Abstract
Microsatellites are DNA sequences of tandem repeats of one to six nucleotides, which are highly polymorphic, and thus the molecular markers of choice in many kinship, population genetic, and conservation studies. There have been significant technical improvements since the early methods for microsatellite isolation were developed, and today the most common procedures take advantage of the hybrid capture methods of enriched-targeted microsatellite DNA. Furthermore, recent advents in sequencing technologies (i.e., next-generation sequencing, NGS) have fostered the mining of microsatellite markers in non-model organisms, affording a cost-effective way of obtaining a large amount of sequence data potentially useful for loci characterization. The rapid improvements of NGS platforms together with the increase in available microsatellite information open new avenues to the understanding of the evolutionary forces that shape genetic structuring in wild populations. Here, we provide detailed methodological procedures for microsatellite isolation based on the screening of GT microsatellite-enriched libraries, either by cloning and Sanger sequencing of positive clones or by direct NGS. Guides for designing new species-specific primers and basic genotyping are also given.
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References
Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445
Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. Trends Ecol Evol 11:424–429
Schlotterer C (2004) The evolution of molecular markers—just a matter of fashion? Nat Rev Genet 5:63–69
Weber JL (1990) Informativeness of human (dC−dA)n.(dG−dT)n polymorphisms. Genomics 7:524–530
Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981
Kassai-Jager E, Ortutay C, Toth G et al (2008) Distribution and evolution of short tandem repeats in closely related bacterial genomes. Gene 410:18–25
Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Lett 9:615–629
Haasl RJ, Payseur BA (2011) Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites. Heredity 106:158–171
Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16
Hamilton MB, Pincus EL, Fleischer RC (1999) Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. Biotechniques 27:500–515
Gardner MG, Cooper SJB, Bull CM et al (1999) Isolation of microsatellite loci from a social lizard, Egernia stojesii, using a modified enrichment procedure. J Hered 90:301–304
Rassmann K, Schlotterer C, Tautz D (1991) Isolation of simple-sequence loci for use in polymerase chain reaction-based DNA fingerprinting. Electrophoresis 12:113–118
Prochazka M (1996) Microsatellite hybrid capture technique for simultaneous isolation of various STR markers. Genome Res 6:646–649
Abdelkrim J, Robertson BC, Stanton JL et al (2009) Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. Biotechniques 46:185–192
Allentoft ME, Schuster SC, Holdaway RN et al (2009) Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data. Biotechniques 46:195–200
Glenn TC, Schable NA (2005) Isolating microsatellite DNA loci. Methods Enzymol 395:202–222
Bachtrog D, Agis M, Imhof M et al (2000) Microsatellite variability differs between dinucleotide repeat motifs—evidence from Drosophila melanogaster. Mol Biol Evol 17:1277–1285
Li YC, Korol AB, Fahima T et al (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11:2453–2465
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, New York
Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Thompson JD, Gibson TJ, Plewniak F et al (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882
Ellegren H (2008) Sequencing goes 454 and takes large-scale genomics into the wild. Mol Ecol 17:1629–1631
Lerner HRL, Fleischer RC (2010) Prospects for the use of next-generation sequencing methods in ornithology. Auk 127:4–15
Gardner MG, Fitch AJ, Bertozzi T et al (2011) Rise of the machines—recommendations for ecologists when using next generation sequencing for microsatellite development. Mol Ecol Resour 11:1093–1101
Jennings TN, Knaus BJ, Mullins TD et al (2011) Multiplexed microsatellite recovery using massively parallel sequencing. Mol Ecol Resour 11:1060–1067
Castoe TA, Poole AW, Gu W et al (2010) Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Mol Ecol Resour 10:341–347
Santana QC, Coetzee MPA, Steenkamp ET et al (2009) Microsatellite discovery by deep sequencing of enriched genomic libraries. Biotechniques 46:217–223
Binladen J, Gilbert MTP, Bollback JP et al (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. Plos One 2:e197
Faircloth BC (2008) MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Mol Ecol Resour 8:92–94
Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawertz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana, Totowa, NJ, pp 365–386
You FM, Huo NX, Gu YQ et al (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253
Meglecz E, Costedoat C, Dubut V et al (2010) QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26:403–404
Holleley CE, Geerts PG (2009) Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR. Biotechniques 46:511–517
Glaubitz JC (2004) CONVERT: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol Ecol Notes 4:309–310
Dieringer D, Schlotterer C (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 3:167–169
Kibbe WA (2007) OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res 35:W43–W46
Vergnaud G, Denoeud F (2000) Minisatellites: mutability and genome architecture. Genome Res 10:899–907
Brownstein MJ, Carpten JD, Smith JR (1996) Modulation of non-templated nucleotide addition by tag DNA polymerase: primer modifications that facilitate genotyping. Biotechniques 20:1004–1006
Gonzalez EG, Zardoya R (2007) Isolation and characterization of polymorphic microsatellites for the sardine Sardina pilchardus (Clupeiformes: Clupeidae). Mol Ecol Notes 7:519–521
Acknowledgments
EGG is sponsored by a postdoctoral fellowship of the Ministerio de Educación Cultura y Deporte (MECD). The research of R.Z. is funded by the Ministerio de Economía y Competitividad (CGL2010-18216).
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Gonzalez, E.G., Zardoya, R. (2013). Microsatellite DNA Capture from Enriched Libraries. In: Kantartzi, S. (eds) Microsatellites. Methods in Molecular Biology, vol 1006. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-389-3_5
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DOI: https://doi.org/10.1007/978-1-62703-389-3_5
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