APPLICATIONS OF NEXT-GENERATION SEQUENCING Reconstructing ancient genomes and epigenomes

被引：136

作者：

Orlando, Ludovic ^{[1
,2
]}

Gilbert, M. Thomas P. ^{[1
,3
]}

Willerslev, Eske ^{[1
]}

机构：

[1] Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen C, Denmark

[2] Univ Toulouse, Univ Paul Sabatier, Lab AMIS, CNRS UMR 5288, F-31000 Toulouse, France

[3] Curtin Univ, Dept Environm & Agr, Trace & Environm DNA Lab, Perth, WA 6102, Australia

来源：

NATURE REVIEWS GENETICS | 2015年 / 16卷 / 07期

基金：

新加坡国家研究基金会;

关键词：

DNA-SEQUENCES; NEANDERTHAL GENOME; MISCODING LESIONS; YERSINIA-PESTIS; READ ALIGNMENT; EVOLUTION; PATTERNS; ANCESTRY; INSIGHTS; HISTORY;

D O I：

10.1038/nrg3935

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：395 / 408

页数：14

共 131 条

[21] Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments [J].

Dabney, Jesse ;

Knapp, Michael ;

Glocke, Isabelle ;

Gansauge, Marie-Theres ;

Weihmann, Antje ;

Nickel, Birgit ;

Valdiosera, Cristina ;

Garcia, Nuria ;

Paeaebo, Svante ;

Arsuaga, Juan-Luis ;

Meyer, Matthias .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (39) :15758-15763

[22] Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries [J].

Dabney, Jesse ;

Meyer, Matthias .

BIOTECHNIQUES, 2012, 52 (02) :87-+

[23] Shotgun microbial profiling of fossil remains [J].

Der Sarkissian, C. ;

Ermini, L. ;

Jonsson, H. ;

Alekseev, A. N. ;

Crubezy, E. ;

Shapiro, B. ;

Orlando, L. .

MOLECULAR ECOLOGY, 2014, 23 (07) :1780-1798

[24] Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array [J].

Devault, Alison M. ;

McLoughlin, Kevin ;

Jaing, Crystal ;

Gardner, Shea ;

Porter, Teresita M. ;

Enk, Jacob M. ;

Thissen, James ;

Allen, Jonathan ;

Borucki, Monica ;

DeWitte, Sharon N. ;

Dhody, Anna N. ;

Poinar, Hendrik N. .

SCIENTIFIC REPORTS, 2014, 4

[25] Second-Pandemic Strain of Vibrio cholerae from the Philadelphia Cholera Outbreak of 1849 [J].

Devault, Alison M. ;

Golding, G. Brian ;

Waglechner, Nicholas ;

Enk, Jacob M. ;

Kuch, Melanie ;

Tien, Joseph H. ;

Shi, Mang ;

Fisman, David N. ;

Dhody, Anna N. ;

Forrest, Stephen ;

Bos, Kirsten I. ;

Earn, David J. D. ;

Holmes, Edward C. ;

Poinar, Hendrik N. .

NEW ENGLAND JOURNAL OF MEDICINE, 2014, 370 (04) :334-340

[26] Testing for Ancient Admixture between Closely Related Populations [J].

Durand, Eric Y. ;

Patterson, Nick ;

Reich, David ;

Slatkin, Montgomery .

MOLECULAR BIOLOGY AND EVOLUTION, 2011, 28 (08) :2239-2252

[27] Ancient Whole Genome Enrichment Using Baits Built from Modern DNA [J].

Enk, Jacob M. ;

Devault, Alison M. ;

Kuch, Melanie ;

Murgha, Yusuf E. ;

Rouillard, Jean-Marie ;

Poinar, Hendrik N. .

MOLECULAR BIOLOGY AND EVOLUTION, 2014, 31 (05) :1292-1294

[28] Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins [J].

Eriksson, Anders ;

Manica, Andrea .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (35) :13956-13960

[29] Major transitions in human evolution revisited: A tribute to ancient DNA [J].

Ermini, Luca ;

Sarkissian, Clio Der ;

Willerslev, Eske ;

Orlando, Ludovic .

JOURNAL OF HUMAN EVOLUTION, 2015, 79 :4-20

[30] Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics [J].

Fabre, Pierre-Henri ;

Vilstrup, Julia T. ;

Raghavan, Maanasa ;

Sarkissian, Clio Der ;

Willerslev, Eske ;

Douzery, Emmanuel J. P. ;

Orlando, Ludovic .

BIOLOGY LETTERS, 2014, 10 (07)

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