title: Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process.
abstract: Genomic methylation is variable under biotic and abiotic stresses in plants. In particular, viral infection is thought to significantly increase genomic methylation with particularly high activity around transposable elements. Here we present the genomic methylation profiles of grains of archaeological barley (Hordeum vulgare) from several strata from a site in southern Egypt, from the Napatan to the Islamic periods (800 BCE - 1812 CE). One sample tested positive for viral infection and exhibits an unusually high degree of genomic methylation compared to the rest. A decreasing trend in global methylation levels according to deposition date shows in-situ de-methylation of 5-methylcytosine, which can be described as a diagenetic process. This is most likely a deamination mediated de-methylation process and is expected to lead to 5 mC > T base modifications in addition to the C > U modifications due to cytosine deamination, so represents a time-dependent process of DNA diagenesis in ancient DNA.
authors.affiliation: School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK.
authors.forename: Oliver
authors.initials: O
authors.lastname: Smith
authors.affiliation: School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK.
authors.forename: Alan J
authors.initials: AJ
authors.lastname: Clapham
authors.affiliation: The Austrian Archaeological Institute; Cairo Branch, Zamalek, Sharia Ismail Muhammed, Apt 62/72, Cairo, Egypt.
authors.forename: Pam
authors.initials: P
authors.lastname: Rose
authors.affiliation: BGI-Europe-UK, 9 Devonshire Square, London, EC2M 4YF, UK.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Liu
authors.affiliation: B BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK.
authors.forename: Robin G
authors.initials: RG
authors.lastname: Allaby
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics / Q000266:history / Q000821:virology; D019175:DNA Methylation; D019143:Evolution, Molecular; D059647:Gene-Environment Interaction; D056426:Genetic Loci; D018745:Genome, Plant; D049668:History, 15th Century; D049669:History, 16th Century; D049690:History, Ancient; D049691:History, Medieval; D001467:Hordeum / Q000235:genetics* / Q000266:history / Q000821:virology; D054884:Host-Pathogen Interactions; D006801:Humans; D009029:Mosaic Viruses / Q000502:physiology; D010935:Plant Diseases / Q000821:virology