Multiplexed microsatellite recovery using massively parallel sequencing

Molecular Ecology Resources

Volumn 11, Issue 6, 2011, Pages 1060-1067

  Jennings, T N ^a   Knaus, B J ^a   Mullins, T D ^b   Haig, S M ^b   Cronn, R C ^a  

^a PACIFIC NORTHWEST RESEARCH STATION   (United States)

^b FOREST AND RANGELAND ECOSYSTEM SCIENCE CENTER   (United States)

Author keywords

Genomic library; Illumina; Microsatellite; Multiplex massively parallel sequencing

Indexed keywords

MICROSATELLITE DNA; PRIMER DNA;

ANIMAL; ARTICLE; BIRD; CEDRUS; DNA BARCODING; DNA SEQUENCE; GENE LIBRARY; GENETICS; METHODOLOGY; SPECTROPHOTOMETRY;

ANIMALS; BIRDS; CEDRUS; DNA BARCODING, TAXONOMIC; DNA PRIMERS; GENOMIC LIBRARY; MICROSATELLITE REPEATS; SEQUENCE ANALYSIS, DNA; SPECTROPHOTOMETRY;

AVES; CONIFEROPHYTA;

EID: 79957480428     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2011.03033.x     Document Type: Article

References (35)

1. Abdelkrim J, Robertson BC, Stanton J-AL, Gemmell NJ (2009) Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. BioTechniques, 46, 185-192.
2. 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.
3. Bentley DR, Balasubramanian S, Swerdlow HP et al. (2008) Accurate whole genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
4. Boomer J, Stow A (2010) Rapid isolation of the first set of polymorphic microsatellite loci from the Australian gummy shark, Mustelus antarcticus, and their utility across divergent shark taxa. Conservation Genetics Resources, 2, 393-395.
5. Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology & Evolution, 18, 249-256.
6. Castoe TA, Poole AW, Gu W et al. (2009) Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources, 10, 341-347.
7. Craig DW, Pearson JV, Szelinger S et al. (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nature Methods, 5, 887-893.
8. Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Research, 36, e122.
9. Csencsics D, Brodbeck S, Holderegger R (2010) Cost-effective, species-specific microsatellite development for the endangered Dwarf Bulrush (Typha minima) using next-generation sequencing technology. Journal of Heredity, 101, 789-793.
10. Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics, 5, 435-445.
11. Elsik CG, Williams CG (2001) Low-copy microsatellite recovery from a conifer genome. Theoretical and Applied Genetics, 103, 1189-1195.
12. Glenn TC, Schable NA (2005) Isolating microsatellite DNA loci. In: Methods in Enzymology 395, Molecular Evolution: Producing the Biochemical Data, Part B (eds Zimmer EA & Roalson EH), pp. 202-222. Academic Press, San Diego, CA. ISBN: 9780121828004.
13. Glover KA, Hansen MM, Lien S, Als TD, Hoyheim B, Skaala O (2010) A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment. BMC Genetics, 11, 2.
14. Haasl RJ, Payseur BA (2011) Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites. Heredity, 106, 158-171.
15. Haig SM, Rhymer JM, Heckel DG (1994) Population differentiation in randomly amplified polymorphic DNA of red-cockaded woodpeckers Picoides borealis. Molecular Ecology, 3, 581-595.
16. Hamblin MT, Warburton ML, Buckler ES (2007) Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS ONE, 2, e1367.
17. Hizume M, Kondo T, Shibata F, Ishizuka R (2001) Flow cytometric determination of genome size in the Taxodiaceae, Cupressaceae sensu stricto and Sciadopityaceae. Cytologia, 66, 307-311.
18. Malausa T, Gilles A, MeglÉcz E et al. (2011) High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Molecular Ecology Resources, doi.
19. Mardis ER (2008) Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics, 9, 387-402.
20. Martin JF, Pech N, Meglecz E et al. (2010) Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing. BMC Genomics, 11, 560.
21. Metzker ML (2010) Sequencing technologies - the next generation. Nature Reviews Genetics, 11, 31-46.
22. Mikheyev AS, Vo T, Wee B, Singer MC, Parmesan C (2010) Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: Performance and a comparison with AFLP-derived distances. PLoS ONE, 5, e11212.
23. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research, 17, 240-248.
24. Morin PA, Luikart G, Wayne RK, SNP Workshop Group (2004) SNPs in ecology, evolution and conservation. Trends in Ecology & Evolution, 19, 208-216.
25. Narum SR, Banks M, Beacham TD et al. (2008) Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms. Molecular Ecology, 17, 3464-3477.
26. Niu BF, Fu LM, Sun SL, Li WZ (2010) Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics, 11, 187. doi:.
27. Organ CL, Shedlock AM, Meade A, Pagel M, Edwards SV (2007) Origin of avian genome size and structure in non-avian dinosaurs. Nature, 446, 180-184.
28. Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma R, Hedrick PW (2010) Conservation genetics in transition to conservation genomics. Trends in Genetics, 26, 177-187.
29. Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics, 11, 180.
30. Pemberton TJ, Sandefur CI, Jakobsson M, Rosenberg NA (2009) Sequence determinants of human microsatellite variability. BMC Genomics, 10, 612.
31. Quail MA, Kozarewa I, Smith F et al. (2008) A large genome center's improvements to the Illumina sequencing system. Nature Methods, 5, 1005-1010.
32. Saarinen EV, Austin JD (2010) When technology meets conservation: increased microsatellite marker production using 454 genome sequencing on the endangered Okaloosa darter (Etheostoma okaloosae). Journal of Heredity, 101, 784-788.
33. Santana QC, Coetzee MPA, Steenkamp ET et al. (2009) Microsatellite discovery by deep sequencing of enriched genomic libraries. BioTechniques, 46, 217-223.
34. Willyard A, Syring J, Gernandt DS, Liston A, Cronn R (2007) Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus. Molecular Biology and Evolution, 24, 620-620.
35. 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.