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Comparative genome

Staphylococcus haemolyticus JCSC1435


reference genomedotplotortholog listcomparative map
Staphylococcus epidermidis ATCC 12228ListMap
Staphylococcus epidermidis RP62AListMap

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Hundreds of microbial genomes have already been completely sequenced including those analyzed at NITE. To further enhance the usefulness of the results of genome analysis, we added a new feature to the DOGAN to present comparative genomics data.
Currently, the data for ten genomes of staphylococcal species are available, including three of those sequenced by us. A large portion of the open reading frames in these species appears to be conserved with respect to their sequence and synteny,(or, their shromosomal gene order)..

We analyzed the relationships among all genes/ORFs in the five staphylococcal genomes and the results were incorporated into the DOGAN.
You can compare genes/ORFs in the genomes listed bellow and get the syntenic regions or points of possible genomic rearrangements displayed in the dotplot viewer. In addition, we provide you with lists of putative orthologs ordered by their genomic locations, with which you may see, for example, if the target genes/ORFs of your interest exist in an operon or in a pathogenicity island etc. and are well conserved amongst the related species or not.


Target genomes
We prepared comparative genomics data for the following genomes, that have been selected for their biomedical interest (note that this analysis does not include ORFs of plasmids.)

Staphylococcus aureus N315 (NITE)
Staphylococcus aureus MW2 (NITE)
These are methicillin-resistant strains of Staphylococcus aureus (MRSA), one of the major causes, respectively, of hospital-acquired or community-acquired infections.

Staphylococcus haemolyticus JCSC1435 (NITE)
A multiply drug-resistant bacterium infecting human that has acquired resistance to methicillin and glycopeptide antibiotics such as Teicoplanin and Vancomycin.

Staphylococcus epidermidis ATCC 12228
Staphylococcus epidermidis RP62A
Two strains of Staphylococcus epidermidis, normally resident on our skin as well as in guts and upper respiratory tract. They are known as opportunistic pathogens.
The ORFs annotated in two S. epidermidis genomes (strains ATCC 12228 and RP62A) were extracted from the NCBI RefSeq and stored into the DOGAN as reference data.

Analytical criteria
Computational analysis was performed based on the following criteria.


Homologs

ORFs of S.aureus, S.epidermidis and S.haemolyticus were classified into mutually homologous groups.


Firstly, ORFs were grouped by using the NCBI-BLAST (blastn) program with a threshold value of 1e-6.
Within each group, ORFs with more than 70% "quality ratio" values reported by the 'Gap' alignment program (GCG Wisconsin package) were classified together to form a homolog group.
The data may be helpful to find ORFs of other species that show similarities with your targets.

A paralogous group was subsequently defined as a homology group that contains more than one ORF derived from a single genome.

Orthologs

For each group of homology, orthologous ORFs were predicted by bidirectional best hits when ORF X of a genome shows highest similarity of all genes of the genome with ORF Y of another genome used as query and vice versa, according to the results obtained by running the 'Gap' program.
We have prepared a list of putative orthologous ORFs of the genomes listed above. You can see the list sorted by gene order of the target genome of your interest.