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.

Figure 1. Histogram showing fragment length distribution of maize GS FLX sequence reads from 3 Arizonan DNA (FLX4-6) samples (blue) in comparison to 3 Arizonan cDNA (FLX1-3) samples (red).

Figure 2. Taxonomic distribution of non-maize HiSeq 2000 reads from cDNA and DNA sets:

(a) represents cDNA sample 935130, (b) represents cDNA sample 935230, and (c) represents a DNA shotgun sample from 100,00 randomly sampled unmapped reads were used to perform BLAST searches and MEGAN was for taxonomic characterization of non-maize reference genome (non-B73) reads.

Figure 3. Histograms showing fragment length distribution of maize GS FLX sequence reads from cDNA samples (FLX1-3), comparing ribosomal RNA (red) to messenger RNA (blue) fragment lengths.