Population Genetics and Genomics of Pathogenic Bacteria Monomorphic Groups

Population Genetics and Genomics of Pathogenic Bacteria Monomorphic Groups

Funding Body (EPA, FP7, etc): SFI

Project type (PhD, post-doc, etc): post-doc

Period (start to end):  Oct-07 – Oct-12

Researcher: Camilla Mazzoni

Project Description 

My work consists mainly on analysing the population structure of monomorphic bacteria species/groups. Due to the lack of variation in the DNA sequence of these groups, we screen entire genomes in order to find polymorphisms in the species. Since the number of genomes is generally low (e.g., 17 for Yersinia pestis), we try to choose genomes that are thought to be representative of the species tree. In this way, we minimize the bias effect on exploiting variation that is limited to the number and evolutionary history of the genomes.

The second phase of the projects consists in genotyping worldwide collections for the positions where variation was found. First, we exclude from the analyses repetitive elements or genes, and any identifiable high complexity region. After the edition of the genotyping data for all the strains collection, we are able to build minimum spanning trees in order to help us understand the population structure of a given species or group. Knowing the evolutionary history based on “neutral” SNPs allow us to infer many of the historical events which the species went through.

Publications

Holt, K.E., Parkhill J., Mazzoni C.J., Roumagnac P., Weill F.X., Goodhead I., Rance R., Baker S., Maskell D.J., Wain J., Dolecek C., Achtman M., Dougan G. (2008). High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nature Genetics 40:987-93.

Mazzoni C.J., Araki A.S., Ferreira G.E.M., Azevedo R.V.D.M., Barbujani G., Peixoto A.A. (2008)Multilocus analysis of introgression between two sand fly vectors of leishmaniasis. BMC Evol Biol. 8:141.

Mazzoni, C. J., Souza, N. A., Andrade-Coelho, C. Kyriacou, C. P., Peixoto, A. A. (2006). Molecular polymorphism, differentiation and introgression in the period gene between Lutzomyia intermedia and Lutzomyia whitmani (Diptera: Psychodidae). BMC Evol Biol. 6:85.

Davila, A.M.R., Lorenzini D.M., Mendes P.N., Satake T.S., Sousa G.R., Campos L.M., Mazzoni C.J., Wagner G.W., Pires P.F., Grisard E.C., Cavalcantis M.C.R., Campos M.L.M. (2005). GARSA: Genomic Analysis Resources for Sequence Annotation. Bioinformatics. 21:4302-4303.

Mazzoni, C. J., Gomes, C. A., Souza, N. A., Queiroz, R. G., Justiniano, S. C. B., Ward, R. D., Kyriacou, C. P., Peixoto, A. A. (2002). Molecular evolution of the period gene in sandflies. Journal of Molecular Evolution. 55(5):553-62.

Environmental Research Institute

University College Cork, Lee Road, Cork

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