Choosing the Best Plant for the Job: A Cost-Effective Assay to Prescreen Ancient Plant Remains Destined for Shotgun Sequencing

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Wales, Nathan ^a,b   Romero Navarro, J Alberto ^b,c,d   Cappellini, Enrico ^b   Gilbert, M Thomas P ^b  

^a UNIVERSITY OF CONNECTICUT   (United States)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^d Cornell University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; FUNGAL DNA; PLANT DNA;

ARTICLE; ASSAY; COST EFFECTIVENESS ANALYSIS; DNA EXTRACTION; DNA SEQUENCE; FOSSIL PLANT; HIGH THROUGHPUT SEQUENCING; MICROORGANISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENE; REAL TIME POLYMERASE CHAIN REACTION; SAMPLE; SHOTGUN SEQUENCING;

BASE SEQUENCE; COST-BENEFIT ANALYSIS; DNA PRIMERS; DNA, PLANT; PLANTS; REAL-TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS);

EID: 84866725421     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0045644     Document Type: Article

References (50)

1. Willerslev E, Cooper A, (2005) Ancient DNA. Proc Biol Sci 272(1558): 3-16.
2. Schlumbaum A, Tensen M, Jaenicke-Després V, (2008) Ancient plant DNA in archaeobotany. Veg Hist Archaeobot 17(2): 233-244.
3. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, et al. (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463(7282): 757-762.
4. Poinar HN, Höss M, Bada JL, Pääbo S, (1996) Amino Acid Racemization and the Preservation of Ancient DNA. Science 272(5263): 864-866.
5. Hofreiter M, Serre D, Poinar HN, Kuch M, Pääbo S, (2001) Ancient DNA. Nat Rev Genet 2(5): 353-359.
6. Heyn P, Stenzel U, Briggs AW, Kircher M, Hofreiter M, et al. (2010) Road blocks on paleogenomes-polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA. Nucleic Acids Res 38: e161.
7. Malmström H, Storå J, Dalén L, Holmlund G, Götherström A, (2005) Extensive Human DNA Contamination in Extracts from Ancient Dog Bones and Teeth. Mol Biol Evol 22(10): 2040-2047.
8. Leonard JA, Shanks O, Hofreiter M, Kreuz E, Hodges L, et al. (2007) Animal DNA in PCR reagents plagues ancient DNA research. J Archaeol Sci 34(9): 1361-1366.
9. Wall JD, Kim SK, (2007) Inconsistencies in Neanderthal Genomic DNA Sequences. PLoS Genet 3(10): 1862-1866.
10. Pääbo S, Poinar H, Serre D, Jaenicke-Després V, Hebler J, et al. (2004) Genetic Analyses from Ancient DNA. Annu Rev Genet 38(1): 645-679.
11. Cooper A, Poinar HN, (2000) Ancient DNA: Do It Right or Not at All. Science 289(5482): 1139.
12. Knapp M, Hofreiter M, (2010) Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives. Genes 1(2): 227-243.
13. Pääbo S, Higuchi RG, Wilson AC, (1989) Ancient DNA and the Polymerase Chain Reaction: The Emerging Field of Molecular Archaeology. J Biol Chem 264(17): 9709-9712.
14. Mardis ER, (2008) Next-Generation DNA Sequencing Methods. Annu Rev Genomics Hum Genet 9(1): 387-402.
15. Poinar HN, Schwarz C, Qi J, Shapiro B, MacPhee RDE, et al. (2006) Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA. Science 311(5759): 392-394.
16. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nat Biotechnol 26(10): 1135-1145.
17. Miller W, Drautz DI, Ratan A, Pusey B, Qi J, et al. (2008) Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456(7220): 387-390.
18. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, et al. (2010) A Draft Sequence of the Neandertal Genome. Science 328(5979): 710-722.
19. Reich D, Green RE, Kircher M, Krause J, Patterson N, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468(7327): 1053-1060.
20. Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, et al. (2011) An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. Science 334(6052): 94-98.
21. Delseny M, Han B, Hsing YI, (2010) High throughput DNA sequencing: The new sequencing revolution. Plant Sci 179(5): 407-422.
22. Briggs AW, Good JM, Green RE, Krause J, Maricic T, et al. (2009) Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes. Science 325(5938): 318-321.
23. Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, et al. (2010) Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture. Science 328(5979): 723-725.
24. Palmer SA, Clapham AJ, Rose P, Freitas FO, Owen BD, et al. (2012) Archaeogenomic Evidence of Punctuated Genome Evolution in Gossypium. Mol Biol Evol 29: 2031-2038.
25. Nielsen R, Paul JS, Albrechtsen A, Song YS, (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12(6): 443-451.
26. Chia J, Song C, Bradbury PJ, Costich D, de Leon N, et al. (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44(7): 803-807.
27. Hufford MB, Xu X, van Heerwaarden J, Pyhajarvi T, Chia J, et al. (2012) Comparative population genomics of maize domestication and improvement. Nat Genet 44(7): 808-811.
28. Ávila-Arcos M, Cappellini E, Romero-Navarro JA, Wales N, Moreno-Mayar JV, et al. (2011) Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Sci Rep 1: 74.
29. Bunning SL, Jones G, Brown TA, (2012) Next generation sequencing of DNA in 3300-year-old charred cereal grains. J Archaeol Sci 39(8): 2780-2784.
30. Lutz K, Wang W, Zdepski A, Michael T, (2011) Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing. BMC Biotechnol 11(1): 54.
31. Cappellini E, Gilbert MTP, Geuna F, Fiorentino G, Hall A, et al. (2010) A multidisciplinary study of archaeological grape seeds. Naturwissenschaften 97(2): 205-217.
32. Wagner A, Blackstone N, Cartwright P, Dick M, Misof B, et al. (1994) Surveys of Gene Families Using Polymerase Chain Reaction: PCR Selection and PCR Drift. Syst Biol 43(2): 250-261.
33. Polz MF, Cavanaugh CM, (1998) Bias in Template-to-Product Ratios in Multitemplate PCR. Appl Environ Microbiol 64(10): 3724-3730.
34. Brown TA, Allaby RG, Sallares R, Jones G, (1998) Ancient DNA in charred wheats: Taxonomic identification of mixed and single grains. Ancient Biomolecules 2(2): 185.
35. Poinar HN, Hofreiter M, Spaulding WG, Martin PS, Stankiewicz BA, et al. (1998) Molecular Coproscopy: Dung and Diet of the Extinct Ground Sloth Nothrotheriops shastensis. Science 281(5375): 402-406.
36. Oskam CL, Haile J, McLay E, Rigby P, Allentoft ME, et al. (2010) Fossil avian eggshell preserves ancient DNA. Proc Biol Sci 277(1690): 1991-2000.
37. Bell AS, Blanford S, Jenkins N, Thomas MB, Read AF, (2009) Real-time quantitative PCR for analysis of candidate fungal biopesticides against malaria: Technique validation and first applications. J Invertebr Pathol 100(3): 160-168.
38. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14): 1754-1760.
39. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 326(5956): 1112-1115.
40. Maier RM, Neckermann K, Igloi GL, Kössel H, (1995) Complete Sequence of the Maize Chloroplast Genome: Gene Content, Hotspots of Divergence and Fine Tuning of Genetic Information by Transcript Editing. J Mol Biol 251(5): 614-628.
41. Pyke K (2009) Plastid biology. Cambridge: Cambridge University Press.
42. Shaver JM, Oldenburg DJ, Bendich AJ, (2006) Changes in chloroplast DNA during development in tobacco, Medicago truncatula, pea, and maize. Planta 224(1): 72-82.
43. Possingham JV, Saurer W, (1969) Changes in chloroplast number per cell during leaf development in spinach. Planta 86(2): 186-194.
44. Maliga P, Bock R, (2011) Plastid biotechnology: food, fuel, and medicine for the 21st century. Plant Physiol 155(4): 1501-1510.
45. Kudo N, Kimura Y, (2001) Flow cytometric evidence for endopolyploidization in cabbage (Brassica oleracea L.) flowers. Sex Plant Reprod 13(5): 279-283.
46. Zoschke R, Liere K, Börner T, (2007) From seedling to mature plant: Arabidopsis plastidial genome copy number, RNA accumulation and transcription are differentially regulated during leaf development. Plant J 50(4): 710-722.
47. Huson DH, Mitra S, Ruscheweyh H, Weber N, Schuster SC, (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res 21(9): 1552-1560.
48. Smith CI, Chamberlain AT, Riley MS, Stringer C, Collins MJ, (2003) The thermal history of human fossils and the likelihood of successful DNA amplification. J Hum Evol 45(3): 203-217.
49. Allaby RG, O'Donoghue K, Sallares R, Jones MK, Brown TA, (1997) Evidence for the survival of ancient DNA in charred wheat seeds from European archaeological sites. Anc Biomol 1(2): 119-129.
50. Palmer SA, Smith O, Allaby RG, (2012) The blossoming of plant archaeogenetics. Ann Anat 20: 146-156.