In silico mining and characterization of simple sequence repeats from gilthead sea bream (Sparus aurata) expressed sequence tags (EST-SSRs); PCR amplification, polymorphism evaluation and multiplexing and cross-species assays

Marine Genomics

Volumn 4, Issue 2, 2011, Pages 83-91

  Vogiatzi, Emmanouella ^a,b   Lagnel, Jacques ^a   Pakaki, Victoria ^a,c   Louro, Bruno ^d   V M Canario, Adelino ^d   Reinhardt, Richard ^e   Kotoulas, Georgios ^a   Magoulas, Antonios ^a   Tsigenopoulos, Costas S ^a  

^a INSTITUTE OF OCEANOGRAPHY   (Greece)

^b DEMOCRITUS UNIVERSITY OF THRACE   (Greece)

^c UNIVERSITY OF CRETE   (Greece)

^d UNIVERSITY OF ALGARVE   (Portugal)

^e MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

Cross species amplification; EST SSRs; Sparidae; Sparus aurata

Indexed keywords

PRIMER DNA;

ANIMAL; ARTICLE; COMPARATIVE STUDY; EXPRESSED SEQUENCE TAG; GENETIC DATABASE; GENETIC MARKER; GENETIC POLYMORPHISM; GENETICS; POLYMERASE CHAIN REACTION; SEA BREAM; SPECIES DIFFERENCE; VARIABLE NUMBER OF TANDEM REPEAT;

ANIMALS; DATABASES, GENETIC; DNA PRIMERS; EXPRESSED SEQUENCE TAGS; GENETIC MARKERS; MINISATELLITE REPEATS; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SEA BREAM; SPECIES SPECIFICITY;

ARCHOSARGUS RHOMBOIDALIS; CLUPEIFORMES; GADIFORMES; PERCIFORMES; SPARIDAE; SPARUS AURATA; TELEOSTEI; TETRA;

EID: 79956354483     PISSN: 18747787     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.margen.2011.01.003     Document Type: Article

References (57)

1. Alarcón J.A., Magoulas A., Georgakopoulos T., Zouros E., Alvarez M.C. Genetic comparison of wild and cultivated European populations of the gilthead sea bream (Sparus aurata). Aquaculture 2004, 230:65-80.
2. Avise J. Molecular Markers, Natural History and Evolution 2004, Sinauer Associates, Sunderland, MA, USA. 2nd ed.
3. Batargias C., Dermitzakis E., Magoulas A., Zouros E. Characterization of six polymorphic microsatellite markers in gilthead seabream, Sparus aurata (Linnaeus 1758). Mol. Ecol. 1999, 8:897-898.
4. Belkhir K., Borsa P., Goudet J., Chikhi L., Bonhomme F. GENETIX, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome et Populations, CNRS UPR 9060, Université de Montpellier II, Montpellier (France) 1998.
5. Bouza C., Hermida M., Millán A., Vilas R., Vera M., Fernández C., Calaza M., Pardo B.G., Martínez P. Characterization of EST-derived microsatellites for gene mapping and evolutionary genomics in turbot. Anim. Genet. 2008, 39:666-670.
6. Brown R.C., Tsalavouta M., Terzoglou V., Magoulas A., McAndrew B.J. Additional microsatellites for Sparus aurata and cross-species amplification within the Sparidae family. Mol. Ecol. Notes 2005, 5:605-607.
7. Castro J., Pino A., Hermida M., Bouza C., Chavarrías D., Merino P., Sánchez L., Martínez P. A microsatellite marker tool for parentage assessment in gilthead seabream (Sparus aurata). Aquaculture 2007, 272:S210-S216.
8. Castro J., Pino-Querido A., Hermida M., Chavarrías D., Romero R., García-Cortés L.A., Toro M.A., Martínez P. Heritability of skeleton abnormalities (lordosis, lack of operculum) in gilthead seabream (Sparus aurata) supported by microsatellite family data. Aquaculture 2008, 279:18-22.
9. Chen S.L., Liu Y.G., Xu M.Y., Li J. Isolation and characterization of polymorphic microsatellite loci from an EST-library of red sea bream (Chrysophrys major) and cross-species amplification. Mol. Ecol. Notes 2005, 5:215-217.
10. Chen S.L., Ma H.Y., Jiang Y., Liao X.L., Meng L. Isolation and characterization of polymorphic microsatellite loci from an EST library of turbot (Scophthalmus maximus) and cross-species amplification. Mol. Ecol. Notes 2007, 7:848-850.
11. Chistiakov D.A., Tsigenopoulos C.S., Lagnel J., Guo Y.M., Hellemans B., Haley C.S., Volckaert F.A.M., Kotoulas G. A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L. Anim. Genet. 2008, 39:623-634.
12. De Innocentiis S., Miggiano E., Ungaro A., Livi S., Sola L., Crosetti D. Geographical origin of individual breeders from gilthead sea bream (Sparus auratus) hatchery broodstocks inferred by microsatellite profiles. Aquaculture 2005, 247:227-232.
13. De Innocentiis S., Miggiano E., Ungaro A., Crosetti D., Sola L. Tracing the geographical origin of individual breeders from gilthead sea bream (Sparus aurata) hatchery broodstocks by multilocus microsatellite profiles. Aquaculture 2005, 247. 11-11.
14. Ellegren H. Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 2004, 5:435-445.
15. Ellis J.R., Burke J.M. EST-SSRs as a resource for population genetic analyses. Heredity 2007, 99:125-132.
16. FAO 2009. FishStat Plus - Universal software for fishery statistical time series, http://www.fao.org/fishery/statistics/software/fishstat/en.
17. Franch R., Louro B., Tsalavouta M., Chatziplis D., Tsigenopoulos C.S., Sarropoulou E., Antonello J., Magoulas A., Mylonas C.C., Babbucci M., Patarnello T., Power D.M., Kotoulas G., Bargelloni L. A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L. Genetics 2006, 174:851-861.
18. Goudet J. Fstat version 1.2: a computer program to calculate F statistics. J. Hered. 1995, 86:485-486.
19. Gupta S., Prasad M. Development and characterization of genic SSR markers in Medicago truncatula and their transferability in leguminous and non-leguminous species. Genome 2009, 52:761-771.
20. Guyomard R., Mauger S., Tabet-Canale K., Martineau S., Genet C., Krieg F., Quillet E. A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics 2006, 7:302.
21. Hirschhorn J.N., Daly M.J. Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet. 2005, 6:95-108.
22. Iseli C., Jongeneel C.V., Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 1999, 138-148.
23. Ju Z., Wells M.C., Martinez A., Hazlewood L., Walter R.B. An in silico mining for simple sequence repeats from expressed sequence tags of zebrafish, medaka, Fundulus, and Xiphophorus. In Silico Biol. 2005, 5:439-463.
24. Kuhl H., Beck A., Wozniak G., Canario A.V.M., Volckaert F.A.M., Reinhardt R. The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. BMC Genomics 2010, 11.
25. Lagnel J., Tsigenopoulos C.S., Iliopoulos I. NOBLAST and JAMBLAST: new options for BLAST and a Java application manager for BLAST results. Bioinformatics 2009, 25:824-826.
26. Launey S., Krieg F., Haffray P., Bruant J.S., Vanniers A., Guyomard R. Twelve new microsatellite markers for gilted seabream (Sparus aurata L.): characterization, polymorphism and linkage. Mol. Ecol. Notes 2003, 3:457-459.
27. Lottaz C., Iseli C., Jongeneel C.V., Bucher P. Modeling sequencing errors by combining Hidden Markov models. Bioinformatics 2003, 19:Ii103-Ii112.
28. Louro, B., Passos, A.L.S., Souche, E.L., Tsigenopoulos, C., Beck, A., Lagnel, J., Bonhomme, F., Cancela, L., Cerdà, J., Clark, M.S., Lubzens, E., Magoulas, A., Planas, J.V., Volckaert, F.A.M., Reinhardt, R., Canario, A.V.M., 2010. Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: Characterization, tissue-specific expression and gene markers. Marine Genomics 3, 179-191.
29. Miggiano E., De Innocentiis S., Ungaro A., Sola L., Crosetti D. AFLP and microsatellites as genetic tags to identify cultured gilthead seabream escapees: data from a simulated floating cage breaking event. Aquacult. Int. 2005, 13:137-146.
30. Miller S.A., Dykes D.D., Polesky H.F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucl. Acids Res. 1988, 16:1215.
31. Navarro A., Badilla R., Zamorano M.J., Pasamontes V., Hildebrandt S., Sαnchez J.J., Afonso J.M. Development of two new microsatellite multiplex PCRs for three sparid species: gilthead seabream (Sparus auratus L.), red porgy (Pagrus pagrus L.) and redbanded seabream (P. auriga, Valenciennes, and their application to paternity studies. Aquaculture 1843, 285(2008):30-37.
32. Navarro A., Zamorano M.J., Hildebrandt S., Ginιs R., Aguilera C., Afonso J.M. Estimates of heritabilities and genetic correlations for growth and carcass traits in gilthead seabream (Sparus auratus L.), under industrial conditions. Aquaculture 2009, 289:225-230.
33. Nei N. Molecular Evolutionary Genetics 1987, Columbia University Press, New York.
34. Ng S.H.S., Chang A., Brown G.D., Koop B.F., Davidson W.S. Type I microsatellite markers from Atlantic salmon (Salmo salar) expressed sequence tags. Mol. Ecol. Notes 2005, 5:762-766.
35. Palma J., Alarcon J.A., Alvarez C., Zouros E., Magoulas A., Andrade J.P. Developmental stability and genetic heterozygosity in wild and cultured stocks of gilthead sea bream (Sparus aurata). J. Mar. Biol. Assoc. U. K. 2001, 81:283-288.
36. Pemberton J.M., Slate J., Bancroft D.R., Barrett J.A. Nonamplifying alleles at microsatellite loci-a caution for parentage and population studies. Mol. Ecol. 1995, 4:249-252.
37. Pinera J.A., Bernardo D., Blanco G., Vazquez E., Sanchez J.A. Usefulness of microsatellite markers developed from Pagellus bogaraveo to genetically study five different species of Sparidae. Mar. Ecol. 2007, 28:184-187.
38. Pujolar J.M., Maes G.E., Van Houdt J.K.J., Zane L. Isolation and characterization of expressed sequence tag-linked microsatellite loci for the European eel (Anguilla anguilla). Mol. Ecol. Resour. 2009, 9:233-235.
39. Qiu X., Xu L., Liu S., Wang X., Meng X. Eleven polymorphic simple sequence repeat markers from expressed sequence tags of Pacific oyster Crassostrea gigas EST database. Conserv. Genet. 2009, 10:1773-1775.
40. Rexroad C.E., Rodriguez M.F., Coulibaly I., Gharbi K., Danzmann R.G., Dekoning J., Phillips R., Palti Y. Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss). BMC Genomics 2005, 6:54.
41. Rice W.R. Analyzing tables of statistical tests. Evolution 1989, 43:223-225.
42. Rozen S., Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Meth. Mol. Biol. 2000, 132:365-386.
43. Sarropoulou E., Franch R., Louro B., Power D.M., Bargelloni L., Magoulas A., Senger F., Tsalavouta M., Patarnello T., Galibert F., Kotoulas G., Geisler R. A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis. BMC Genomics 2007, 8:44.
44. Schlotterer C. Evolutionary dynamics of microsatellite DNA. Chromosoma 2000, 109:365-371.
45. Selkoe K.A., Toonen R.J. Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol. Lett. 2006, 9:615-629.
46. Senger F., Priat C., Hitte C., Sarropoulou E., Franch R., Geisler R., Bargelloni L., Power D., Galibert F. The first radiation hybrid map of a perch-like fish: the gilthead seabream (Sparus aurata L). Genomics 2006, 87:793-800.
47. Serapion J., Kucuktas H., Feng J., Liu Z. Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Mar Biotechnol NY 2004, 6:364-377.
48. Sha Z., Wang S., Zhuang Z., Wang Q., Wang Q., Li P., Ding H., Wang N., Liu Z., Chen S. Generation and analysis of 10 000 ESTs from the half-smooth tongue sole Cynoglossus semilaevis and identification of microsatellite and SNP markers. J. Fish Biol. 2010, 76:1190-1204.
49. Slate J., Hale M., Birkhead T. Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: a new resource for evolutionary genetic studies of passerines. BMC Genomics 2007, 8:52.
50. Tóth G., Gáspári Z., Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 2000, 10:967-981.
51. Van Oosterhout C., Hutchinson W.F., Wills D.P.M., Shipley P. micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 2004, 4:535-538.
52. Vasemägi A., Nilsson J., Primmer C.R. Seventy-five EST-linked Atlantic salmon (Salmo salar L.) microsatellite markers and their cross-amplification in five salmonid species. Mol. Ecol. Notes 2005, 5:282-288.
53. Vidal R., Peñaloza C., Urzúa R., Toro J.E. Screening of ESTs from Mytilus for the detection of SSR markers in Mytilus californianus. Mol. Ecol. Resour. 2009, 9:1409-1411.
54. Wang D., Liao X., Cheng L., Yu X., Tong J. Development of novel EST-SSR markers in common carp by data mining from public EST sequences. Aquaculture 2007, 271:558-574.
55. Wang Y., Ren R., Yu Z. Bioinformatic mining of EST-SSR loci in the Pacific oyster, Crassostrea gigas. Anim. Genet. 2008, 39:287-289.
56. Yu H., Li Q. Development of EST-SSRs in the Mediterranean blue mussel, Mytilus galloproviancialis. Mol. Ecol. Notes 2007, 7:1308-1310.
57. Yue G.H., Ho M.Y., Orban L., Komen J. Microsatellites within genes and ESTs of common carp and their applicability in silver crucian carp. Aquaculture 2004, 234:85-98.