Sequencing of the Japanese soybean cultivar 'Enrei'

To establish the basic research resources for whole genome analysis and domestic soybean breeding, we have sequenced the entire genome of a Japanese soybean cultivar ‘Enrei’ with a next-generation sequencer, Roche/454 GS-FLX Titanium. The sequenced genome size of soybean is 950 Mb. After sequencing and assembling the whole genome shotgun sequence data, we obtained an ‘Enrei’ data set with about 800 Mb total bases and 221,674 contigs with an average size is 3.6 kb. This sequence has a high quality score for each nucleotide, so it is appropriate to use in searching for differences in single nucleotide polymorphisms and insertions/deletions between genomes of ‘Williams 82’ and ‘Enrei’. These sequence data, the derived SNPs and In/Dels, and additional data will be installed into the previously reported DaizuBase. DaizuBase includes “Unified map”, which indicates the relationship between the linkage map and the physical map, and “Gbrowse”, which exhibits aligned Enrei-BAC clones on the Glyma 1 assembly, and facilitates comparative genome analyses. It will show ‘Enrei’ draft genome sequence data. Next, we attempted to develop a method for comparative analysis among domestic soybeans. The fragmented DNAs prepared from domestic soybean were hybridized with synthetic oligonucleotides designed from end-sequences of mapped Enrei-BAC clones by the NimbleGen sequence capture method. Hybridized DNA was recovered and sequenced with Roche/454 GS-FLX Titanium. To validate this method, sequenced data were assembled and mapped by Blast searches of DaizuBase. Captured sequences corresponded well to the original BAC sequences (Fig. 1), suggesting that this method is suitable for genome-wide analysis of target regions in domestic soybeans.