Small RNA Activity in Archeological Barley Shows Novel Germination Inhibition in Response to Environment

Abstract

The recovery of ancient RNA from archeological material could enable the direct study of microevolutionary processes. Small RNAs are a rich source of information because their small size is compatible with biomolecular preservation, and their roles in gene regulation make them likely foci of evolutionary change. We present here the small RNA fraction from a sample of archeological barley generated using high-throughput sequencing that has previously been associated with localized adaptation to drought. Its microRNA profile is broadly similar to 19 globally distributed modern barley samples with the exception of three microRNAs (miRNA159, miRNA319, and miR396), all of which are known to have variable expression under stress conditions. We also found retrotransposon activity to be significantly reduced in the archeological barley compared with the controls, where one would expect the opposite under stress conditions. We suggest that the archeological barley’s conflicting stress signals could be the result of long-term adaptation to its local environment.

Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA

“…These findings were consistent with a proposed origin of domesticated barley in the Upper Jordan Valley, as well as with gene flow between cultivated and wild populations during the early domestication phase [104]. In addition to aDNA, plant subfossils can also provide ancient RNA (including small RNAs) and epigenetic (i.e., DNA methylation) signatures [143–146]. Barley is the ancient crop that has garnered most of the attention at the DNA, RNA, and epigenetic levels.…”

“…Barley is the ancient crop that has garnered most of the attention at the DNA, RNA, and epigenetic levels. A series of investigations have addressed the complex process of local adaptation and domestication, or have identified the presence of barley stripe mosaic virus, one of the major diseases affecting this major crop [101, 144–146].…”

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

“…Despite the dominance of DNA, in recent years several studies have begun to explore whether or not RNA survives in archaeological substrates, particularly in the context of plant materials. Next-generation sequencing (NGS) approaches have uncovered viral RNA genomes in barley grains and faecal matter [11,12], environmentally induced differential regulation patterns of microRNA and RNA-induced genome modifications in barley grain [13,14], and general transcriptomics in maize kernels [15]. All but one of these datasets, however, have been derived from plant seed endosperm, which often facilitates exceptional preservation [16,17] and is known to be predisposed to nucleic acid compartmentalisation [18], thus allowing for reasonable expectations of such preservation.…”

Ancient microRNA profiles of a 14,300-year-old canid are taxonomically informative and give glimpses into gene regulation from the Pleistocene

“…With the availability of powerful and sensitive sequencing approaches, a small number of recent studies have capitalised on early observations of very short RNA fragments surviving in some archaeological plant and mummified materials (Rollo 1985;Venanzi and Rollo 1990), and have recovered sequenceable amounts of aRNA from historic plant and feces samples. In doing so they have detected, for instance, viral RNA genomes (Ng et al 2014;Smith et al 2014), microRNAs (Smith et al 2017) and even fragments of protein-coding transcripts (Fordyce et al 2013). While these studies represent a proof of concept for aRNA sequencing, or paleotranscriptomics, they are limited to relatively recent (<1000 years old) samples and, except for one study, restricted on seedmaterial that conveys highly preservative conditions.…”

“…MicroRNAs are 22 nucleotide short RNA molecules that are excellent cell-and tissue markers (Christodoulou et al 2010;McCall et al 2017;de Rie et al 2017), and stable in historic samples (Keller et al 2017;Smith et al 2017). They are produced when RNA hairpin structures ('precursor microRNAs') are cleaved into functional regulatory molecules ('mature microRNAs') and biogenesis by-products ('star microRNAs').…”