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processes in a large number of species (
Kassen and Rainey, 2004
;
Mes, 2008
).
Until recently, however, population genetics studies have mostly employed a
very limited number of loci due to sequencing and labor expenses (
Butlin, 2010
).
With the present flood of new data unleashed by the arrival of affordable,
rapid, high-quality sequencing technologies, the focus is rapidly shifting from the
mechanics of generating sequence data to the problems of analyzing it. This cre-
ates an urgent need for better ways to compare and visualize genomic data (
Field
et al., 2006
). By analogy with the application of the Human Variome Database
(
Ring et al., 2006
), an important aim of microbial pathogenomics would be devel-
opment of a Microbial Variome Database (
Chattopadhyay et al., 2013
). Such a
database would constitute a species-specific genomic resource. The information
about all the changes in sequence, origin of isolation of the strains where such
changes accumulated and their potential adaptive values will bring bacterial evo-
lutionary genomics to a new level, both quantitatively and qualitatively, offering
broad applicability of population genomics tools to experimental research, clini-
cal diagnostics, epidemiology, and environmental control of pathogens. Similar
to the case with the human genome, such a database would be extremely helpful
to associate genetic variation in bacteria (such as gene presence/absence or muta-
tion) with the bacterial ability to cause disease and, thus, greatly contribute to
understanding virulence evolution. It would provide genome-wide information on
potential targets for vaccines, antibiotics, and other therapeutics development on
one hand, while on the other it would offer a global surveillance system to enable
rapid determination of newly emerging pathogenic clones and genetic mecha-
nisms behind the emergence.
REFERENCES
Escherichia coli
CoIV plasmid pRK100: genetic organization, stability and conjugal transfer.
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