0 Mb) was assembled with Velvet  and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 152.9 Mb of 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package  selleck chemical was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution , Dupfinisher , or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI).
Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F.Chang, unpublished). A total of 24 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI . The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 219.5 �� coverage of the genome. The final assembly contained 438,623 pyrosequence and 43,957,307 Illumina reads. Genome annotation Genes were identified using Prodigal  as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline .
The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes – Expert Review (IMG-ER) platform . Genome properties The genome consists of a 2,157,835 bp long chromosome with a 36% GC content and a 58,717 bp plasmid with 31% GC content (Table 3 and Figures 3a and and3b).3b). Of the 2,278 genes predicted, 2,128 were protein-coding genes, and 50 RNAs; 27 pseudogenes were identified. The majority of the protein-coding genes (76.5%) were assigned with a putative function while the remaining ones were annotated as hypothetical proteins.
The distribution of genes into COGs functional categories is presented in Table 4. Table 3 Genome Statistics Figure 3a Graphical circular map of the chromosome. From outside to the center: Genes on forward strand (color by COG Cilengitide categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew. Figure 3b Graphical circular map of the plasmid (not drown to scale with chromosome).