Mycobacterium ulcerans
Mycobacterium marinum
Mycobacterium smegmatis
M.ulcerans genome
See GC%
M.marinum genome
See GC%
M.smegmatis genome
See GC%
MYCOBACTERIAL IDENTIFICATION BY MEANS OF MYCOLIC ACID HPLC
Mycobacterium ulcerans
Mycobacterium marinum
Mycobacterium smegmatis
I am of the opinion that Mycobacterium marinum may be the valid alternative to Mycobacterium smegmatis for growing and isolating phages with a potential action on Mycobacterium ulcerans.
The reasons are:
1)Short duplication time ( about 4 hours respect to 32 hours for M.ulcerans),
2)The supposed descent from M.marinum.
!!!These two last features represent a new direction for my research.
Some information:
Mycobacterium marinum from Wikipedia
Mycobacterium smegmatis from Wikipedia
Mycobacterium marinum from Medscape(1)
Mycobacterium marinum from Medscape(2)
My "in silico " results:
Alignments by MAUVE software
By Mauve software: Alignment of Conserved Genomic Sequence with Rearrangements from Multiple Genome Evolution Laboratory ( University Wisconsin-Madison) it is possible to verify this supposition in easy way because this alignment software uses the Locally Collinear Blocks .
Locally Collinear Blocks (LCBs )
Because recombination can cause genome rearrangements, orthologous regions of one genome may be reordered or inverted relative to another genome. During the alignment process, Mauve identifies conserved segments that appear to be internally free from genome rearrangements. Such regions are referred to as Locally Collinear Blocks (LCBs). Mauve requires that each collinear region of the alignment meets a "minimum weight" criteria. The weight of an LCB is defined as the sum of the lengths of matches in that LCB. Mauve removes matches composing low-weight LCBs from the set of alignment anchors before completing the alignment. The minimum LCB weight is a user-definable parameter, and by default Mauve chooses this value to be 3 times the minimum match size. The minimum LCB weight must be manually determined for accurate estimation of genomic rearrangement.
Genome sequence files can be given to Mauve in any of FastA, Multi-FastA, GenBank flat file, or raw formats. A display mode is available that colors regions conserved among all genomes differently than regions conserved among subsets of the genomes.
M.ulcerans and M.marinum:
M.marinum and M.smegmatis:
M.ulcerans and M.smegmatis:
M.ulcerans ,M.smegmatis and M.marinum:
Identity Matrix
Sequence Identity Matrix:
basebybase software:
NB: the percentage of identity betwen M. marinum and M.smegmatis is higher than percentage betwen M.marinum and M.ulcerans.
Dot plot by Gepard software
M.ulcerans and M.marinum:
M.marinum and M.smegmatis:
M.ulcerans and M.smegmatis:
