90 bp paired end sequencing technology

The DNA of the parental lines (V71-370 and PI407162) was isolated and sequenced at a depth of 15× using Illumina 90 bp paired-end sequencing technology with insert sizes of around 500 bp. The data were processed after filtering out low-quality reads and duplicate reads. The processed data were aligned to the William 82 G. max v1.1 from Phytozome as the reference genome [2 (link)]. SNPs and Indels were identified using an in-house built pipeline using GATK v3.0 [80 (link)] and were analyzed for possible synonymous/non-synonymous SNP variation annotations using SnpEFF [81 ] and v9.0 gene models from Phytozome. To detect small insertions and deletions, Indels (1-5 bp) were called by SOAP (Short Oligonucleotide Analysis Package) indel 1.09 (http://soap.genomics.org.cn/soapindel.html). The non-synonymous SNP variations were only considered for comparison among 17 Chinese and 1 Korean wild soybeans, and can be viewed using SNPViz tool [82 (link)] available in SoyKB.

Genomic DNA samples were sequenced using standard bisulfite sequencing protocols and Illumina 90-bp paired-end sequencing technology at BGI, China. Sequencing reads were aligned to the Arabidopsis reference genome (TAIR10) using Bismark alignment software v.0.7.7 (Krueger and Andrews 2011 (link)) with a maximum of two mismatches, and only uniquely aligned reads were retained. Bisulfite conversion rates (Supplemental Table S4) were estimated based on reads that uniquely aligned to the lambda phage genome.