Genome sequencing of the BtE555 variant strain. (a) Reference genome coverage. BtE555 short reads were aligned against the BtE264 reference. Y-axis: percentage nucleotide coverage of the BtE264 genome. X-axis: number of reads covering each nucleotide. Vertical blue line indicates 20× coverage, corresponding to 90% coverage of the BtE264 genome. The inset graph is a close-up of the intersect. (b) Functional enrichment of Bt genes with nonsynonymous SNPs (Nsy SNPs). COG functional categories are indicated on the y-axis, and the percentage of genes in each COG category is shown on the x-axis. Dark blue columns represent Bt genes with Nsy SNPs relative to BtE264, and light blue columns indicate all Bt genes with COG annotations. COG categories exhibiting a significant enrichment of Bt genes with Nsy SNPs are highlighted by asterisks (*P < 0.05 or **P < 0.01, binomial test; after Bonferroni correction). (c) Sequence coverage gaps in BtE264 are associated with GIs and nGis. Shown are coverage maps of BtE264 chromosome 1 (top) and chromosome 2 (bottom). Graph: median fold-coverage of BtE555 sequence reads using a 10-kb moving window. Genomic track: genomic locations of predicted GIs and nGsi in green and red bars, respectively. aCGH track: aCGH hybridization patterns of BtE555 against BtE264. The x-axis shows the BtE264 genome co-ordinates (bp). (d) Confirmation of the Bp-likeCPS gene cluster in BtE555. Row 1: genomic coordinates of the BtE264 EPS cluster (chromosome I BTH_I1321 to BTH1344). Bt EPS cluster genes are shown in blue. Row 2: coverage map shows a drop of BtE555 sequence reads corresponding to Bt EPS genes. Row 3: genomic locations of predicted BtE555 genes in contig 19, showing genes conserved with BtE264 (orange) and Bp-likeCPS cluster genes (red). Row 4: genomic location of BtE555 contig 19 (34 kb) showing conserved (orange) and BtE555-specific regions (red).