7-9 0 with an optimum at pH 7 0 [1] Figure 2 Transmission electr

7-9.0 with an optimum at pH 7.0 [1]. Figure 2 Transmission electron micrograph of S. novella ATCC 8093T. Scale bar: 500 nm Table 1 Classification and general features of S. novella according to the MIGS recommendations [47] and the NamesforLife database [48]. Chemotaxonomy The lipopolysaccharide of strain ATCC 8093T lacks heptoses and has only 2,3-diamino-2,3-dideoxyglucose http://www.selleckchem.com/products/epz-5676.html as the backbone sugar [1]; other data on the cell wall structure of strain ATCC 8093T are not available. The major isoprenoid quinone is ubiquinone Q-10 [1], and the major cellular fatty acids are octadecenoid acid (C18:1) and C19 cyclopropane acid; no hydroxyl acids are present [1]. Cells contain putrescine and homospermidine. Genome sequencing and annotation Genome project history This organism was selected for sequencing on the basis of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.

The genome project is deposited in the Genomes On Line Database [39] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2. Table 2 Genome sequencing project information Growth conditions and DNA isolation Strain ATCC 8093T was grown from a culture of DSMZ 506 in DSMZ medium 69 at 28��Cg DNA was purified using the Genomic-tip 100 System (Qiagen) following the directions provided by the supplier. The purity, quality and size of the bulk gDNA preparation were assessed by JGI according to DOE-JGI guidelines.

Genome sequencing and assembly The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [57]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 13 contigs in one scaffold was converted into a phrap [58] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (211.3 Mb) were assembled with Velvet [59] 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 259.9 Mb 454 draft data and all of the 454 paired-end data. Newbler parameters were -consed -a 50 -l 350 -g -m -ml 20.

The Phred/Phrap/Consed software package [58] 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 [58], Brefeldin_A Dupfinisher [60], or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished).

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