, deletion cost=3, insertion open cost=6, deletion open cost=6, deletion extend cost=1, length fraction=0.5, similarity fraction=0.8, auto-detection of paired distances=yes, non-specific matches= ignored (due to the ancestrally polyploid nature of soybean). The two lanes of mappings were then merged within CLC genomics workbench.