Sequencing, assembly and comparative genomics of several Staphylococcus aureus strains

Laurent FALQUET, Sandra Calderon, Valérie Vogel, Patrick Basset, Dominique Blanc


Staphylococcus aureus is a well known opportunistic bacteria often found in hospital acquired infections. Understanding its microevolution should highlight the mechanism by which genetic factors might be transmitted, resulting in the emergence of new clones with specific biological characteristics, such as pathogenicity, virulence, or antibiotic resistance. Comparative genomics of different strains should allow the identification of the genetic basis of such characteristics. When the strains are closely related, the direct comparison of the contigs obtained by de novo assembly might be unsatisfactory and the comparison with a reference genome could be required. However assembling by mapping onto a reference genome often only identifies the similarities, one must carefully analyse the non-matched orphaned reads in order to identify the real differences.We present preliminary results of Ultra High Throughput Illumina sequencing and comparison by mapping onto a reference genome, as well as de novo assembly of non-mapped reads.


Ultra High Throughput Sequencing; Comparative genomics; Staphylococcus aureus;


Klucar, L., Stano, M., Hajduk, M. (2010): phiSITE: Database of Gene Regulation in Bacteriophages. Nucleic Acids Res. 38(Database Issue): D366-D370.


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