Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts

@article{Gilbert2007WholeGenomeSS,
  title={Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts},
  author={M. Thomas P. Gilbert and Lynn P. Tomsho and Snjezana Rendulic and Mike Packard and Daniela I. Drautz and Andrei V. Sher and Alexei Tikhonov and Love Dal{\'e}n and Tatyana Kuznetsova and Pavel A Kosintsev and Paula F. Campos and Thomas F.G. Higham and Matthew James Collins and Andrew Wilson and Fyodor Shidlovskiy and Bernard Buigues and Per G. P. Ericson and Mietje Germonpr{\'e} and Anders G{\"o}therstr{\"o}m and Paola Iacumin and V. I. Nikolaev and Malgosia Nowak-Kemp and Eske Willerslev and James R. Knight and Gerard P. Irzyk and Clotilde Perbost and Karin M. Fredrikson and Timothy T. Harkins and Sharon Sheridan and Webb Miller and Stephan C. Schuster},
  journal={Science},
  year={2007},
  volume={317},
  pages={1927 - 1930}
}
Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in… 

Analysis of Whole Mitogenomes from Ancient Samples.

This protocol was designed for enrichment of mitochondrial DNA in ancient or other degraded samples, and can be easily adapted for using for building libraries for shotgun-sequencing of whole genomes, or enrichment of other genomic regions.

True single-molecule DNA sequencing of a pleistocene horse bone.

The first "true single molecule sequencing" of ancient DNA is reported, suggesting that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third-generation sequencing approaches.

Comment on "Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts"

When experimental parameters are carefully controlled for, including adequate sampling, quantitative polymerase chain reaction analysis, and modeling the decay of DNA, the general importance of this claim is not supported.

Response to Comment on "Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts"

The authors are misreading and misinterpreting the conclusions of the study; they claim nothing further than that hair shaft represents an excellent source material for the shotgun sequencing of mitochondrial DNA genomes.

Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples

While both methods recovered DNA from ancient soft tissue, the laboratory method performed better overall in terms of DNA yield and quality, which was primarily due to the poorer performance of the commercial binding buffer in recovering aDNA.

Mitogenomic analyses from ancient DNA.

Characterising the potential of sheep wool for ancient DNA analyses

The data suggest that wool offers a promising source for future ancient mitochondrial DNA studies, and short fragments of both mitochondrial and single-copy nuclear DNA can be PCR-amplified from wool derived from a variety of breeds, regardless of the body location or natural pigmentation.

Rapid assembly of taxonomically validated mitochondrial genomes from historical insect collections

Contiguous sequences are difficult to obtain from degraded DNA with Sanger technology but the Illumina short reads are a natural fit for dry-collection specimens and the obvious possibility for scaling up this protocol provides exciting prospects for the large-scale indexing of natural history collections using partial or full mitochondrial genomes.

A rapid column‐based ancient DNA extraction method for increased sample throughput

The results on Pleistocene cave bear samples show that DNA yields are quantitatively comparable, and in fact even slightly better than with silica batch extraction, while at the same time the number of samples that can conveniently be processed in parallel increases and both bench time and costs decrease using this method.
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