Deep sequencing of RNA from ancient maize kernels

Sarah Louise Fordyce; Maria del Carmen Avila Arcos; Morten Rasmussen; Enrico Cappellini; J. Alberto Romero-Navarro; Nathan Wales; David Eugenio Alquezar Planas; Steven Penfield; Terence A. Brown; Jean-Philippe Vielle-Calzada; Rafael Montiel; Tina Jørgensen; Nancy Odegaard; Michael Jacobs; Bernardo Arriaza; Thomas F. G. Higham; Christopher Bronk Ramsey; Eske Willerslev; Tom Gilbert

doi:10.1371/journal.pone.0050961

Deep sequencing of RNA from ancient maize kernels

Sarah Louise Fordyce, Maria del Carmen Avila Arcos, Morten Rasmussen, Enrico Cappellini, J. Alberto Romero-Navarro, Nathan Wales, David Eugenio Alquezar Planas, Steven Penfield, Terence A. Brown, Jean-Philippe Vielle-Calzada, Rafael Montiel, Tina Jørgensen, Nancy Odegaard, Michael Jacobs, Bernardo Arriaza, Thomas F. G. Higham, Christopher Bronk Ramsey, Eske Willerslev, Tom Gilbert

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Abstract

The characterization of biomolecules from ancient samples can shed otherwise unobtainable insights into the past. Despite the fundamental role of transcriptomal change in evolution, the potential of ancient RNA remains unexploited - perhaps due to dogma associated with the fragility of RNA. We hypothesize that seeds offer a plausible refuge for long-term RNA survival, due to the fundamental role of RNA during seed germination. Using RNA-Seq on cDNA synthesized from nucleic acid extracts, we validate this hypothesis through demonstration of partial transcriptomal recovery from two sources of ancient maize kernels. The results suggest that ancient seed transcriptomics may offer a powerful new tool with which to study plant domestication.

Original language	English
Article number	e50961
Journal	PLoS ONE
Volume	8
Issue number	1
Number of pages	9
ISSN	1932-6203
DOIs	https://doi.org/10.1371/journal.pone.0050961
Publication status	Published - 17 Jan 2013

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Deep Sequencing of RNA from Ancient Maize KernelsFinal published version, 338 KBLicence: CC BY

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Fordyce, S. L., Avila Arcos, M. D. C., Rasmussen, M., Cappellini, E., Romero-Navarro, J. A., Wales, N., Alquezar Planas, D. E., Penfield, S., Brown, T. A., Vielle-Calzada, J-P., Montiel, R., Jørgensen, T., Odegaard, N., Jacobs, M., Arriaza, B., Higham, T. F. G., Ramsey, C. B., Willerslev, E., & Gilbert, T. (2013). Deep sequencing of RNA from ancient maize kernels. PLoS ONE, 8(1), [e50961]. https://doi.org/10.1371/journal.pone.0050961

Fordyce, SL, Avila Arcos, MDC, Rasmussen, M, Cappellini, E, Romero-Navarro, JA, Wales, N, Alquezar Planas, DE, Penfield, S, Brown, TA, Vielle-Calzada, J-P, Montiel, R, Jørgensen, T, Odegaard, N, Jacobs, M, Arriaza, B, Higham, TFG, Ramsey, CB, Willerslev, E & Gilbert, T 2013, 'Deep sequencing of RNA from ancient maize kernels', PLoS ONE, vol. 8, no. 1, e50961. https://doi.org/10.1371/journal.pone.0050961

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title = "Deep sequencing of RNA from ancient maize kernels",

abstract = "The characterization of biomolecules from ancient samples can shed otherwise unobtainable insights into the past. Despite the fundamental role of transcriptomal change in evolution, the potential of ancient RNA remains unexploited - perhaps due to dogma associated with the fragility of RNA. We hypothesize that seeds offer a plausible refuge for long-term RNA survival, due to the fundamental role of RNA during seed germination. Using RNA-Seq on cDNA synthesized from nucleic acid extracts, we validate this hypothesis through demonstration of partial transcriptomal recovery from two sources of ancient maize kernels. The results suggest that ancient seed transcriptomics may offer a powerful new tool with which to study plant domestication.",

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AU - Fordyce, Sarah Louise

AU - Avila Arcos, Maria del Carmen

AU - Rasmussen, Morten

AU - Cappellini, Enrico

AU - Romero-Navarro, J. Alberto

AU - Wales, Nathan

AU - Alquezar Planas, David Eugenio

AU - Penfield, Steven

AU - Brown, Terence A.

AU - Vielle-Calzada, Jean-Philippe

AU - Montiel, Rafael

AU - Jørgensen, Tina

AU - Odegaard, Nancy

AU - Jacobs, Michael

AU - Arriaza, Bernardo

AU - Higham, Thomas F. G.

AU - Ramsey, Christopher Bronk

AU - Willerslev, Eske

AU - Gilbert, Tom

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AB - The characterization of biomolecules from ancient samples can shed otherwise unobtainable insights into the past. Despite the fundamental role of transcriptomal change in evolution, the potential of ancient RNA remains unexploited - perhaps due to dogma associated with the fragility of RNA. We hypothesize that seeds offer a plausible refuge for long-term RNA survival, due to the fundamental role of RNA during seed germination. Using RNA-Seq on cDNA synthesized from nucleic acid extracts, we validate this hypothesis through demonstration of partial transcriptomal recovery from two sources of ancient maize kernels. The results suggest that ancient seed transcriptomics may offer a powerful new tool with which to study plant domestication.

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DO - 10.1371/journal.pone.0050961

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Deep sequencing of RNA from ancient maize kernels

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