Deep Sequencing of RNA from Ancient Maize Kernels

Fordyce, Sarah L.; Ávila-Arcos, María C.; Rasmussen, Morten; Cappellini, Enrico; Romero-Navarro, J. Alberto; Wales, Nathan; Penfield, Steven; Brown, Terence A.; Vielle‐Calzada, Jean‐Philippe; Montiel, Rafaél; Jørgensen, Tina; Odegaard, Nancy; Jacobs, Michael A.; Arriaza, Bernardo; Higham, Thomas; Ramsey, Christopher Bronk; Willerslev, Eske; Gilbert, M. Thomas P.

doi:10.1371/journal.pone.0050961

Cited by 42 publications

(36 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Besides delivering ancient genomes and epigenomes, new methodological developments have also provided access to ancient transcriptomes 113,114 and proteomes 17,115,116 . Owing to the biochemical processes inherent in animal cell death, animal tissues are unlikely to represent good reservoirs for long-term RNA survival.…”

Section: Discussionmentioning

confidence: 99%

“…Materials still exist in other organisms that do not undergo autolysis. One example is plant seed, a tissue that requires RNA survival for germination and that has demonstrated ancient RNA survival going back hundreds to thousands of years 113,114 . Such materials may contribute to our understanding of how gene expression pathways have been remodelled during domestication.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Reconstructing ancient genomes and epigenomes

2015

Self Cite

View full text Add to dashboard Cite

Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Reconstructing ancient genomes and epigenomes

2015

Self Cite

View full text Add to dashboard Cite

show abstract

“…Mitochondrial DNA from one species can comprise just 10 -8 percent of the total eDNA in freshwater (Turner et al 2014a); thus, low template quantity and background interference present challenges for functional genomic analysis of macrobial eDNA, particularly for single-copy nuclear loci (Morin et al 2007). However, paleogenetic studies have demonstrated that these types of functional genomic data can be obtained from biomaterial exposed to substantial DNA/RNA decay (Fordyce et al 2013). Furthermore, microbial metagenomics has paved the way for functional genomic analysis of eDNA, demonstrating how to analyze functional genomic data from complex environmental mixtures of individuals and species (Mendoza et al 2015).…”

Section: Functional Genetics and Genomicsmentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

View full text Add to dashboard Cite

Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the ''ecology'' of eDNA-myriad interactions between extraorganismal genetic material and its environment-and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.

show abstract

“…RNA is highly prone to hydrolytic attack relative to DNA, partly because of its single stranded nature. However, while more labile than DNA, ancient RNA still occurs in useful quantities (Fordyce et al, 2013;Smith et al, 2014a). Furthermore, methylation can be detected in archaeological samples (Briggs et (Palmer et al, 2012) mapped to Arabidopsis thaliana metabolic pathways.…”

Section: The Challenge Of Understanding How Plant Community Systems Bmentioning

confidence: 99%

Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant–hominin co-evolution back to the Pliocene

Allaby

Kistler

Gutaker

et al. 2015

Journal of Human Evolution

View full text Add to dashboard Cite

The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant-human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively small selective value, punctuated by periods in which changes in one-half of the plant-hominin relationship cause rapid, low-complexity adaptation in the other. A corollary of a single plant-hominin co-evolutionary process is that clues about the initiation of the domestication process may well lie deep within the hominin lineage.

show abstract

Deep Sequencing of RNA from Ancient Maize Kernels

Cited by 42 publications

References 37 publications

Reconstructing ancient genomes and epigenomes

Reconstructing ancient genomes and epigenomes

The ecology of environmental DNA and implications for conservation genetics

Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant–hominin co-evolution back to the Pliocene

Contact Info

Product

Resources

About