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Assessing the utility of whole genome amplified DNA for next-generation molecular ecology.

Publication ,  Journal Article
Blair, C; Campbell, CR; Yoder, AD
Published in: Molecular ecology resources
September 2015

DNA quantity can be a hindrance in ecological and evolutionary research programmes due to a range of factors including endangered status of target organisms, available tissue type, and the impact of field conditions on preservation methods. A potential solution to low-quantity DNA lies in whole genome amplification (WGA) techniques that can substantially increase DNA yield. To date, few studies have rigorously examined sequence bias that might result from WGA and next-generation sequencing of nonmodel taxa. To address this knowledge deficit, we use multiple displacement amplification (MDA) and double-digest RAD sequencing on the grey mouse lemur (Microcebus murinus) to quantify bias in genome coverage and SNP calls when compared to raw genomic DNA (gDNA). We focus our efforts in providing baseline estimates of potential bias by following manufacturer's recommendations for starting DNA quantities (>100 ng). Our results are strongly suggestive that MDA enrichment does not introduce systematic bias to genome characterization. SNP calling between samples when genotyping both de-novo and with a reference genome are highly congruent (>98%) when specifying a minimum threshold of 20X stack depth to call genotypes. Relative genome coverage is also similar between MDA and gDNA, and allelic dropout is not observed. SNP concordance varies based on coverage threshold, with 95% concordance reached at ~12X coverage genotyping de-novo and ~7X coverage genotyping with the reference genome. These results suggest that MDA may be a suitable solution for next-generation molecular ecological studies when DNA quantity would otherwise be a limiting factor.

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Published In

Molecular ecology resources

DOI

EISSN

1755-0998

ISSN

1755-098X

Publication Date

September 2015

Volume

15

Issue

5

Start / End Page

1079 / 1090

Related Subject Headings

  • Polymorphism, Single Nucleotide
  • Nucleic Acid Amplification Techniques
  • High-Throughput Nucleotide Sequencing
  • Genomics
  • Evolutionary Biology
  • Cheirogaleidae
  • Animals
  • 06 Biological Sciences
 

Citation

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Blair, C., Campbell, C. R., & Yoder, A. D. (2015). Assessing the utility of whole genome amplified DNA for next-generation molecular ecology. Molecular Ecology Resources, 15(5), 1079–1090. https://doi.org/10.1111/1755-0998.12376
Blair, Christopher, C Ryan Campbell, and Anne D. Yoder. “Assessing the utility of whole genome amplified DNA for next-generation molecular ecology.Molecular Ecology Resources 15, no. 5 (September 2015): 1079–90. https://doi.org/10.1111/1755-0998.12376.
Blair C, Campbell CR, Yoder AD. Assessing the utility of whole genome amplified DNA for next-generation molecular ecology. Molecular ecology resources. 2015 Sep;15(5):1079–90.
Blair, Christopher, et al. “Assessing the utility of whole genome amplified DNA for next-generation molecular ecology.Molecular Ecology Resources, vol. 15, no. 5, Sept. 2015, pp. 1079–90. Epmc, doi:10.1111/1755-0998.12376.
Blair C, Campbell CR, Yoder AD. Assessing the utility of whole genome amplified DNA for next-generation molecular ecology. Molecular ecology resources. 2015 Sep;15(5):1079–1090.
Journal cover image

Published In

Molecular ecology resources

DOI

EISSN

1755-0998

ISSN

1755-098X

Publication Date

September 2015

Volume

15

Issue

5

Start / End Page

1079 / 1090

Related Subject Headings

  • Polymorphism, Single Nucleotide
  • Nucleic Acid Amplification Techniques
  • High-Throughput Nucleotide Sequencing
  • Genomics
  • Evolutionary Biology
  • Cheirogaleidae
  • Animals
  • 06 Biological Sciences