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Marine Biotechnology

, Volume 8, Issue 5, pp 521–533 | Cite as

New Resources for Marine Genomics: Bacterial Artificial Chromosome Libraries for the Eastern and Pacific Oysters (Crassostrea virginica and C. gigas)

  • Charles CunninghamEmail author
  • Jun-ichi Hikima
  • Matthew J. Jenny
  • Robert W. Chapman
  • Guang-Chen Fang
  • Chris Saski
  • Mats L. Lundqvist
  • Rod A. Wing
  • Pauline M. Cupit
  • Paul S. Gross
  • Greg W. Warr
  • Jeff P. Tomkins
Original Article

Abstract

Large-insert genomic bacterial artificial chromosome (BAC) libraries of two culturally and economically important oyster species, Crassostrea virginica and C. gigas, have been developed as part of an international effort to develop tools and reagents that will advance our ability to conduct genetic and genomic research. A total of 73,728 C. gigas clones with an average insert size of 152 kb were picked and arrayed representing an 11.8-fold genome coverage. A total of 55,296 clones with an average insert size of 150 kb were picked and arrayed for C. virginica, also representing an 11.8-fold genome coverage. The C. gigas and C. virginica libraries were screened with probes derived from selected oyster genes using high-density BAC colony filter arrays. The probes identified 4 to 25 clones per gene for C. virginica and 5 to 50 clones per gene for C. gigas. We conducted a preliminary analysis of genetic polymorphism represented in the C. gigas library. The results suggest that the degree of divergence among similar sequences is highly variable and concentrated in intronic regions. Evidence supporting allelic polymorphism is reported for two genes and allelic and/or locus specific polymorphism for several others. Classical inheritance studies are needed to confirm the nature of these polymorphisms. The oyster BAC libraries are publicly available to the research community on a cost-recovery basis at www.genome.clemson.edu.

Keywords

BAC library crassostrea gigas crassostrea virginica oysters 

Notes

Acknowledgments

We thank members of the Oyster Genome Consortium whose efforts resulted in the funding of the White Paper (http://www.genome.gov/10001852) advocating the construction of the oyster BAC libraries. Construction of the libraries was supported by the NIH Healthy People 2010 BAC library construction program of the National Human Genome Research Institute. The characterization of the libraries was supported as part of an Oceans and Human Health Initiative award from NOAA and by the Ernest F. Hollings Visiting Scholar Program at the Hollings Marine Laboratory, Charleston, SC. We thank Barry Ledford for access to his dock on Wadmalaw Sound for the collection of Eastern oysters.

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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Charles Cunningham
    • 1
    • 5
    • 7
    Email author
  • Jun-ichi Hikima
    • 1
  • Matthew J. Jenny
    • 1
    • 6
  • Robert W. Chapman
    • 2
  • Guang-Chen Fang
    • 3
  • Chris Saski
    • 3
  • Mats L. Lundqvist
    • 1
  • Rod A. Wing
    • 4
  • Pauline M. Cupit
    • 1
    • 5
  • Paul S. Gross
    • 1
  • Greg W. Warr
    • 1
  • Jeff P. Tomkins
    • 3
  1. 1.Marine Biomedicine and Environmental Sciences Center and Department of Biochemistry and Molecular BiologyMedical University of South Carolina, Hollings Marine LaboratoryCharlestonUSA
  2. 2.Marine Resources Research InstituteSouth Carolina Department of Natural ResourcesCharlestonUSA
  3. 3.Clemson University Genomics InstituteClemsonUSA
  4. 4.Arizona Genomics InstituteTucsonUSA
  5. 5.Department of BiologyUniversity of New MexicoAlbuquerqueUSA
  6. 6.Department of BiologyWoods Hole Oceanographic InstitutionWoods HoleUSA
  7. 7.Department of BiologyUniversity of New MexicoNMUSA

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