Complete genome sequence of Lactococcus lactis subsp. lactis A12, a strain isolated from wheat sourdough. L.lactis A12

3-kb long paired-end library of total DNA was constructed and sequenced on the 454 GS FLX platform, generating 192,126 reads. These reads were used in combination with the 228,613 reads previously obtained from shotgun 454 GS FLX sequencing for the assembly step using the integrated processing environment NG6. A total of 10 scaffolds were generated and five could be ordered and oriented against the high-resolution NheI optical map of the chromosome. Chromosomal sequences corresponding to each ribosomal operon (six), gaps (five), nucleotide ambiguities (19 regions), and pseudogenes (78 putative) were determined by Sanger sequencing of appropriate PCR products. Annotation of the assembled chromosome and plasmids was performed using the integrated bacterial genome annotation platform AGMIAL, followed by a manual curation process.