Deep Sequencing of RNA from Ancient Maize Kernels

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Fordyce, Sarah L ^a   Ávila Arcos, Maria C ^a   Rasmussen, Morten ^a   Cappellini, Enrico ^a   Romero Navarro, J Alberto ^a,b   Wales, Nathan ^a,c   Alquezar Planas, David E ^a   Penfield, Steven ^d   Brown, Terence A ^e   Vielle Calzada, Jean Philippe ^f   Montiel, Rafael ^f   Jørgensen, Tina ^a   Odegaard, Nancy ^g   Jacobs, Michael ^g   Arriaza, Bernardo ^h   Higham, Thomas F G ⁱ   Ramsey, Christopher Bronk ⁱ   Willerslev, Eske ^a   Gilbert, M Thomas P ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^c UNIVERSITY OF CONNECTICUT   (United States)

^d UNIVERSITY OF YORK   (United Kingdom)

^e UNIVERSITY OF MANCHESTER   (United Kingdom)

^f DEPARTAMENTO DE FÍSICA   (Mexico)

^g UNIVERSITY OF ARIZONA   (United States)

^h UNIVERSIDAD DE TARAPACÁ   (Chile)

ⁱ UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; NUCLEIC ACID; PLANT RNA; TRANSCRIPTOME;

ARTICLE; BIOINFORMATICS; DNA SYNTHESIS; GERMINATION; MAIZE; NONHUMAN; PLANT GENETICS; RNA DEGRADATION; RNA SEQUENCE; SEED KERNEL; TRANSCRIPTOMICS; VALIDATION PROCESS;

DNA, COMPLEMENTARY; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GERMINATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; RNA, PLANT; SEEDS; TIME FACTORS; TRANSCRIPTOME; ZEA MAYS;

ZEA MAYS;

EID: 84872224484     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0050961     Document Type: Article

References (40)

1. Wang Z, Gerstein M, Snyder M, (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev 10: 57-63.
2. Wang RL, Stec A, Hey J, Lukens L, Doebley J, (1999) The limits of selection during maize domestication. Nature 398: 236-239.
3. Wright SI, Vroh Bi I, Schroeder SG, Yamasaki M, Doebley JF, et al. (2005) The effects of artificial selection on the maize genome. Science 308: 1310-1314.
4. Yamasaki M, Tenaillon MI, Vroh Bi I, Schroeder SG, Sanchez-Villeda H, et al. (2005) A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. The Plant Cell 17: 2859-2872.
5. Studer A, Zhao Q, Ross-Ibarra J, Doebley J, (2011) Idenitification of functional transposon insertion in the maize domestication gene tb1. Nat Genet 43: 1160-1165.
6. Jaenicke-Despres V, Buckler ES, Smith ES, Gilbert MTP, Cooper A, et al. (2003) Early allelic selection in maize as revealed by ancient DNA. Science 302: 1206-1208.
7. Freitas FO, Bendel G, Allaby RG, Brown TA, (2003) DNA from primitive maize landraces and archaeological remains: implications for the domestication of maize and its expansion into South America. J Arch Sci 30: 901-908.
8. O'Donoghue K, Clapham A, Evershed RP, Brown TA, (1996) Remarkable preservation of biomolecules in ancient radish seeds. Proc R Soc Lond B 263: 541-547.
9. Li P, Ponnala L, Gandotra, Wang L, Si Y, et al. (2010) The developmental dynamics of the maize leaf transcriptome. Nat Genet 42: 1060-1067.
10. Buitink J, Leger JJ, Guisle I, Vu BL, Wuilleme S, et al. (2006) Transcriptome profiling uncovers metabolic and regulatory processes occurring during the transition from desiccation-sensitive to desiccation-tolerant stages in Medicago truncatula seeds. Plant J 47: 735-750.
11. Kan Y, Wan Y Beaudoin F, Leader DJ, Edwards K, et al. (2006) Transcriptome analysis reveals differentially expressed storage protein transcripts in seeds of Aegilops and wheat. J Cereal Sci 44: 75-85.
12. Prioul JL, Méchin V, Lessard P, Thévenot C, Grimmer M, et al. (2008) A joint transcriptomic, proteomic and metabolic analysis of maize endosperm development and starch filling. Plant Biotechnology J 6: 855-869.
13. Holdsworth MJ, Finch-Savage WE, Grappin P, Job D, (2007) Post-genomics dissection of seed dormancy and germination. Trends Plant Sci 13: 7-13.
14. Rasmussen M, Li Y, Lindgreen S, Skou Pedersen J, Albrechtsen A, et al. (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463: 757-762.
15. Green R, Krause J, Briggs AW, Maricic T, Stenzel U, et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710-722.
16. 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: 1053-1060.
17. Rasmussen M, Guo X, Wang Y, Lohmueller, Rasmussen S, et al. (2011) An aboriginal Australian genome reveals separate human dispersals into Asia. Science 334: 94-98.
18. Lindahl T, (1993) Instability and decay of the primary structure of DNA. Nature 362: 709-715.
19. Almoguera C, Jordano J, (1992) Developmental and environmental concurrent expression of sunflower dry-seed-stored low-molecular-weight heat-shock protein and Lea mRNAs. Plant Molecular Biol 19: 781-792.
20. Masaki S, Yamada T, Hirasawa T, Todaka D, Kanekatsu M, (2008) Proteomic analysis of RNA-binding proteins in dry seeds of rice after fractionation by ssDNA affinity column chromatography. Biotechnol Lett 30: 955-60.
21. Rollo F, (1985) Characterization by molecular hybridization of RNA fragments isolated from ancient (1400 B.C.) seeds. Theor Appl Genet 41: 330.
22. Venanzi FM, Rollo F, (1990) Mummy RNA lasts longer. Nature 343: 25-26.
23. Rollo F, Venanzi FM, Amici A, (1991) Nucleic acids in mummified plant seeds: biochemistry and molecular genetics of pre-Columbian maize. Genet Res 58: 193-201.
24. Sallon S, Solowey E, Korchinsky R, Egli M, Woodhatch I, et al. (2008) Germination, genetics, and growth of an ancient date seed. Science 320: 1464.
25. Bannister B, Dean JS, Robinson WJ, (1968) Tree-ring dates from Arizona C-D: Eastern Grand Canyon-Tsegi Canyon-Kayenta Area. Tucson: Lab. Tree-Ring Res.
26. 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. Scientific Reports 1doi. 10.1038/srep00074.
27. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
28. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
29. Kent WJ, (2002) BLAT- the BLAST-like alignment tool. Genome Res 12: 656-64.
30. Babraham Bioinformatics website. Available: http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/. Accessed: 2011 Nov.
31. Ginolhac A, Rasmussen M, Gilbert MTP, Willerslev E, Orlando L, (2011) mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 27: 2153-2155.
32. RepeatMasker website, RepeatModeler Open-1.0. Available: http://www.repeatmasker.org.
33. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Bio 215: 403-410.
34. Huson DH, Mitra S, Weber N, Ruscheweyh H, Schuster SC, (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res 21: 1552-1560.
35. Buescher PJ, Phillips RL, Brambl R, (1984) Ribosomal RNA contents of maize genotypes with different ribosomal RNA gene numbers. Biochem Genet 22: 923-930.
36. Miller W, Drautz DI, Ratan A, Pusey B, Qi J, et al. (2008) Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456: 387-390.
37. Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, et al. (2007) Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A 104: 14616-14621.
38. Dure L, Waters L, (1965) Long-lived messenger RNA: Evidence from cotton seed germination. Science 147: 410-412.
39. Hammett JR, Katterman FR, (1975) Storage and metabolism of poly(adenylic acid)-mRNA in germinating cotton seeds. Biochem 14: 4375-4379.
40. Nakabayashi K, Okamoto M, Koshiba T, Kamiya Y, Nambara E, (2005) Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed. Plant J 41: 697-709.