New Resources for Marine Genomics: Bacterial Artificial Chromosome Libraries for the Eastern and Pacific Oysters (Crassostrea virginica and C. gigas)
- 250 Downloads
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.
KeywordsBAC library crassostrea gigas crassostrea virginica oysters
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.
- Ammiraju, JS, Luo, M, Goicoechea, JL, Wang, W, Kudrna, D, Mueller, C, Talag, J, Kim, H, Sisneros, NB, Blackmon, B, Fang, E, Tomkins, JB, Brar, D, MacKill, D, McCouch, S, Kurata, N, Lambert, GH, Galbraith, DW, Arumuganathan, K, Rao, K, Walling, JG, Gill, N, Yu, Y, San Miguel, P, Soderlund, C, Jackson, S, Wing, RA 2006The 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 Res16140147CrossRefGoogle 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
- Hedgecock, D, Li, G, Hubert, SK, Buckli, A, Ribes, V 2004Widespread null alleles and poor cross-species amplification of microsatellite DNA loci cloned from the Pacific oyster, Crassostrea gigas J Shellfish Res23379385Google Scholar
- Hedgecock, D, Gaffney, PM, Goulletquer, P, Gou, X, Reece, K, Warr, GW 2005The case for sequencing the Pacific oyster genomeJ Shellfish Res24429441Google Scholar
- Herpin, A, Lelong, C, Becker, T, Rosa, FM, Favrel, P, Cunningham, C 2005Structural 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 bilateriaMech Dev122695705CrossRefGoogle Scholar
- Herpin, A, Lelong, C, Becker, T, Rosa, F, Favrel, P, Cunningham, C 2005Structural and functional evidence for a singular repertoire of BMP receptor signal transducing proteins in the lophotrochozoan Crassostrea gigas suggests a shared ancestral BMP/activin pathwayFEBS J27234243440CrossRefGoogle 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. 536–546Google Scholar
- 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)