Eggplant whole-genome sequencing. Solanum virginianum

Genome sequencing of Solanum melongena L. (eggplant) was performed by using Illumina HiSeq2000 and Roche 454 reads. The genic-regions enriched genome library were sequenced for the four cultivars, Nakate-shinkuro, LS1934, WCGR112-8, and AE-P03 by Roche 454 GS FLX+. All of the 454 reads including the four cultivars were assembled into contigs (454 Newbler contigs) by Newbler 2.7. The illumina reads sequenced for a cultivar, Nakate-shinkuro were assembled into scaffolds (SOAPdenovo scaffolds) by SOAPdenovo v1.05. The gap-filled scaffolds (illumina consensus sequences) were obtained by using GapCloser 1.10. To obtain the genomic regions of Nakate-shinkuro, the scaffolds mapped by the illumina reads (454 consensus sequences) were obtained by BWA 0.6.2. Next, the hybrid-assembly was performed for the 454 consensus sequences and the illumina consensus sequences by PCAP.rep. Finally, the super-scafflods were connected using the mate-pair reads of HiSeq2000 by SSPACE 2.0. After the assembly, the integrated linkage map was constructed using the SNP and SSR markers. The draft genome sequences of eggplant (SME_r2.5) were compared with those of tomato (SL2.40).