(Mimosoideae) [28]. Genome sequencing and annotation information Genome project history This organism was selected for sequencing on the basis http://www.selleckchem.com/products/Oligomycin-A.html of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the Community Sequencing Program at the U.S. Department of Energy, Joint Genome Institute (JGI) for projects of relevance to agency missions. The genome project is deposited in the Genomes OnLine Database [27] and an improved-high-quality-draft genome sequence in IMG. Sequencing, finishing and annotation were performed by the JGI. A summary of the project information is shown in Table 2.

Table 2 Genome sequencing project information for ��Burkholderia sprentiae�� strain WSM5005T Growth conditions and DNA isolation ��Burkholderia sprentiae�� strain WSM5005T was grown to mid logarithmic phase in TY rich medium [29] on a gyratory shaker at 28��C. DNA was isolated from 60 mL of cells using a CTAB (Cetyl trimethyl ammonium bromide) bacterial genomic DNA isolation method [30]. Genome sequencing and assembly The genome of ��Burkholderia sprentiae�� strain WSM5005T was sequenced at the Joint Genome Institute (JGI) using a combination of Illumina [31] and 454 technologies [32]. An Illumina GAii shotgun library which generated 76,247,610 reads totaling 5,794.8 Mb, and a paired end 454 library with an average insert size of 13 kb which generated 612,483 reads totaling 112.9 Mb of 454 data were generated for this genome. All general aspects of library construction and sequencing performed at the JGI can be found at [30].

The initial draft assembly contained 420 contigs in 8 scaffolds. The 454 paired end data was assembled with Newbler, version 2.3. The Newbler consensus sequences were computationally shredded into 2 kb overlapping fake reads (shreds). Illumina sequencing data were assembled with VELVET, version 1.0.13 [33], and the consensus sequences were computationally shredded into 1.5 kb overlapping fake reads (shreds). We integrated the 454 Newbler consensus shreds, the Illumina VELVET consensus shreds and the read pairs in the 454 paired end library using parallel phrap, version SPS – 4.24 Carfilzomib (High Performance Software, LLC). The software Consed [34-36] was used in the following finishing process. Illumina data was used to correct potential base errors and increase consensus quality using the software Polisher developed at JGI (Alla Lapidus, unpublished). Possible mis-assemblies were corrected using gapResolution (Cliff Han, unpublished), Dupfinisher [37], or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR (J-F Cheng, unpublished) primer walks.