Comparison of random and SSR-enriched shotgun pyrosequencing for microsatellite discovery and single multiplex PCR optimization in Acacia harpophylla F. Muell. Ex Benth

Molecular Ecology Resources

Volumn 11, Issue 4, 2011, Pages 711-724

  Lepais, Olivier ^a   Bacles, Cecile F E ^a  

^a UNIVERSITY OF STIRLING   (United Kingdom)

Author keywords

454 GS FLX Titanium; Brigalow acacia; High throughput genotyping; Next generation sequencing; Short sequence repeats

Indexed keywords

MICROSATELLITE DNA; PRIMER DNA;

ACACIA; ARTICLE; AUSTRALIA; CLASSIFICATION; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; VALIDATION STUDY;

ACACIA; AUSTRALIA; DNA PRIMERS; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION;

ACACIA; ACACIA HARPOPHYLLA;

EID: 79959254890     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2011.03002.x     Document Type: Article

References (60)

1. Abdelkrim J, Robertson BC, Stanton JAL, Gemmell NJ (2009) Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. BioTechniques, 46, 185-192.
2. Alberto F (2009) MsatAllele-1.0: an R package to visualize the binning of microsatellite alleles. Journal of Heredity, 100, 394-397.
3. 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.
4. Altschul SF, Madden TL, Schäffer AA et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
5. Arnaud-Haond S, Duante CM, Alberto F, Serrao EA (2007) Standardizing methods to address clonality in population studies. Molecular Ecology, 16, 5115-5139.
6. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier (France).
7. Bennett MD, Leith IJ (2005) Angiosperm DNA C-values database (release 6.0, Oct. 2005).
8. Bertorelle G, Benazzo A, Mona S (2010) ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Molecular Ecology, 19, 2609-2625.
9. 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. Molecular Ecology Resources, 10, 341-347.
10. Chandler TS, Buckley YM, Dwyer JM (2007) Restoration potential of Brigalow regrowth: insights from a cross-sectional study in southern Queensland. Ecological Management & Restoration, 8, 218-221.
11. Chybicki IJ, Burczyk J (2009) Simultaneous estimation of null alleles and inbreeding coefficients. Journal of Heredity, 100, 106-113.
12. Cryer NC, Butler DR, Wilkinson MJ (2005) High throughput, high resolution selection of polymorphic microsatellite loci for multiplex analysis. Plant Methods, 1, 3.
13. 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.
14. Dewoody J, Nason JD, Hipkins VD (2006) Mitigating scoring errors in microsatellite data from wild populations. Molecular Ecology Notes, 6, 951-957.
15. Dubut V, Grenier R, Meglécz E et al. (2010) Development of 55 novel polymorphic microsatellite loci for the critically endangered Zingel asper L. (Actinopterygii: Perciformes: Percidae) and cross-species amplification in five other percids. European Journal of Wildlife Research, 56, 931-938.
16. Dwyer JM, Fensham R, Buckley YM (2010a) Restoration thinning accelerates structural development and carbon sequestration in an endangered Australian ecosystem. Journal of Applied Ecology, 47, 681-691.
17. Dwyer JM, Fensham R, Buckley YM (2010b) Agricultural legacy, climate, and soil influence the restoration and carbon potential of woody regrowth in Australia. Ecological Applications, 20, 1838-1850.
18. El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L) Skeels] endemic to Morocco. Theoretical and Applied Genetics, 92, 832-839.
19. Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics, 5, 435-445.
20. EPBC (1999). Environmental Protection and Biodiversity Conservation Act. Threatened Species & Ecological Communities. Brigalow (Acacia harpophylla dominant and co-dominant). Listed on 4 April 2001. Australian Government - Department of Sustainability, Environment, Water, Population and Communities. Accessed 12 November 2010.
21. Erbert D, Peakall R (2009) Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Molecular Ecology Resources, 9, 673-690.
22. Gaggiotti OE, Foll M (2010) Quantifying population structure using the F-model. Molecular Ecology Resources, 10, 821-830.
23. Gerber S, Chabrier P, Kremer A (2003) FAMOZ: a software for parentage analysis using dominant, codominant and uniparentally inherited markers. Molecular Ecology Notes, 3, 479-481.
24. Goldstein DB, Schlötterer C (1999) Microsatellites: Evolution and Applications. Oxford University Press, Oxford, UK.
25. Goudet J (1995) FSTAT (Version 1.2): a computer program to calculate F-statistics. Journal of Heredity, 86, 485-486.
26. Gupta PK, Balyan IS, Sharma PC, Ramesh B (1996) Microsatellites in plants: a new class of molecular markers. Current Science, 70, 45-54.
27. Guichoux E, Lagache L, Wagner S et al. (in press) Current trends in microsatellite genotyping. Molecular Ecology Resources.
28. Holleley CE, Geerts PG (2009) Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR. BioTechniques, 46, 511-517.
29. Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. Trends in Ecology & Evolution, 11, 424-429.
30. Johnson PCD, Haydon DT (2007) Maximum-likelihood estimation of allelic dropout and false allele error rates from microsatellite genotypes in the absence of reference data. Genetics, 175, 827-842.
31. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16, 1099-1106.
32. Kelkar YD, Strubczewski N, Hile SE, Chiaromonte F, Eckert KA, Makova KD (2010) What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats. Genome Biology and Evolution, 2, 620-635.
33. Kruglyak S, Durrett RT, Schug MD, Aquadro CF (1998) Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proceeding of the National Academy of Sciences of the United States of America, 95, 10774-10778.
34. 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:.
35. Martin JF, Pech N, Meglécz E et al. (2010) Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing. BMC Genomics, 11, 560.
36. Meglécz E, Martin JF (2009) QDD for Windows and Linux version 1. Software documentation. Accessed 10 November 2010.
37. Meglécz 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.
38. Metzker ML (2010) Sequencing technologies - the next generation. Nature Reviews Genetics, 11, 31-46.
39. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nature Genetics, 30, 194-200.
40. 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.
41. Perry JC, Rowe L (2010) Rapid microsatellite development for water striders by next-generation sequencing. Journal of Heredity, 102, 125-129.
42. R Development Core Team (2009) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Accessed 10 November 2010.
43. Rasmussen DA, Noor MAF (2009) What can you do with 0.1× genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae). BMC Genomics, 10, 382.
44. Ray N, Excoffier L (2010) A first step towards inferring levels of long-distance dispersal during past expansions. Molecular Ecology Resources, 10, 902-914.
45. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology, 132, 365-386.
46. Santana QC, Coetzee MPA, Steenkamp ET et al. (2009) Microsatellite discovery by deep sequencing of enriched genomic libraries. BioTechniques, 46, 217-223.
47. Saski C, Lee SB, Daniell H et al. (2005) Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Molecular Biology, 59, 309-322.
48. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology, 18, 233-234.
49. Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecology Letters, 9, 615-629.
50. Spear SF, Balkenhol N, Fortin MJ, McRae BH, Scribner K (2010) Use of resistance surfaces for landscape genetic studies: considerations for parameterization and analysis. Molecular Ecology, 19, 3576-3591.
51. Squirrell J, Hollingsworth PM, Woodhead M et al. (2003) How much effort is required to isolate nuclear microsatellites from plants? Molecular Ecology, 12, 1339-1348.
52. Tangphatsornruang S, Somta P, Uthaipaisanwong P et al. (2009) Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biology, 9, 137.
53. Tangphatsornruang S, Sangsrakru D, Chanprasert J et al. (2010) The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Research, 17, 11-22.
54. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research, 11, 1441-1452.
55. Toonen RJ, Hughes S (2001) Increased throughput for fragment analysis on ABI Prism 377 automated sequencer using a membrane comb and STRand software. BioTechniques, 31, 1320-1324.
56. Tóth G, Gáspári Z, Jurka J (2000) Microsatellites in different Eukaryotic genomes: survey and analysis. Genome Research, 10, 967-981.
57. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535-538.
58. Vanpé C, Buschiazzo E, Abdelkrim J, Morrow G, Nicol SC, Gemmell NJ (2009) Development of microsatellite markers for the short-beaked echidna using three different approaches. Australian Journal of Zoology, 57, 219-224.
59. Wang Z, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theoretical and Applied Genetics, 88, 1-6.
60. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Molecular Ecology, 11, 1-16.