The Virtual Genome Project

The Virtual Genome Project (VGP) was established as a free resource on the world wide web for people interested in the process of horizontal gene transfer (HGT) between bacteria and its ecological and evolutionary significance. The “virtual genome” (VG) is the genetic information that is shared by a broad spectrum of bacterial species by means of various mechanisms of horizontal gene transfer. It is a pool of genes that is not restricted to specific bacteria, but is widely accessible by many. The focus of the site is on plasmids. For basic information on bacteria, DNA, and gene transfer mechanisms, we have created the Teachers/Students section, which also includes links to exciting lesson plans and definitions of many relevant terms. For those interested in digging deeper into current research about horizontal gene transfer and mobile genetic elements, we've created the Plasmids and Phage sections, as well as About Top Lab, which gives insight into one of the premier plasmid research laboratories, that of Dr. Eva Top at the University of Idaho. As an additional tool for those interested in groundbreaking plasmid research, we have created an active blog that hosts posts and comments about recently published research in the field of HGT.


We should no longer think of bacteria as having static genomes that only change slowly over time due to mutations. It is now clear that horizontal (or lateral) gene transfer between closely and even very distantly related bacteria plays a very important role in their evolution, and in their rapid adaptation to changing environments. The most well-known example of bacterial adaptation by HGT is the rapid spread of resistance against all kinds of antibiotics among pathogens, which makes it increasingly difficult to treat infections that used to be easily cured with a few days' worth of drugs. Another example that is relevant to our daily lives is the transfer of genes that let bacteria degrade some of the harmful pollutants that we use and that seep into our environment, like the herbicides you may spray on your lawn, or compounds in petroleum products (1).

The genes that code for antibiotic resistance and metal resistance, UV resistance pollutant degradation, virulence and many other traits are part of the virtual genome. The VG also includes the mobile genetic elements (MGE) that mediate the horizontal transfer of these genes. These can be divided in two groups. First there are the MGE that can transfer BETWEEN bacterial cells, and therefore are critical in horizontal gene transfer, such as plasmids, bacteriophages, conjugative transposons, and other integrative and conjugative elements (ICE). Plasmids mediate transfer by conjugation, and phage mediate transfer be way of transduction. The second group of MGE promotes gene movement WITHIN bacterial cells, for example within a chromosome, within a plasmid, or between a chromosome and plasmid. This group consists of various classes of transposons, integronsw, and insertion sequences (IS elements). Together, all these MGE and ICE provide the mechanisms needed for bacteria to access the Virtual Genome.

References:

  1. Thomas, C. M. 2000. The horizontal gene pool. Bacterial plasmids and gene spread. Harwood Academic Publishers, Amsterdam.

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The Virtual Genome Project is funded by the National Science Foundation Microbial Genome Sequencing Program, Grant number: EF-0627988.
For more information contact: Dr. Eva Top, Professor of Biology, Department of Biological Sciences, University of Idaho, Moscow, I.D. 83844-3051 U.S.A.
email: etop [at] uidaho.edu

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