Compared with other members of the Cryomorphaceae, the strain most similar to strain UST20020801T with respect to the content of straight-chain fatty acids and branched-chain hydroxy fatty acids is Cryomorpha ignava 1-22T [1]. In addition to phosphatidylethanolamine third as major polar lipid, six unidentified lipids, one unidentified aminolipid, one unidentified aminophospholipid and one unidentified glycolipid were found in strain UST20020801T [15]. MK-6 was detected as a major respiratory quinone in strain UST20020801T [1]. Genome sequencing and annotation Genome project history This organism was selected for sequencing on the basis of its phylogenetic position [41], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [42].

The genome project is deposited in the Genomes On Line Database [27] 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 O. hongkongensis strain UST20020801T, DSM 17368, was grown in DSMZ medium 1168 (YPS medium) [43] at 30��C. DNA was isolated from 0.5-1 g of cell paste using Jetflex Genomic DNA Purification kit (GENOMED 600100) following the standard protocol as recommended by the manufacturer with an extended cell-lysis procedure, i.e. incubation with additional 80 ��l protease K for one hour at 58��C. DNA is available through the DNA Bank Network [44].

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 [45]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly, consisting of 39 contigs in one scaffold, was converted into a phrap [46] assembly by making fake reads from the consensus to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (5,738.3 Mb) was assembled with Velvet [47] 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 81.1 Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20.

The Phred/Phrap/Consed software package [46] 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 [45], Dupfinisher [48], or sequencing cloned bridging PCR fragments with Drug_discovery subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished).