16S rRNA sequences were retrieved from Genbank (NCBI), and accession numbers are given in parentheses. Strains from which www.selleckchem.com/products/MLN-2238.html a … Genome project history Table 2 presents the project information in compliance to MIGS version 2.0 . Table 2 Project information Growth conditions and DNA isolation Dehalobacter restrictus strain PER-K23, DSM9455, was cultivated anaerobically as previously described . DNA was extracted from bacterial pellets using the protocol recommended by the JGI. In brief, cell walls were digested with lysozyme before DNA was purified with hexadecyltrimethylammonium bromide, phenol and chloroform, and precipitated with isopropanol. Quality and quantity of the obtained DNA were checked by running aliquots on agarose gels using lambda phage DNA as mass standard and HindIII digested lambda phage DNA as a size marker.
Genome sequencing and assembly The draft genome of Dehalobacter restrictus PER-K23 was generated at the DOE Joint genome Institute (JGI) using a combination of Illumina , and 454 technologies . For this, genome we constructed and sequenced an Illumina GAii shotgun library which generated 77,929,756 reads totaling 5,922.7 Mb, and 1 paired end 454 library with an average insert size of 10 kb which generated 318,117 reads totaling 59.3 Mb of 454 data. All general aspects of library construction and sequencing performed at the JGI can be found at the JGI website . The initial draft assembly contained 90 contigs in 1 scaffold. The 454 paired end data were assembled together with Newbler, version 2.3-PreRelease-6/30/2009.
The Newbler consensus sequences were computationally shredded into 2 kb overlapping fake reads (shreds). Illumina sequencing data was assembled with VELVET, version 1.0.13 , and the consensus sequence 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, 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potential base errors and increase consensus quality using the software Polisher developed at JGI (Alla Lapidus, unpublished).
Possible mis-assemblies were corrected using gapResolution (Cliff Han, unpublished), Dupfinisher , or sequencing cloned bridging PCR fragments with subcloning.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 134 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. The total size Dacomitinib of the genome is 2,943,336 bp and the final assembly is based on 24.6 Mb of 454 draft data which provides an average 8.