Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1(T): chromosome II is a true chromosome

The photosynthetic bacterium Rhodobacter sphaeroides 2.4.1(T) has two chromosomes, CI (similar to 3.0 Mb) and CII (similar to 0.9 Mb). In this study a low-redundancy sequencing strategy was adopted to analyse 23 out of 47 cosmids from an ordered CII library. The sum of the lengths of these 23 cosmid inserts was similar to 495 kb, which comprised similar to 417 kb of unique DNA. A total of 1145 sequencing runs was carried out, with each run generating 559+/-268 bases of sequence to give similar to 640 kb of total sequence. After editing, similar to 2.8% bases per run were estimated to be ambiguous. After the removal of vector and Escherichia coli sequences, the remaining similar to 565 kb of R. sphaeroides sequences were assembled, generating similar to 291 kb of unique sequences. BLASTX analysis of these unique sequences suggested that similar to 131 kb (45% of the unique sequence) had matches to either known genes, or database ORFs of hypothetical or unknown function (dORFs). A total of 144 strong matches to the database was found; 101 of these matches represented genes encoding a wide variety of functions, e.g. amino acid biosynthesis, photosynthesis, nutrient transport, and various regulatory functions. Two rRNA operons (rrnB and rrnC) and five tRNAs were also identified. The remaining 160 kb of DNA sequence which did not yield database matches was then analysed using CODONPREFERENCE from the GCG package. This analysis suggested that 122 kb (42% of the total unique DNA sequence) could encode putative ORFs (pORFs), with the remaining 38 kb (13%) possibly representing non-coding intergenic DNA. From the data so far obtained, CII does not appear to be specialized for encoding any particular metabolic function, physiological state or growth condition. These data suggest that CII contains genes which are functionally as diverse as those found on any other bacterial chromosome and also contains sequences (pORFs) which may prove to be unique to this organism.