The genome project is deposited in the Genomes OnLine Database [24] and the complete genome sequence 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 for Mesorhizobium australicum http://www.selleckchem.com/products/Gemcitabine-Hydrochloride(Gemzar).html strain WSM2073T Growth conditions and DNA isolation M. australicum strain WSM2073T was grown to mid logarithmic phase in TY medium (a rich medium) [25] on a gyratory shaker at 28��C. DNA was isolated from 60 mL of cells using a CTAB (Cetyl trimethylammonium bromide) bacterial genomic DNA isolation method. Genome sequencing and assembly The draft genome of M. australicum strain WSM2073T was generated at the DOE Joint genome Institute (JGI) using a combination of Illumina [26] and 454 technologies [27].

For this, genome we constructed and sequenced an Illumina GAii shotgun library which generated 10,509,788 reads totaling 378.4 Mb, a 454 Titanium standard library which generated 235,807 reads and paired end 454 libraries with an average insert sizes of 26.3 Kb /10.9 Kb which generated 221,877/139,171 reads totaling 257.0 Mb of 454 data. All general aspects of library construction and sequencing performed in this project can be found at the DOE Joint Genome Institute website. The initial draft assembly contained 14 contigs in 1 scaffold. The 454 Titanium standard data and the 454 paired end data were assembled together with Newbler, version 2.3. The Newbler consensus sequences were computationally shredded into 2 Kb overlapping fake reads (shreds).

Illumina sequencing data was assembled with VELVET, version 0.7.63 [28], 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 (High Performance Software, Entinostat LLC). The software Consed [29-31] 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potential base errors and increase consensus quality using the software Polisher developed at JGI (Alla Lapidus, unpublished). Possible mis-assemblies were corrected using gapResolution (Cliff Han, unpublished), Dupfinisher [32], or sequencing cloned bridging PCR fragments with subcloning.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. A total of 59 additional reactions were necessary to close gaps and to raise the quality of the finished sequence.