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Bacterial Genomes Dynamics

Starting from a common pool of highly conserved genetic information, still shared by all the extant life forms, genomes have been shaped to a considerable extent during their 4/3.5 billion years long  evolution, leading to the great diversification of life (and genomes) that we observe nowadays. This raises the intriguing question of how both genome complexity and size could have been increased during evolution. In other words, which are the molecular mechanisms that drove the evolution of the earliest genes and genomes? We are deeply interested in understanding  these evolutionary dynamics and the molecular mechanisms that shape and have shaped genomes. Beside its evolutionary relevance, this topic has also other drawbacks. Indeed, the mechanisms that have permitted genome expansion and metabolism assembly are the very same that are responsible for other phenomena that we daily observe around us, such as the emergence of multidrug resistant bacteria or the occurrence of genetic disorders in humans. Sometimes, the molecular events responsible for these processes leave their traces on the chromosomes of living organisms. As a consequence, their incidence, their frequency and even their smallest details can be studied and modelled combining genomics and computational biology tools (see here a definition of computational biology and/or bioinformatics, http://en.wikipedia.org/wiki/Computational_biology) to scan sequenced genomes. 

 

Bacterial genomics 

We are currently involved in several genomics projects, including those focused on Sinorhizobium melilotiAcinetobacter venetianus and Pseudoalteromonas haloplankits bacterial species.

1471-2164-12-235-3 1471-2164-12-235-4

L-R: Structure of S. meliloti genomes - Regions of Rm1021 pSymA megaplasmid (red circle) and regions ansent in the genomes of strains AK83 and BL225C (green bars) 

 

Horizontal gene transfer and bacterial evolution 

Furthermore, our research is also focused on the study of the degree of horizontal gene transfer HGT within bacterial communities with a special interest in the intra- and interspecific transfer of plasmid molecules harbouring genes involved in catabolic and in antibiotic resistance processes. In particular, we have developed and we are still implementing softwares for a network-oriented representation of HGT events.

actinogamma_small                  plasnet_small

L-R: Horizontal gene transfer between Actinobacteria and Gammaproteobacteria plasmids  -  Gene sharing network among bacterial plasmids

 

Genomics software development

Finally, the in-house development of computational biology tools to be used for comparative studies is another major goal in our research activity (see Developed Software section)

 
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