Graphical Comparison between MG and MG:
MP/MG-Comparison-Map This map shows the
MP-ORF map and the corresponding ORFs of MG.
Since the order of the genes is conserved within six DNA segments (coloured), we
looked at the recombination sites. All DNA segments are flanked by a repetitive
DNA Region which could be the recombination site for the genome rearangement.
A characteristic feature of these repetitive DNA regions is an increase
of the GC-content within the DNA-sequence.
Legend of the figure:
The complete gene map of the M.pneumoniae genome and the alignment of the corresponding M.genitalium ORFs.
The thick, coloured arrows represent the position, size and direction of transcription of the proposed ORFs of M.pneumoniae. The official name of an ORF can be deduced from the cosmid name above the horizontal scale-line and the black number directly below the thick arrows, e.g. the correct ORF name represented by the first complete green arrow is E07_orf1113. For more details see.
The second number in colour below the black number indicates the corresponding ORF number (e.g. MG141) of M.genitalium, except for the yellow segment, where the M.genitalium ORFs were also drawn in black for better visibility. Throughout the genome map the ORFs of M.genitalium are oriented in the same direction as the ORFs of M.pneumoniae.
The genes of the M.genitalium map are named in numerical order, starting with MG001 localized in this comparative map around nucleotide position 206.000 (dnaA region). Any divergence in the order of orthologous genes can be recognized by the discontinuity of the numbers of the M.genitalium ORFs. In all cases where the consecutive order of M.genitalium orthologs is conserved, coloured thin horizontal lines connect the first and last gene in the particular genome region. The order of genes is conserved in both bacteria within six DNA segments each marked by the distinct strong color. Interspaced M.pneumoniae ORFs without significant similarities to M.genitalium are shown by thick arrows in white. M.pneumoniae-specific ORFs representing amplification of M.genitalium homologs were indicated by thick arrows in light colors . Each of these six conserved DNA segments of M.pneumoniae (strong colours) is bordered by repetitive DNA sequences. Rectangles with various patterns above the scale-line indicate size, position and direction of transcription for repetitive DNA sequences derived ORFs.
The GC-Curve compares the the the GC-content
between MP and MG ( *for this analysis the MG sequence was reverse complemented
and had a new start-position). At the flanks of the blocks you can see an
increase of the GC-content.
Legend of the figure:
Low resolution G+C-plot of the complete genomes of M.pneumoniae and M.genitalium. The G+C-content was calculated within a windowsize of 1000 bp and an increment of each 250 bp. The positions of the segments of conserved gene order are indicated as coloured bars. The black dots mark the position of the putative origins of replication and rrn the position of the rRNA operon. The black triangles indicate repetitive DNA sequences. The gaps between the segments and a black triangles above mark a proposed site of translocation. The start point of the M.genitalium genome sequence was changed to MG068 and the sequence was reverse complemented. The M.genitalium ORF names (e.g. MG068) below the M.genitalium G+C plot indicate the new orientation of the genomic sequence and the frist and the last ORF of each segment e.g. the green segment reaches from MG140-MG185.
Below the plots is a schematic illustration of the different order of the genomic segments in these two bacteria.
The order the blocks within two genomes is
also illustrated in circular Form.
Legend of the figure:
Comparative presentation of the organization of DNA segments with conserved gene order and general direction of transcription in M.pneumoniae and M.genitalium. Segments with conserved gene order in both bacteria are shown in the same colour. Gaps within the coloured block and triangles in the red segments represent repetitive DNA sequences. The black arrows starting in two opposite directions from the proposed origin of replication (black dot) indicate the general direction of transcription, the two arrowheads mark the region on the genome where the direction of transcription is frequently changing. The numbers inside the coloured circle indicate the first and last M.genitalium ORF (MG is omitted) of each of the six DNA segments with conserved gene order. For this illustration the M.genitalium sequence was reverse complemented and the putative origin of replication was oriented in the "3 'o' clock" position.
This figure shows that the general transcription orientation is very conserved in these two bacteria and that the proposed genomic recombination took only place in one half of the genome. For clearness, the ORFs which are transcribed contrary to the general direction of transcription have not been indicated.
In a higher resolution you can see here the MP-Genome with the ORFs
and GC-curve in segments of each 100 kB.
The GC content of each ORF is listed in
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