Literature DB >> 24531081

Ancient whole genome enrichment using baits built from modern DNA.

Jacob M Enk1, Alison M Devault, Melanie Kuch, Yusuf E Murgha, Jean-Marie Rouillard, Hendrik N Poinar.   

Abstract

We report metrics from complete genome capture of nuclear DNA from extinct mammoths using biotinylated RNAs transcribed from an Asian elephant DNA extract. Enrichment of the nuclear genome ranged from 1.06- to 18.65-fold, to an apparent maximum threshold of ∼80% on-target. This projects an order of magnitude less costly complete genome sequencing from long-dead organisms, even when a reference genome is unavailable for bait design.

Entities:  

Keywords:  ancient DNA; targeted enrichment; whole-genome capture

Mesh：

Substances：

Year:  2014        PMID： 24531081     DOI： 10.1093/molbev/msu074

Source DB:  PubMed          Journal:  Mol Biol Evol        ISSN： 0737-4038            Impact factor:   16.240


  35 in total

1.  Partial uracil-DNA-glycosylase treatment for screening of ancient DNA.

Authors:  Nadin Rohland; Eadaoin Harney; Swapan Mallick; Susanne Nordenfelt; David Reich
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2015-01-19       Impact factor: 6.237

Review 2.  Reconstructing ancient genomes and epigenomes.

Authors:  Ludovic Orlando; M Thomas P Gilbert; Eske Willerslev
Journal:  Nat Rev Genet       Date:  2015-06-09       Impact factor: 53.242

3.  Modeling genome coverage in single-cell sequencing.

Authors:  Timothy Daley; Andrew D Smith
Journal:  Bioinformatics       Date:  2014-08-08       Impact factor: 6.937

4.  Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme insular change within a morphologically conservative radiation.

Authors:  Roseina Woods; Samuel T Turvey; Selina Brace; Ross D E MacPhee; Ian Barnes
Journal:  Proc Natl Acad Sci U S A       Date:  2018-11-12       Impact factor: 11.205

Review 5.  Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions.

Authors:  Alex D Greenwood; Yasuko Ishida; Sean P O'Brien; Alfred L Roca; Maribeth V Eiden
Journal:  Microbiol Mol Biol Rev       Date:  2017-12-13       Impact factor: 11.056

6.  Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing.

Authors:  Kojun Kanda; James M Pflug; John S Sproul; Mark A Dasenko; David R Maddison
Journal:  PLoS One       Date:  2015-12-30       Impact factor: 3.240

Review 7.  Targeted capture in evolutionary and ecological genomics.

Authors:  Matthew R Jones; Jeffrey M Good
Journal:  Mol Ecol       Date:  2015-07-30       Impact factor: 6.185

Review 8.  Human evolution: a tale from ancient genomes.

Authors:  Bastien Llamas; Eske Willerslev; Ludovic Orlando
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-02-05       Impact factor: 6.237

9.  Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.

Authors:  Pablo Librado; Clio Der Sarkissian; Luca Ermini; Mikkel Schubert; Hákon Jónsson; Anders Albrechtsen; Matteo Fumagalli; Melinda A Yang; Cristina Gamba; Andaine Seguin-Orlando; Cecilie D Mortensen; Bent Petersen; Cindi A Hoover; Belen Lorente-Galdos; Artem Nedoluzhko; Eugenia Boulygina; Svetlana Tsygankova; Markus Neuditschko; Vidhya Jagannathan; Catherine Thèves; Ahmed H Alfarhan; Saleh A Alquraishi; Khaled A S Al-Rasheid; Thomas Sicheritz-Ponten; Ruslan Popov; Semyon Grigoriev; Anatoly N Alekseev; Edward M Rubin; Molly McCue; Stefan Rieder; Tosso Leeb; Alexei Tikhonov; Eric Crubézy; Montgomery Slatkin; Tomas Marques-Bonet; Rasmus Nielsen; Eske Willerslev; Juha Kantanen; Egor Prokhortchouk; Ludovic Orlando
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-23       Impact factor: 11.205

10.  Episodic Diversifying Selection Shaped the Genomes of Gibbon Ape Leukemia Virus and Related Gammaretroviruses.

Authors:  Niccolò Alfano; Sergios-Orestis Kolokotronis; Kyriakos Tsangaras; Alfred L Roca; Wenqin Xu; Maribeth V Eiden; Alex D Greenwood
Journal:  J Virol       Date:  2015-12-04       Impact factor: 5.103
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