Review
BAC libraries and comparative genomics of aquatic chordate species

https://doi.org/10.1016/j.cca.2004.07.001Get rights and content

Abstract

The bacterial artificial chromosome (BAC) system is useful for creating a representation of the genomes of target species. The system is advantageous in that it can accommodate exogenous inserts that are very large (>100 kilobases, kb), thereby allowing entire eukaryotic genes (including flanking regulatory regions) to be encompassed in a single clone. The interest in BACs has recently been spawned by vast improvements in high throughput genomic sequencing such that comparisons of orthologous regions from different genomes (comparative genomics) are being routinely investigated, and comprise a significant component, of all major sequencing centers. In this review, we discuss the general principles of BAC cloning, the resources that are currently available, and some of the applications of the technology. It is not intended to be an exhaustive treatise; rather our goal is to provide a primer of the BAC technology in order to make readers aware of these resources and how they may utilize them in their own research programs.

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).

References (91)

  • T. Miya et al.

    An ascidian homologue of vertebrate BMPs 5–8 is expressed in the midline of the anterior neuroectoderm and in the midline of the ventral epidermis of the embryo

    Mech. Dev.

    (1996)
  • K. Osoegawa et al.

    An improved approach for construction of bacterial artificial chromosome libraries

    Genomics

    (1998)
  • T.P. Powers et al.

    Evidence for Hox 14 paralog group in vertebrates

    Curr. Biol.

    (2004)
  • G.H. Thorgaard et al.

    Status and opportunities for genomics research with rainbow trout

    Comp. Biochem. Physiol., B

    (2002)
  • C.T. Amemiya et al.

    Zebrafish YAC, BAC, and PAC genomic libraries

    Methods Cell Biol.

    (1999)
  • A. Amores et al.

    Zebrafish hox clusters and vertebrate genome evolution

    Science

    (1998)
  • A. Amores et al.

    Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish

    Genome Res.

    (2004)
  • S. Baxendale et al.

    Comparative sequence analysis of the human and pufferfish Huntington's disease genes

    Nat. Genet.

    (1995)
  • S. Brenner et al.

    Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome

    Nature

    (1993)
  • A. Brownlie et al.

    Positional cloning of the zebrafish sauternes gene: a model for congenital sideroblastic anaemia

    Nat. Genet.

    (1998)
  • R.L. Carroll

    Vertebrate Paleontology and Evolution

    (1988)
  • R. Chen et al.

    Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project

    Genome Res.

    (2004)
  • C.H. Chiu et al.

    Molecular evolution of the HoxA cluster in the three major gnathostome lineages

    Proc. Natl. Acad. Sci. U. S. A.

    (2002)
  • C.H. Chiu et al.

    Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution

    Genome Res.

    (2004)
  • J.A. Clark

    Gaining ground: the origin and early evolution of tetrapods

    (2002)
  • M.J. Cohn

    Lamprey Hox genes and the origin of jaws

    Nature

    (2002)
  • F.S. Collins et al.

    A vision for the future of genomics research

    Nature

    (2003)
  • J. Danke et al.

    Genome resource for the indonesian coelacanth. Latimeria menadoensis

    J. Exp. Zool.

    (2004)
  • G.R. de Beer

    The Development of the Vertebrate Skull

    (1985)
  • P. Dehal et al.

    The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins

    Science

    (2002)
  • R.J. DiLeone et al.

    Efficient studies of long-distance Bmp5 gene regulation using bacterial artificial chromosomes

    Proc. Natl. Acad. Sci. U. S. A.

    (2000)
  • A. Donovan et al.

    Positional cloning of zebrafish ferroportin1 identifies a conserved vertebrate iron exporter

    Nature

    (2000)
  • A. Force et al.

    Preservation of duplicate genes by complementary, degenerative mutations

    Genetics

    (1999)
  • Force, A., Shashikant, C., Stadler, P., and Amemiya, C.T., Comparative genomics, cis-regulatory elements, and gene...
  • P. Forey et al.

    Agnathans and the origin of jawed vertebrates

    Nature

    (1993)
  • S. Gong et al.

    A gene expression atlas of the central nervous system based on bacterial artificial chromosomes

    Nature

    (2003)
  • A. Gorbman et al.

    Early development of oral, olfactory and adenohypophyseal structures of reproduction in hagfish

  • B.K. Hall

    Developmental processes underlying heterochrony as an evolutinary mechanism

    Can. J. Zool.

    (1984)
  • B.K. Hall

    Evolutionary Developmental Biology

    (1998)
  • B.K. Hall

    The Neural Crest in Development and Evolution

    (1999)
  • M. Hammerschmidt et al.

    Genetic analysis of dorsoventral pattern formation in the zebrafish: requirement of a BMP-like ventralizing activity and its dorsal repressor

    Genes Dev.

    (1996)
  • J.D. Hansen et al.

    Lymphocyte development in fish and amphibians

    Immunol. Rev.

    (1998)
  • G.S. Helfman et al.

    The diversity of fishes

    (1997)
  • P.W. Holland et al.

    Evolution of regional identity in the vertebrate nervous system

    Perspect. Dev. Neurobiol.

    (1995)
  • N.D. Holland et al.

    Engrailed expression during develpment of a lamprey, Lampetra japonica: a possible clue to homologies between agnathan and gnathostome muscles of the mandibular arch

    Dev. Growth Differ.

    (1993)
  • Cited by (0)

    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.

    View full text