Deep Sequencing of RNA from Ancient Maize Kernels

Sarah L. Fordyce; Maria C. Ávila-Arcos; Morten Rasmussen; Enrico Cappellini; J. Alberto Romero-Navarro; Nathan Wales; David E. 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; M. Thomas P. Gilbert

doi:10.1371/journal.pone.0050961

Deep Sequencing of RNA from Ancient Maize Kernels

Sarah L. Fordyce, Maria C. Ávila-Arcos, Morten Rasmussen, Enrico Cappellini, J. Alberto Romero-Navarro, Nathan Wales, David E. 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, M. Thomas P. 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 (US)
Article number	e50961
Journal	PloS one
Volume	8
Issue number	1
DOIs	https://doi.org/10.1371/journal.pone.0050961
State	Published - Jan 17 2013
Externally published	Yes

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Fordyce, S. L., Ávila-Arcos, M. 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, M. T. P. (2013). Deep Sequencing of RNA from Ancient Maize Kernels. PloS one, 8(1), Article e50961. https://doi.org/10.1371/journal.pone.0050961

Fordyce, SL, Ávila-Arcos, MC, Rasmussen, M, Cappellini, E, Romero-Navarro, JA, Wales, N, Alquezar-Planas, DE, Penfield, S, Brown, TA, Vielle-Calzada, JP, Montiel, R, Jørgensen, T, Odegaard, N, Jacobs, M, Arriaza, B, Higham, TFG, Ramsey, CB, Willerslev, E & Gilbert, MTP 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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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 - Wales, Nathan

AU - Alquezar-Planas, David E.

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AU - Odegaard, Nancy

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AU - Arriaza, Bernardo

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Deep Sequencing of RNA from Ancient Maize Kernels

Abstract

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