Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridization.
Two closely related strains of the Gram-positive, cellulolytic ruminal bacterium Ruminococcus flavefaciens were compared at the genomic level by suppressive subtractive hybridization. The two strains investigated in this study differ by 1.94% in their respective 16S rDNA genes. Three hundred and eighty-four PCR-amplified products were cloned and then screened for their strain identity by dot blot hybridization. Based on redundancy percentages of the clones sequenced, 9.5% of the genome of the R. flavefaciens FD-1 strain is not present in the JM1 strain. The majority of identities of individual cloned subtracted products (642 bp average length) bore no relation to deposited sequences in GenBank (42% of the subtracted library), whereas of those with putative assigned functions 7% are loosely associated with fibre-degradation, 6% with insertion elements, transposons and phage-like ORFs, 5% with cell membrane associated proteins and 3% with signal transduction. Subtracted sequences were then supplemented with the draft (2 x coverage) genome sequence of R. flavefaciens FD-1 to indicate potential regions of rearrangement within the genome, including a novel insertion sequence.
Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 West Gregory Dr, Urbana, IL 61801, USA.
Dionysios A
DA
Antonopoulos
Karen E
KE
Nelson
Mark
M
Morrison
Bryan A
BA
White
D001483:Base Sequence; D002480:Cellulase / Q000235:genetics; D004251:DNA Transposable Elements; D030561:Databases, Nucleic Acid; D015723:Gene Library; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D045857:Ruminococcus / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA
D004251:DNA Transposable Elements; D012336:RNA, Ribosomal, 16S; D002480:Cellulase