Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

Molecular Ecology Resources
Carly F GrahamChristopher M Somers

Abstract

Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double-digest RADSeq approach (3RAD). We generated libraries using genomic DNA serially extracted from the muscle tissue of 8 individual lake whitefish (Coregonus clupeaformis) following 0-, 12-, 48- and 96-h incubation at room temperature posteuthanasia. This treatment of the tissue resulted in input DNA that ranged in quality from nearly intact to highly sheared. All samples were sequenced as a multiplexed pool on an Illumina MiSeq. Libraries created from low to moderately degraded DNA (12-48 h) performed well. In contrast, the number of RADtags per individual, number of variable sites, and percentage of identical RADtags retained were all dramatically reduced when libraries were made using highly degraded DNA (96-h group). This reduction in performance was largely due to a significant and unexpected loss of raw reads as a result of poor quality scores. Our findings remained consistent after changes in restriction enzymes, modif...Continue Reading

References

Oct 19, 2004·Molecular Ecology·A BoninP Taberlet
Apr 9, 2005·Molecular Ecology·L R PrughC J Krebs
Jan 3, 2006·Genetics·Eric C Anderson, John Carlos Garza
Aug 24, 2007·Proceedings of the National Academy of Sciences of the United States of America·Adrian W BriggsSvante Pääbo
Feb 12, 2008·Trends in Genetics : TIG·Elaine R Mardis
May 27, 2008·Trends in Ecology & Evolution·Craig D MillarDavid M Lambert
Jul 29, 2008·Nucleic Acids Research·Juliane C DohmHeinz Himmelbauer
Oct 15, 2008·PloS One·Nathan A BairdEric A Johnson
Jan 28, 2009·Journal of Evolutionary Biology·P VonlanthenO Seehausen
Dec 10, 2009·Nature Reviews. Genetics·Michael L Metzker
May 5, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Louis BernatchezJérôme St-Cyr
Jan 20, 2011·Briefings in Bioinformatics·Christian Ledergerber, Christophe Dessimoz
Jan 20, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sean MylesEdward S Buckler
Feb 24, 2011·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·W F PfenderM B Slabaugh
Apr 13, 2011·Molecular Ecology Resources·David Martín-GálvezJuan J Soler
May 17, 2011·PloS One·Robert J ElshireSharon E Mitchell
May 18, 2011·Nucleic Acids Research·Kensuke NakamuraShigehiko Kanaya
May 20, 2011·Molecular Ecology Resources·Travis C Glenn
May 26, 2011·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Daniele TrebbiRoberto Tuberosa
Jun 15, 2011·BMC Genomics·Lorenzo BarchiGiuseppe Leonardo Rotino
Jun 18, 2011·Nature Reviews. Genetics·John W DaveyMark L Blaxter
Jun 30, 2011·Bioinformatics·Eva-Maria WillingChristine Dreyer
Apr 21, 2012·Trends in Biotechnology·Søren Overballe-PetersenEske Willerslev
May 23, 2012·Nature Methods·Shi WangMikhail V Matz
Nov 1, 2012·Molecular Ecology·John W DaveyMark L Blaxter
Nov 22, 2012·Molecular Ecology·Nian WangRichard J A Buggs
Feb 23, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Tobias WürschumJochen C Reif

❮ Previous
Next ❯

Citations

Jan 6, 2016·Nature Reviews. Genetics·Kimberly R AndrewsPaul A Hohenlohe
Sep 24, 2015·Molecular Ecology Resources·John E McCormackBrant C Faircloth
Jul 16, 2016·Molecular Ecology Resources·Sandra L HoffbergTravis C Glenn
Jun 12, 2016·Systematic Biology·Michael G HarveyRobb T Brumfield
Oct 22, 2016·Molecular Ecology Resources·Lauren M SchiebelhutMichael N Dawson
Jan 27, 2019·Molecular Ecology Resources·Mariah H Meek, Wesley A Larson
Sep 25, 2019·Molecular Ecology·Nicolas C RochetteJulian M Catchen
Jun 15, 2017·Oncotarget·Elizabeth B PerryRichard M White
Mar 11, 2020·Molecular Ecology Resources·Jocelyn P ColellaMatthew D MacManes
Jun 1, 2017·BMC Genomics·Arpita KonarJeanne Romero-Severson
Feb 26, 2019·Ecology and Evolution·Joseph B PfallerStuart F McDaniel
Aug 21, 2020·BMC Biology·Igor FilipovićGordana Rašić
Jul 21, 2017·PLoS Neglected Tropical Diseases·Luis E Hernandez-CastroMartin S Llewellyn
Oct 17, 2019·PeerJ·Natalia J Bayona-VásquezBrant C Faircloth
Jun 8, 2019·Bioinformatics·Davoud TorkamanehFrançois Belzile
Sep 5, 2019·Proceedings of the National Academy of Sciences of the United States of America·J P LawrenceBrice P Noonan
May 1, 2020·Applications in Plant Sciences·Ingrid E Jordon-ThadenCarl J Rothfels
May 8, 2018·Applications in Plant Sciences·Michael R McKainYa Yang
Jan 16, 2021·The Journal of Heredity·Tyler A BrownMercedes Burns
May 23, 2020·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Troy J KieranTravis C Glenn
Aug 15, 2021·The New Phytologist·Drew A LarsonChristopher W Dick

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.