Xanthomonas oryzae pv. oryzae str. KACC10331 (KXO85), a representative Korean race 1 strain that is virulent to rice carrying the Xa21 resistance gene, was used in this study. The genome sequence was determined through the whole-genome shotgun approach (20 ). The nucleotide sequence of the inserts carried by 49 087 clones with 1–2 kb inserts (8.6-fold genome coverage) and 14 783 clones with 8–10 kb inserts (2.4-fold genome coverage) in pUC18 SmaI/BAP vector (Invitrogen, USA) were determined from both ends using BigDye™ terminator (Applied Biosystems, USA) and an ABI3700 automated sequencer. In addition to the above sequences, nucleotide sequences were obtained from both ends of 3025 inserts carried by fosmid clones constructed using 40 kb genome fragments in the pEpiFOS™-5 vector (Epicentre technologies, USA) and 2895 BAC clones with 112 kb genome fragments generated in the pIndigoBAC-5 vector (Epicentre technologies, USA). The inserts in these libraries covered 98% of the genome and the sequences from both ends of fosmid and BAC clones were used to confirm the orientation and integrity of the sequence contigs to validate the final sequence assembly. The reported sequence (GenBank accession no. AE013598) was assembled from 70 689 115 bp of accumulated nucleotide sequence using Phred/Phrap/Consed software package (). The scaffolds were created using mate information between contig groups. Gap closures between scaffolds or contigs were accomplished by primer-walking on BAC, cosmid or plasmid templates spanning Xoo genome and direct sequencing of PCR products. Assembly was confirmed by comparing PacI, PmeI and SwaI restriction maps to computational predictions.