The genome project is deposited in the Genomes On Line Database [11] and the complete genome sequence is deposited in GenBank and the Integrated Microbial Genomes database (IMG) [31]. Sequencing, finishing and annotation were performed by the selleck chem inhibitor DOE Joint Genome Institute (JGI) using state of the art sequencing technology [32]. A summary of the project information is shown in Table 2. Table 2 Genome sequencing project information Growth conditions and DNA isolation A culture of DSM 14336T was grown aerobically in DSMZ medium 514 [33] at 20��C. Genomic DNA was isolated using a Jetflex Genomic DNA Purification Kit (GENOMED 600100) following the standard protocol provided by the manufacturer but modified by an incubation time of 40 min, the incubation on ice over night on a shaker, the use of additional 10 ��l proteinase K, and the addition of 100 ��l protein precipitation buffer.

DNA is available from DSMZ through the DNA Bank Network [34]. Genome sequencing and assembly The draft genome sequence was generated using Illumina sequencing technology. For this genome, we constructed and sequenced an Illumina short-insert paired-end library with an average insert size of 270 bp, which generated 10,989,662 reads. In addition, an Illumina long-insert paired-end library with an average insert size of 9,000 bp was constructed, generating 1,005,012 reads for a total of 1,798 Mb of Illumina data (Feng Chen, unpublished). All general aspects of library construction and sequencing performed can be found at the JGI web site [35]. The initial draft assembly contained 16 contigs in 6 scaffold(s).

The initial draft data was assembled with Allpaths [36] and the consensus was computationally shredded into 10 kbp overlapping fake reads (shreds). The Illumina draft data was also assembled with Velvet [37], and the consensus sequences were computationally shredded into 1.5 kbp overlapping fake reads (shreds). The Illumina draft data was assembled again with Velvet using the shreds from the first Velvet assembly to guide the next assembly. The consensus from the second Velvet assembly was shredded into 1.5 kbp overlapping fake reads. The fake reads from the Allpaths assembly and both Velvet assemblies and a subset of the Illumina CLIP paired-end reads were assembled using parallel phrap (High Performance Software, LLC) [38]. Possible mis-assemblies were corrected with manual editing in Consed [38].

Gap closure was accomplished using repeat resolution software (Wei Gu, unpublished), and sequencing AV-951 of bridging PCR fragments with Sanger technologies. A total of 15 additional sequencing reactions were completed to close gaps and to raise the quality of the final sequence. The total size of the genome is 4,630,996 bp and the final assembly is based on 1,798 Mb of Illumina draft data, which provides an average 382.5 �� coverage of the genome.