High-resolution alignment of a 1-megabase-long genome region of three strains of Rhodobacter capsulatus.
A detailed restriction map of the genome of Rhodobacter capsulatus SB1003 was constructed recently by using an ordered set of overlapping cosmids. Pulsed-field gel electrophoresis-generated restriction patterns of the chromosomes of 14 other R. capsulatus strains were compared. Two of them, St. Louis and 2.3.1, were chosen for high-resolution alignment of their genomes with that of SB1003. A 1-Mb segment of the R. capsulatus SB1003 cosmid set was used as a source of ordered probes to group cosmids from the other strains. Selected cosmids were linked into one 800-kb contig and two smaller contigs of 100 kb each. EcoRV and BamHI restriction maps of the newly ordered cosmids were constructed by using lambda terminase. Long-range gene order in the new strains was mainly conserved for the regions studied. However, one large genome rearrangement inverted a 470-kb DNA fragment of the St. Louis strain between the rrnA and rrnB operons. A 50-kb deletion covering three SB1003 probes was found in strain 2.3.1 near rrnB. Conservation of about 50% of the positions of restriction sites in all these strains and nearly 80% for the pair 2.3.1- St. Louis made it possible to produce high-resolution alignment of the contiguous 800-kb genome segment. Ten deletions of 2 to 27 kb, one 30-kb inversion, and three translocations were found in this region. Strong clustering of the positions of polymorphic restriction sites was observed. For a 50-kb size interval, two patterns of the distribution of restriction sites were found, one with about 90% and the other with 5 to 30% conservation of sites. This structure may be explained by independent acquisition of these divergent regions from other Rhodobacter strains.
Fonstein
M
M
Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA.
Nikolskaya
T
T
Haselkorn
R
R
D007446:Chromosome Inversion; D002874:Chromosome Mapping / Q000379:methods*; D003360:Cosmids; D016521:Electrophoresis, Gel, Pulsed-Field; D015723:Gene Library; D015321:Gene Rearrangement; D016680:Genome, Bacterial; D009693:Nucleic Acid Hybridization; D015183:Restriction Mapping; D016354:Rhodobacter capsulatus / Q000145:classification / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D013045:Species Specificity