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http://dx.doi.org/10.9710/kjm.2014.30.3.197

Transferability of Cupped Oyster EST (Expressed Sequence Tag)-Derived SNP (Single Nucleotide Polymorphism) Markers to Related Crassostrea and Ostrea Species  

Kim, Woo-Jin (Biotechnology Research Division, National Fisheries Research and Development Institute)
Jung, Hyungtaek (Science and Engineering Faculty, Queensland University of Technology)
Shin, Eun-Ha (Biotechnology Research Division, National Fisheries Research and Development Institute)
Baek, Ilseon (Division of Marine Technology, Chonnam National University)
Publication Information
The Korean Journal of Malacology / v.30, no.3, 2014 , pp. 197-210 More about this Journal
Abstract
Single nucleotide polymorphisms (SNPs) are widely acknowledged as the marker of choice for many genetic and genomic applications because they show co-dominant inheritance, are highly abundant across genomes and are suitable for high-throughput genotyping. Here we evaluated the applicability of SNP markers developed from Crassostrea gigas and C. virginica expressed sequence tags (ESTs) in closely related Crassostrea and Ostrea species. A total of 213 putative interspecific level SNPs were identified from re-sequencing data in six amplicons, yielding on average of one interspecific level SNP per seven bp. High polymorphism levels were observed and the high success rate of transferability show that genic EST-derived SNP markers provide an efficient method for rapid marker development and SNP discovery in closely related oyster species. The six EST-SNP markers identified here will provide useful molecular tools for addressing questions in molecular ecology and evolution studies including for stock analysis (pedigree monitoring) in related oyster taxa.
Keywords
SNPs; EST; Crassostrea; Ostrea; Transferability; Type I markers;
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1 Reece, K.S., Cordes, J.F., Stubbs, J.B., Hudson, K.L. and Francis, E.A. (2008) Molecular phylogenies help resolve taxonomic confusion with Asian Crassostrea oyster species. Marine Biotechnology, 153: 709-721.
2 Ronquist, F. and Huelsenbeck, J.P. (2003) MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1572-1574.   DOI   ScienceOn
3 Small, K.S., Brudno, M, Hill, M.M. and Sidow, A. (2007) Extreme genomic variation in a natural population. Proceedings of the National Academy Sciences of the United States of America, 104: 5698-5703.   DOI   ScienceOn
4 Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22: 2688-2690.   DOI   ScienceOn
5 Takahashi, N., Hayano, T. and Suzuki, M. (1989) Peptidyl-prolylcis-trans isomerase is the cyclosporin A-binding protein cyclophilin. Nature, 337: 473-475.   DOI   ScienceOn
6 Tamura, K., Peterson, D., Peterson, N., Nei, G. and Kumar, S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology Evolution, 28: 2731-2739.   DOI   ScienceOn
7 Zhang, L.S. and Guo, X.M. (2010) Development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea virginica Gmelin by mining ESTs and resequencing. Aquaculture, 302: 124-129.   DOI   ScienceOn
8 Zhang, G., Fang, Z., Guo, X., Luo, R., Xu, F., Yang, P. and Zhang, L. et al. (2012) The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 490: 49-54.   DOI
9 Amaral, A.R., Coelho, M.M., Marugan-Lobon, J. and Rohlf, F.J. (2009) Cranial shape differentiation in three closely related delphinid cetacean species: insights into evolutionary history. Zoology, 112: 38-47.   DOI   ScienceOn
10 Behereqaray, L.B. (2008) Twenty years of phylogeography: The state of the field and the challenges for the Southern Hemisphere. Molecular Ecology, 17: 3754-3774.
11 Baldauf, S.L., Palmer, J.D. and Doolittle, W.F. (1996) The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proceedings of the National Academy Sciences of the United States of America, 93: 7749-7754.   DOI   ScienceOn
12 Ban, N., Nissen, P., Hansen, J., Moore, P.B. and Steitz, T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science, 289: 905-920.   DOI   ScienceOn
13 Barbazuk, W.B., Emrich, S.J., Chen, H.D., Li, L. and Schnable, P.S. (2007) SNP discovery via 454 transcriptome sequencing. Plant Journal, 51: 910-918.   DOI   ScienceOn
14 Gadagkar, S.R., Rosenberg, M.S. and Kumar, S. (2005) Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree. Journal of Experimental Zoology Part B: Molecular and Development Evolution, 304: 64-74.
15 Bouck, A. and Vision, T. (2007) The molecular ecologist's guide to expressed sequence tags. Molecular Ecology, 16: 907-924.
16 Jenny, M., Chapman, R., Mancia, A., Chen, Y.-A., McKillen, D., Trent, H., Lang, P., Escoubas, J.-M., Bachere, E., Boulo, V., Liu, J., Cunningham, C., Cupit, P., Tanguy, A., Guo, X., Moraga, D., Boutet, I., Huvet, A., De Guise, S., Almeida, J. and Warr, G.A. (2007) A cDNA Microarray for Crassostrea virginica and C. gigas. Marine Biotechnology, 9: 577-591.   DOI   ScienceOn
17 Cutter, A.D., Baird, S.E. and Charlesworth, D. (2006) High nucleotide polymorphism and rapid decay of linkage disequilibrium in wild populations of Caenorhabditis remanei. Genetics, 174: 901-913.   DOI   ScienceOn
18 FAO. (2013) Fisheries and Aquaculture Statistical Databases, Global Aquaculture Production (online query).
19 Galat, A. (1999) Variations of sequences and amino acid compositions of proteins that sustain their biological functions: An analysis of the cyclophilin family of proteins. Archives of Biochemistry and Biophysics, 371: 149-162.   DOI   ScienceOn
20 Kim, W.J., Dammannagoda, S.T., Jung, H., Baek, I.S., Yoon, H.S. and Choi, S.D. (2014) Mitochondrial DNA sequence analysis from multiple gene fragments reveals genetic heterogeneity of Crassostrea ariakensis in East Asia. Genes and Genomics, 36: 611-627   DOI   ScienceOn
21 Jung, H., Kim, W.J. and Gaffney, P.M. (2006) Development of single nucleotide polymorphisms (SNPs) in Crassostrea ariakensis and related Crassostrea species. Journal of Shellfish Research, 25: 742.
22 Jung, H., Lyons, R.E., Li, Y., Thanh, N.M., Dinh, H., Hurwood, D.A., Salin, K.R. and Mather, P.B. (2014) A candidate association study for growth performance in an improved giant freshwater prawn (Macrobrachium rosenbergii) culture line. Marine Biotechnology, 16: 161-180.   DOI   ScienceOn
23 Lee, H., Cha, S., Lee, M., Cho, G.J., Choi, W.S. and Suk, H. (2003) Role of antiproliferative B cell translocation gene-1 as an apoptotic sensitizer in activation-induced cell death of brain microglia. Journal of Immumology, 171: 5802-5811.
24 Kim, W.J., Jung, H. and Gaffney, P.M. (2011) Development of type I genetic markers from expressed sequence tags in highly polymorphic species. Marine Biotechnology, 13: 127-132.   DOI
25 Lambeth, D.O., Mehus, J.G., Ivey, M.A. and Milavetz, B.I. (1997) Characterization and cloning of a nucleotide-diphosphate kinase targeted to matrix of mitochondrial in Pigeon. Journal of Biological Chemistry, 272: 24604-24611.   DOI   ScienceOn
26 Langdon, C., Evans, F., Jacobson, D. and Michael. B. (2003) Yields of cultured Pacific oysters Crassostrea gigas Thunberg improved after one generation of selection. Aquaculture, 220: 227-244.   DOI   ScienceOn
27 Li, L. and Guo, X. (2004) AFLP-based genetic linkage maps of the Pacific oyster Crassostrea gigas Thunberg. Marine Biotechnology, 6: 26-36.   DOI   ScienceOn
28 Librado, P. and Rozas, J. (2009) DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25: 1451-1452.   DOI   ScienceOn
29 Li, W., Rusiniak, M.E., Chintala, S., Gautam, R., Novak, E.K. and Swank, R.T. (2004) Murine Hermansky-Pudlak syndrome genes: regulators of lysosome-related organelles. BioEssays, 26: 616-628.   DOI   ScienceOn
30 Li, Q. and Wan, J. M. (2005) SSRHunter: development of a local searching software for SSR sites. Hereditas, 27: 808-810.
31 Li, Q., Liu, S. and Kong, L. (2009) Microsatellites within genes and ESTs of the Pacific oyster Crassostrea gigas and their transferability in five other Crassostrea species. Electronic Journal of Biotechnology, 12: 1-7.
32 Obata, M., Shimizu, M., Sano, N. and Komaru, A. (2008) Maternal inheritance of mitochondrial DNA (mtDNA) in the Pacific oyster (Crassostrea gigas): a preliminary study using mtDNA sequence analysis with evidence of random distribution of MitoTracker-stained sperm mitochondira in fertilized eggs. Zoological Science, 25: 248-254.   DOI   ScienceOn
33 Morin, P.A., Luikart, G., Wayne, R.K. and the SNP workshop group. (2004) SNPs in ecology, evolution and conservation. Trends in Ecology and Evolution, 19: 208-216.   DOI   ScienceOn
34 Morin, P. A. and McCarthy, M. (2007) Highly accurate SNP genotyping from historical and low-quality samples. Molecular Ecology Notes, 7: 937-946.   DOI   ScienceOn
35 Morton, B.R., Bi, I.V., McMullen, M.D. and Gaut, B.S. (2006) Variation in mutational dynamics across the maize genome as a function of regional and flanking base composition. Genetics, 172: 569-577.
36 Peters, I.R., Peeters, D., Helps, C.R. and Day, M.J. (2007) Development and application of multiple internal reference (housekeeper) gene assays for accurate normalization of canine gene expression studies. Veterinary Immunology Immunopathology, 117: 55-66.   DOI   ScienceOn
37 Sauvage, C., Bierne, N. and Boudry, P. (2007) Single nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas. Gene, 406: 13-22.   DOI   ScienceOn
38 Quilang, W., Wang, S., Li, P., Abernathy, J., Peatman, E., Wang, Y., Wang, L., Shi, Y., Wallace, R., Guo, X. and Liu, Z. (2007) Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers. BMC Genomics, 8: 157-167.   DOI   ScienceOn
39 Fleury, E., Huvet, A. Lelong, C., de Lorgeril, J., Boulo, V., Gueguen, Y., Bachere, E., Tanguy, A., Moraga, D., Fabioux, C., Lindeque, P., Shaw, J., Reinhardt, R., Prunet, P., Davey, G., Lapegue, S., Sauvage, C., Corporeau, C., Moal, J., Gavory, F., Wincker, P., Moreews, F., Klopp, C., Mathieu, M., Boudry, P. and Favrel, P. (2009) Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the Gigas Database. BMC Genomics, 10: 341-355.   DOI   ScienceOn