Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology
ReviewBAC libraries and comparative genomics of aquatic chordate species☆
Section snippets
What are BAC libraries?
Bacterial artificial chromosomes are based on plasmid vectors that are essentially composed of an F-factor origin of replication with a chloramphenicol resistance gene (Fig. 1) (Shizuya et al., 1992, Osoegawa et al., 1998, Amemiya et al., 1999). The F-factor replicon allows propagation of the bacterial plasmid as a single copy entity in Escherichia coli, thus permitting stable propagation of cloned inserts greater than 100 kilobase pairs (kb).1
Who sponsors BAC library construction?
Due to the high cost and considerable expertise required in making BAC libraries, most libraries are generated in specialty laboratories5 through contract-type mechanisms from federal granting agencies (predominantly NIH and NSF). In this
What BAC libraries are currently available?
BAC libraries have now been generated from several metazoan species, including both protostomes and deuterostomes. Table 1 lists BAC libraries from aquatic chordate species, many of these libraries being constructed in our laboratory. While it is difficult to keep an accurate accounting of all the libraries that are now in existence, BAC libraries made or being made as part of the NSF BAC program are listed at http://www.nsf.gov/bio/pubs/awards/bachome.htm; libraries made or being made as part
Utility of BAC libraries and comparative genomics
BAC libraries are very useful for many applications in modern biology: isolation of intact genes or gene clusters from regions of interest (Kim et al., 2000, Chiu et al., 2002, Chiu et al., 2004, Powers and Amemiya, 2004), whole genome physical mapping (Chen et al., 2004), elucidating gene organization (Amores et al., 1998, Strong et al., 1999), positional cloning (Brownlie et al., 1998, Donovan et al., 2000), long range DNA sequencing and anchoring (Mahairas et al., 1999, Lander et al., 2001,
Summary
BAC libraries are collections of large exogenous DNA inserts cloned into stable plasmid vectors and propagated in E. coli. The libraries are extremely useful for biological investigation and programs have been initiated to develop more BAC resources for the community. BACs have become exceedingly useful for the comparative genomic approach wherein orthologous regions are compared and contrasted between different taxa in order to begin to understand the logic of genome organization and
Acknowledgements
We thank the members of the Amemiya laboratory. Our laboratory is funded, in part, by National Institutes of Health (RR14085, HG02526-01), the National Science Foundation (IBN-0207870, IBN-0321461) and the United States Department of Energy (DE-FG03-01ER63273).
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This paper is based on a presentation given at the conference: Aquatic Animal Models of Human Disease hosted by the American Type Culture Collection and the University of Miami in Manassas, Virginia, USA, September 29–October 2, 2003.