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J. Bacteriol., 05 1995, 2368-2372, Vol 177, No. 9
Copyright © 1995, American Society for Microbiology

High-resolution alignment of a 1-megabase-long genome region of three strains of Rhodobacter capsulatus

M Fonstein, T Nikolskaya and R Haselkorn
Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA.

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.(ABSTRACT TRUNCATED AT 250 WORDS)

This article has been cited by other articles:

• Vlcek, C., Paces, V., Maltsev, N., Haselkorn, R., Fonstein, M. (1997). Sequence of a 189-kb segment of the chromosome of Rhodobacter capsulatus SB1003. Proc. Natl. Acad. Sci. USA 94: 9384-9388 [Abstract] [Full Text]