Characterization of expressed sequence tag-derived single-nucleotide polymorphisms in the bay scallop Argopecten irradians irradians

Fisheries Science

Volumn 75, Issue 6, 2009, Pages 1389-1400

  Li, Ronghua ^a   Li, Qi ^a   Kong, Lingfeng ^a  

^a OCEAN UNIVERSITY OF CHINA   (China)

Author keywords

Argopecten irradians irradians; Codon bias; Parentage; Single nucleotide polymorphism

Indexed keywords

ARGOPECTEN IRRADIANS; ARGOPECTEN IRRADIANS IRRADIANS; TETRA;

EID: 76349100282     PISSN: 09199268     EISSN: 14442906     Source Type: Journal    
DOI: 10.1007/s12562-009-0167-0     Document Type: Article

References (38)

1. Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA, Boyce-Jacino M (1999) Mining SNPs from EST databases. Genome Res 9: 167-174.
2. Gupta PK, Roy JK, Prasad M (2001) Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr Sci 80: 524-535.
3. Rafalski JA (2002) Application of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5: 94-100.
4. Morin PA, Luikart G, Wayne RK, the SNP Workshop Group (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19: 208-216.
5. Landegren U, Nilsson M, Kwok PY (1998) Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. Genome Res 8: 769-776.
6. Kota R, Varshney RK, Thiel T, Dehmer KJ, Graner A (2001) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135: 145-151.
7. Useche FJ, Gao G, Harafey M, Rafalski A (2001) High-throughput identification, database storage and analysis of SNPs in EST sequences. Genome Inform 12: 194-203.
8. Ye S, Dhillon S, Ke X, Collins AR, Day IN (2001) An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Res 29: e88.
9. Zhang FS, He YC, Liu XS, Ma JH, Li SY, Qi LX (1986) A report on the introduction, spat rearing and experimental culture of bay scallop, Argopecten irradians Lamarck. Ocean Limn Sin 17: 367-374 (in Chinese).
10. Zhang FS (2003) China aquaculture industry development in modern times and contemporary age: status and prospects. World Sci Tech R& D 25: 5-13 (in Chinese).
11. You FM, Huo N, Gu YQ, Luo M, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9: 253.
12. Li Q, Park C, Kijima A (2002) Isolation and characterization of microsatellite loci in the Pacific abalone, Haliotis discus hannai. J Shellfish Res 21: 811-815.
13. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16: 1099-1106.
14. Li R, Li Q, Yu R (2008) A set of polymorphic expressed sequence tag-derived microsatellites from the bay scallop, Argopecten irradians irradians, and their transportability in three other scallop species. J World Aquac Soc 39: 138-141.
15. Rice RW (1989) Analyzing tables of statistical tests. Evolution 43: 223-225.
16. Duret L, Mouchiroud D (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci 96: 4482-4487.
17. Song L, Xu W, Li C, Li H, Wu L, Xiang J, Guo X (2006) Development of expressed sequence tags from the Bay Scallop, Argopecten irradians irradians. Mar Biotechnol 8: 161-169.
18. Stenico MA, Lloyd T, Sharp PM (1994) Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucleic Acids Res 22: 2437-2446.
19. Umashankar V, Arunkumar V, Dorairaj S (2007) ACUA: a software tool for automated codon usage analysis. Bioinformation 2: 62-63.
20. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D (2001) A map of human genome sequence variation containing 1. 42 million single nucleotide polymorphisms. Nature 409: 928-933.
21. Hayes B, Laerdahl JK, Lien S, Moen T, Berg P, Hindar K, Davidson WS, Koop BF, Adzhubei A, Høyheim B (2007) An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences. Aquaculture 265: 82-90.
22. Sauvage C, Bierne N, Lapègue S, Boudry P (2007) Single nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas. Gene 406: 13-22.
23. Dantec LL, Chagné D, Pot D, Cantin O, Garnier-Ger P, Bedon F, Frigerio JM, Chaumeil P, Leger P, Garcia V, Laigret F, Daruvar A, Plomion C (2004) Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences. Plant Mol Biol 54: 461-470.
24. Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett H, Bowatte DR, Lawrence TJ, Rikkerink EHA, Gardiner SE, Korban SS (2008) Development of a set of SNP markers present in expressed genes of the apple. Genomics 92: 353-358.
25. Kim S, Misra A (2007) SNP genotyping: technologies and biomedical applications. Annu Rev Biomed Eng 9: 289-320.
26. Chiapparino E, Lee D, Donini P (2004) Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS-PCR. Genome 47: 414-420.
27. Syvanen AC (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2: 930-942.
28. Wang LL, Song LS, Zhang H, Gao Q, Guo XM (2007) Genetic linkage map of bay scallop, Argopecten irradians irradians (Lamarck 1819). Aquac Res 38: 409-419.
29. O'Reilly PT, Herbinger CM, Wright JM (1998) Analysis of parentage determination in Atlantic salmon (Salmo salar) using microsatellites. Anim Genet 29: 363-370.
30. Miggiano E, Deinnocentiis S, Ungaro A, Sola L, Crosetti D (2005) AFLP and microsatellites as genetic tags to identify cultured gilthead seabream escapees: data from a simulated floating cage breaking event. Aquac Int 13: 137-146.
31. Li Q, Park C, Kijima A (2003) Allelic transmission of microsatellites and application to kinship analysis in newly hatched Pacific abalone larvae. Fish Sci 69: 883-889.
32. Anderson EC, Garza JC (2006) The power of single nucleotide polymorphisms for large-scale parentage inference. Genetics 172: 2567-2582.
33. Vignal A, Milan D, SanCristobal M, Eggen A (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 34: 275-305.
34. Grantham R, Gautier C, Gouy M, Mercier R, Pave A (1980) Codon catalog usage and the genome hypothesis. Nucleic Acids Res 8: r49-r62.
35. Moriyama EN (2003) Codon usage, encyclopedia of the human genome. Macmillan Publishers, Nature Publishing Group, London. http://www. ehgonline. net.
36. Shields DC, Sharp PM, Higgins DG, Wright F (1988) 'Silent' sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol Biol Evol 5: 704-716.
37. Musto H, Cruveiller S, D'Onofrio G, Romero H, Bernardi G (2001) Translational selection on codon usage in Xenopus laevis. Mol Biol Evol 18: 1703-1707.
38. Tanguy A, Bierne N, Saavedra C, Pina B, Bachère E, Kube M, Bazin E, Bonhomme F, Boudry P, Boulo V, Boutet I, Cancela L, Dossat C, Favrel P, Huvet A, Jarque S, Jollivet D, Klages S, Lapègue S, Leite R, Moal J, Moraga D, Reinhardt R, Samain JF, Zouros E, Canario A (2008) Increasing genomic information in bivalves through new EST collections in four species: development of new genetic markers for environmental studies and genome evolution. Gene 408: 27-36.