Biology subjects

Ella Reiter

Publications and source records attributed to Ella Reiter.

3 recordsLinked to original sources

bioRxiv2020

Comparison of target enrichment strategies for ancient pathogen DNA

In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA, and targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods - (1) array-based hybridization capture and in-solution capture using either (2) RNA or (3) DNA baits - have different characteristics that may influence the capture efficiency, specificity, and reproducibility. Here, we compared their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum of 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens, and RNA baits usually perform better than DNA baits. Method summaryWe compared three targeted DNA enrichment strategies used in ancient DNA research for the specific enrichment of pathogen DNA regarding their efficiency, specificity, and reproducibility for ancient and modern Mycobacterium leprae and Treponema pallidum samples. Array-based capture and in-solution capture with RNA and DNA baits were all tested in three independent replicates.

genetics↗

bioRxiv2016

Extraction of ultrashort DNA molecules from herbarium specimens

DNA extracted from herbarium specimens is highly fragmented and decays at a faster rate than DNA from ancient bones. Therefore, it is crucial to utilize extraction protocols that retrieve short DNA molecules. Improvements in extraction and library preparation protocols for animal remains have allowed efficient retrieval of molecules shorter than 50 bp. We adapted those improvements to extraction protocols for herbarium specimens and evaluated their performance by shotgun sequencing, which allows an accurate estimation of the distribution of fragment lengths. Extraction with PTB buffer decreased median fragment length by 35% when compared to CTAB. Modifying the binding conditions of DNA to silica allowed for an additional decrease of 10%. We did not observe a further decrease in length when we used single-stranded instead of double-stranded library preparation methods. Our protocol enables the retrieval of ultrashort molecules from herbarium specimens and will help to unlock the genetic information stored in herbaria.

Genomics↗

bioRxiv2015

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens

Herbaria archive a record of changes of worldwide plant biodiversity harboring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation -length and base composition at breaking points-, and nucleotide misincorporation by analyzing 86 herbarium samples spanning the last 300 years using Illumina shot-gun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 x 10-4 per year, which is ten times faster than the rate estimated for fossilized bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar of what has been found analyzing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine (C) to thymine (T) substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

Evolutionary Biology↗