Genome sequencing The genome sequences of H. pylori strains F16, F30, F32 and F57 were determined by a whole-genome shotgun strategy. We constructed small-insert (2 kb) and large-insert (10 kb) plasmid libraries from genomic DNA, and sequenced both ends of the clones to obtain 26,112 (F16 and F57), 30,720 (F30) and 33,792 (F32) sequences using ABI 3730xl sequencers (Applied Biosystems),
with coverage of 10.0 (F16)-, 11.5 (F30)-, 12.7 (F32)- and 10.0 (F57)-fold. Sequence reads were assembled with the Phred-Phrap-Consed program, and gaps were closed by direct sequencing of clones that spanned the gaps or with PCR products amplified using oligonucleotide primers designed against Transferase inhibitor the ends of neighboring contigs. The overall accuracy of the finished sequence was estimated to have an error rate of less than 1 per 10,000 bases (Phrap score of ≥40). Sequences of the molybdenum-related genes and the genes in the acetate pathway of the four Japanese strains were verified by resequencing PCR fragments directly amplified selleck chemicals llc from genomic DNA (primers are in Additional file 4 (= Table S3)). The genome sequences of other strains were obtained from National Center for Biotechnology Information (NCBI) . Accession numbers
are in Table 1. Gene finding and annotation We used the same protocol to identify genes in the four new strains and 16 other complete genomes (Table 1; gene assignment differences are in Additional file 8 (= Table 6)). Protein-coding genes were identified by integrating predictions from programs GeneMarkS  and GLIMMER3 . All ORFs longer than 10 amino acids were searched using BLASTP  against two databases, one composed of genes of 6 H. pylori genomes in RefSeq database at NCBI (“”close”" database), and the other composed of genes of 300 complete prokaryote genomes (one genome per one genus) available at the end of 2008, except for those in the Helicobacter genus (“”distant”" database). When the predicted start position differed in GeneMarkS and GLIMMER3, assignments were made by consensus of hits, with consensus against the “”distant”" database taking
priority over the “”close”" one. The consensus start position among bidirectional best hits with 50% or more amino acid sequence identity for each matched region for each genome pair BIBF-1120 was determined by majority rule. Overlap of genes was resolved by comparing the results from four prediction programs. Genes encoding fewer than 100 amino acids and predicted only by Glimmer3 were dropped except for the microcin gene. tRNA genes were detected using tRNAscan-SE . rRNA genes were identified based on sequence conservation. Putative replication origins were predicted by GC-skew (window size 500 bp, window shift 250 bp). Core genome analysis The common core structure conserved among 20 H. pylori genomes was identified based on conservation of gene order among orthologs using the CoreAligner program  SB273005 implemented in the RECOG system.