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

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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.

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References

  • JS Ammiraju M Luo JL Goicoechea W Wang D Kudrna C Mueller J Talag H Kim NB Sisneros B Blackmon E Fang JB Tomkins D Brar D MacKill S McCouch N Kurata GH Lambert DW Galbraith K Arumuganathan K Rao JG Walling N Gill Y Yu P San Miguel C Soderlund S Jackson RA Wing (2006) ArticleTitleThe Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza Genome Res 16 140–147 Occurrence Handle10.1101/gr.3766306

    Article  Google Scholar 

  • Curole JP, Hedgecock D (2005) High frequency of SNPs in the Pacific oyster genome. Available at: http://intl-pag. org/13/abstracts/PAG13_W026.html

  • Y Gueguen JP Cadoret D Flament C Barreau-Roumiguiee A Girardot J Garnier A Hoareau E Bachere JM Escoubas (2003) ArticleTitleImmune gene discovery by expressed sequence tags generated from hemocytes of the bacteria-challenged oyster, Crassostrea gigas Gene 303 139–145 Occurrence Handle10.1016/S0378-1119(02)01149-6

    Article  Google Scholar 

  • D Hedgecock G Li SK Hubert A Buckli V Ribes (2004) ArticleTitleWidespread null alleles and poor cross-species amplification of microsatellite DNA loci cloned from the Pacific oyster, Crassostrea gigas J Shellfish Res 23 379–385

    Google Scholar 

  • D Hedgecock PM Gaffney P Goulletquer X Gou K Reece GW Warr (2005) ArticleTitleThe case for sequencing the Pacific oyster genome J Shellfish Res 24 429–441

    Google Scholar 

  • A Herpin P Favrel C Cunningham (2002) ArticleTitleGene structure and expression of cg-ALR1, a type I activin-like receptor from the bivalve mollusc Crassostrea gigas Gene 301 21–30 Occurrence Handle10.1016/S0378-1119(02)01082-X

    Article  Google Scholar 

  • A Herpin C Lelong T Becker FM Rosa P Favrel C Cunningham (2005) ArticleTitleStructural and functional evidences for a type 1 TGF-beta sensu stricto receptor in the lophotrochozoan Crassostrea gigas suggest conserved molecular mechanisms controlling mesodermal patterning across bilateria Mech Dev 122 695–705 Occurrence Handle10.1016/j.mod.2004.12.004

    Article  Google Scholar 

  • A Herpin C Lelong T Becker F Rosa P Favrel C Cunningham (2005) ArticleTitleStructural and functional evidence for a singular repertoire of BMP receptor signal transducing proteins in the lophotrochozoan Crassostrea gigas suggests a shared ancestral BMP/activin pathway FEBS J 272 3424–3440 Occurrence Handle10.1111/j.1742-4658.2005.04761.x

    Article  Google Scholar 

  • S Hubert D Hedgecock (2004) ArticleTitleLinkage maps of microsatellite DNA markers for the Pacific oyster Crassostrea gigas Genetics 168 351–362 Occurrence Handle10.1534/genetics.104.027342

    Article  Google Scholar 

  • MJ Jenny AH Ringwood ER Lacy AJ Lewitus JW Kempton PS Gross GW Warr RW Chapman (2002) ArticleTitleIndicators of stress response identified by expressed sequence tag analysis of hemocytes and embryos from the American Oyster, Crassostrea virginica Mar Biotechnol 4 81–93 Occurrence Handle10.1007/s10126-001-0072-8

    Article  Google Scholar 

  • MJ Jenny AH Ringwood K Schey GW Warr RW Chapman (2004) ArticleTitleDiversity of metallothioneins in the American oyster, Crassostrea virginica, revealed by transcriptomic and proteomic approaches Eur J Biochem 271 1702–1712 Occurrence Handle10.1111/j.1432-1033.2004.04071.x

    Article  Google Scholar 

  • M Luo Y Wang D Frisch T Joobeur R Wing R Dean (2001) ArticleTitleMelon BAC library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium Wilt (Fom-2) Genome 44 154–162 Occurrence Handle10.1139/gen-44-2-154

    Article  Google Scholar 

  • CA Milbury PM Gaffney (2005) ArticleTitleComplete mitochondrial DNA sequence of the eastern oyster Crassostrea virginica Mar Biotechnol 7 697–712 Occurrence Handle10.1007/s10126-005-0004-0

    Article  Google Scholar 

  • Newell RIE (1988) Ecological changes in Chesapeake Bay: are they the result of overharvesting the eastern oyster (Crassostrea virginica)? In: Understanding the Estuary: Advances in Chesapeake Bay Research, Lynch MP, Krome EC, eds. Chesapeake Research Consortium Publication 129 (CBP/TRS 24/88), pp. 536–546

  • Peterson DG, Tomkins JP, Frisch DA, Wing RA, Paterson AH (2000) Construction of plant bacterial artificial chromosome (BAC) libraries: an illustrated guide. J Agric Genomics Vol 5. (http://www.ncgr.org/research/jag/index.html)

  • A Tanguy D Moraga (2001) ArticleTitleCloning and characterization of a gene coding for a novel metallothionein in the Pacific oyster Crassostrea gigas (CgMT2): a case of adaptive response to metal-induced stress? Gene 273 123–130 Occurrence Handle10.1016/S0378-1119(01)00577-7

    Article  Google Scholar 

  • A Tanguy X Guo SE Ford (2004) ArticleTitleDiscovery of genes expressed in response to Perkinsu0s marinus challenge in eastern (Crassostrea virginica) and Pacific (C. gigas) oysters Gene 38 121–131 Occurrence Handle10.1016/j.gene.2004.05.019

    Article  Google Scholar 

  • Y Wang Z Xu JC Pierce X Guo (2005) ArticleTitleCharacterization of eastern oyster (Crassostrea virginica Gmelin) chromosomes by fluorescence in situ hybridization with bacteriophage P1 clones Mar Biotechnol 7 207–214 Occurrence Handle10.1007/s10126-004-0051-y

    Article  Google Scholar 

  • Q Zhang SK Allen SuffixJr KS Reece (2005) ArticleTitleGenetic variation in wild and hatchery stocks of Suminoe Oyster (Crassostrea ariakensis) assessed by PCR-RFLP and microsatellite markers Mar Biotechnol 7 588–599 Occurrence Handle10.1007/s10126-004-5105-7

    Article  Google Scholar 

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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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  1. Charles Cunningham

    Present address: Department of Biology, University of New Mexico, NM, 87131, USA

Authors and Affiliations

  1. Marine Biomedicine and Environmental Sciences Center and Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Hollings Marine Laboratory, Charleston, SC, 29412, USA

    Charles Cunningham, Jun-ichi Hikima, Matthew J. Jenny, Mats L. Lundqvist, Pauline M. Cupit, Paul S. Gross & Greg W. Warr

  2. Marine Resources Research Institute, South Carolina Department of Natural Resources, Charleston, SC, 29412, USA

    Robert W. Chapman

  3. Clemson University Genomics Institute, Clemson, SC, 29634, USA

    Guang-Chen Fang, Chris Saski & Jeff P. Tomkins

  4. Arizona Genomics Institute, 303 Forbes Hall, Tucson, AZ, 85721, USA

    Rod A. Wing

  5. Department of Biology, University of New Mexico, 216 Castetter Hall, Albuquerque, NM, 87131, USA

    Charles Cunningham & Pauline M. Cupit

  6. Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543-1050, USA

    Matthew J. Jenny

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  1. Charles Cunningham
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Correspondence to Charles Cunningham.

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Cunningham, C., Hikima, Ji., Jenny, M.J. et al. New Resources for Marine Genomics: Bacterial Artificial Chromosome Libraries for the Eastern and Pacific Oysters (Crassostrea virginica and C. gigas). Mar Biotechnol 8, 521–533 (2006). https://doi.org/10.1007/s10126-006-6013-9

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  • DOI: https://doi.org/10.1007/s10126-006-6013-9

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