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

다국어 초록 (Multilingual 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.

참고문헌 (Reference)

1 Langdon, C., "Yields of cultured Pacific oysters Crassostrea gigas Thunberg improved after one generation of selection" 220 : 227-244, 2003

2 Galat, A., "Variations of sequences and amino acid compositions of proteins that sustain their biological functions: An analysis of the cyclophilin family of proteins" 371 : 149-162, 1999

3 Morton, B. R., "Variation in mutational dynamics across the maize genome as a function of regional and flanking base composition" 172 : 569-577, 2006

4 Behereqaray, L. B., "Twenty years of phylogeography: The state of the field and the challenges for the Southern Hemisphere" 17 : 3754-3774, 2008

5 Baldauf, S. L., "The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny" 93 : 7749-7754, 1996

6 Zhang, G., "The oyster genome reveals stress adaptation and complexity of shell formation" 490 : 49-54, 2012

7 Bouck, A., "The molecular ecologist’s guide to expressed sequence tags" 16 : 907-924, 2007

8 Ban, N., "The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution" 289 : 905-920, 2000

9 Sauvage, C., "Single nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas" 406 : 13-22, 2007

10 Li, Q., "SSRHunter: development of a local searching software for SSR sites" 27 : 808-810, 2005

11 Morin, P. A., "SNPs in ecology, evolution and conservation" 19 : 208-216, 2004

12 Barbazuk, W. B., "SNP discovery via 454transcriptome sequencing" 51 : 910-918, 2007

13 Lee, H., "Role of antiproliferative B cell translocation gene-1 as an apoptotic sensitizer in activation-induced cell death of brain microglia" 171 : 5802-5811, 2003

14 Stamatakis, A., "RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models" 22 : 2688-2690, 2006

15 Takahashi, N., "Peptidyl-prolylcis–trans isomerase is the cyclosporin A-binding protein cyclophilin" 337 : 473-475, 1989

16 Li, W., "Murine Hermansky-Pudlak syndrome genes: regulators of lysosome-related organelles" 26 : 616-628, 2004

17 Ronquist, F., "MrBayes 3:bayesian phylogenetic inference under mixed models" 19 : 1572-1574, 2003

18 Reece, K. S., "Molecular phylogenies help resolve taxonomic confusion with Asian Crassostrea oyster species" 153 : 709-721, 2008

19 김우진, "Mitochondrial DNA sequence analysis from multiple gene fragments reveals genetic heterogeneity of Crassostrea ariakensis in East Asia" 한국유전학회 36 (36): 611-624, 2014

20 Li, Q., "Microsatellites within genes and ESTs of the Pacific oyster Crassostrea gigas and their transferability in five other Crassostrea species" 12 : 1-7, 2009

21 Obata, M., "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" 25 : 248-254, 2008

22 Tamura, K., "MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods" 28 : 2731-2739, 2011

23 Gadagkar, S. R., "Inferring species phylogenies from multiple genes:Concatenated sequence tree versus consensus gene tree" 304 : 64-74, 2005

24 Morin, P. A., "Highly accurate SNP genotyping from historical and low-quality samples" 7 : 937-946, 2007

25 Cutter, A. D., "High nucleotide polymorphism and rapid decay of linkage disequilibrium in wild populations of Caenorhabditis remanei" 174 : 901-913, 2006

26 Fleury, E., "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" 10 : 341-355, 2009

27 Quilang, W., "Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers" 8 : 157-167, 2007

28 FAO, "Fisheries and Aquaculture Statistical Databases, Global Aquaculture Production (online query)"

29 Small, K. S., "Extreme genomic variation in a natural population" 104 : 5698-5703, 2007

30 Librado, P., "DnaSP v5: A software for comprehensive analysis of DNA polymorphism data" 25 : 1451-1452, 2009

31 Kim, W. J., "Development of type I genetic markers from expressed sequence tags in highly polymorphic species" 13 : 127-132, 2011

32 Jung, H., "Development of single nucleotide polymorphisms (SNPs) in Crassostrea ariakensis and related Crassostrea species" 25 : 742-, 2006

33 Zhang, L.S., "Development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea virginica Gmelin by mining ESTs and resequencing" 302 : 124-129, 2010

34 Peters, I. R., "Development and application of multiple internal reference (housekeeper) gene assays for accurate normalization of canine gene expression studies" 117 : 55-66, 2007

35 Amaral, A. R., "Cranial shape differentiation in three closely related delphinid cetacean species:insights into evolutionary history" 112 : 38-47, 2009

36 Lambeth, D. O., "Characterization and cloning of a nucleotide-diphosphate kinase targeted to matrix of mitochondrial in Pigeon" 272 : 24604-24611, 1997

37 Li, L., "AFLP-based genetic linkage maps of the Pacific oyster Crassostrea gigas Thunberg" 6 : 26-36, 2004

38 Jung, H., "A candidate association study for growth performance in an improved giant freshwater prawn (Macrobrachium rosenbergii) culture line" 16 : 161-180, 2014

39 Jenny, M., "A cDNA Microarray for Crassostrea virginica and C. gigas" 9 : 577-591, 2007