Advertisement

Conservation Genetics Resources

, Volume 10, Issue 3, pp 313–315 | Cite as

Trehalose improves PCR amplification of vertebrate nuclear DNA from historical allozymes

  • Michael L. Yuan
  • Guinevere O. U. Wogan
  • Ian J. Wang
Technical Note

Abstract

Historical tissue collections represent potential resources for temporal genetic studies in evolutionary and conservation biology. Unfortunately, DNA from historical samples stored without modern genetic analyses in mind, such as frozen allozyme homogenates, are often degraded and contaminated with PCR inhibitors. Here, we report the successful use of trehalose for improving PCR amplification of degraded, vertebrate nuclear DNA extracted from cryopreserved allozymes. We amplified and sequenced two nuclear genes (MLC2a and RPL12) from allozymes of the Shasta salamander, Hydromantes shastae. Our results demonstrate the potential of trehalose as a tool for utilizing historical allozyme collections in modern genetic studies.

Keywords

Conservation Degraded DNA PCR enhancer Museum samples Salamander 

Notes

Acknowledgements

We thank David Wake, Carol Spencer, and the Museum of Vertebrate Zoology (MVZ) for allozyme and tissue samples. We thank the MVZ’s Evolutionary Genetics Lab and Lydia Smith for access to sequencing facilities. We also thank an anonymous reviewer for providing thoughtful feedback on this manuscript. This work was supported by a grant from the Hellman Fellows Fund, the California Agricultural Experiment Station, and the USDA National Institute of Food and Agriculture, Hatch project 1007819.

References

  1. Arbetman MP, Premoli AC (2011) Oldies (but goldies!): extracting DNA from cryopreserved allozyme homogenates. J Hered 102:764–769. doi: 10.1093/jhered/esr096 CrossRefPubMedGoogle Scholar
  2. Bezrukavnikov S, Mashaghi A, van Wijk RJ et al (2014) Trehalose facilitates DNA melting: a single-molecule optical tweezers study. Soft Matter 10:7269–7277. doi: 10.1039/C4SM01532K CrossRefPubMedGoogle Scholar
  3. Butler SL, Falke JJ (1996) Effects of protein stabilizing agents on thermal backbone motions: a disulfide trapping study. Biochemistry 35:10595–10600. doi: 10.1021/bi961107v CrossRefPubMedPubMedCentralGoogle Scholar
  4. Ellegren H (1994) Genomic DNA from museum bird feathers. In: Herrmann B, Hummel S (eds) Ancient DNA. Springer New York, pp 211–217CrossRefGoogle Scholar
  5. Fisher-Reid MC, Wiens JJ (2011) What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades. BMC Evol Biol 11:300. doi: 10.1186/1471-2148-11-300 CrossRefPubMedPubMedCentralGoogle Scholar
  6. Gilbert MTP, Wilson AS, Bunce M et al (2004) Ancient mitochondrial DNA from hair. Curr Biol 14:R463–R464. doi: 10.1016/j.cub.2004.06.008 CrossRefPubMedGoogle Scholar
  7. Holmes MW, Hammond TT, Wogan GOU et al (2016) Natural history collections as windows on evolutionary processes. Mol Ecol 25:864–881. doi: 10.1111/mec.13529 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Hykin SM, Bi K, McGuire JA (2015) Fixing formalin: a method to recover genomic-scale DNA sequence data from formalin-fixed museum specimens using high-throughput sequencing. PLoS ONE 10:e0141579. doi: 10.1371/journal.pone.0141579 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Mundy NI, Unitt P, Woodruff DS (1997) Skin from feet of museum specimens as a non-destructive source of DNA for avian genotyping. Auk 114:126–129. doi: 10.2307/4089075 CrossRefGoogle Scholar
  10. R Development Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org/
  11. Samarakoon T, Wang SY, Alford MH (2013) Enhancing PCR amplification of DNA from recalcitrant plant specimens using a trehalose-based additive. Appl Plant Sci. doi: 10.3732/apps.1200236 PubMedPubMedCentralCrossRefGoogle Scholar
  12. Schlötterer C (2004) The evolution of molecular markers—just a matter of fashion? Nat Rev Genet 5:63–69. doi: 10.1038/nrg1249 CrossRefPubMedGoogle Scholar
  13. Snyder-Mackler N, Majoros WH, Yuan ML et al (2016) Efficient genome-wide sequencing and low-coverage pedigree analysis from noninvasively collected samples. Genetics 203:699–714. doi: 10.1534/genetics.116.187492 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Spiess A-N, Mueller N, Ivell R (2004) Trehalose is a potent PCR enhancer: lowering of DNA melting temperature and thermal stabilization of Taq polymerase by the disaccharide trehalose. Clin Chem 50:1256–1259. doi: 10.1373/clinchem.2004.031336 CrossRefPubMedGoogle Scholar
  15. Suarez AV, Tsutsui ND (2004) The value of museum collections for research and society. Bioscience 54:66–74. doi: 10.1641/0006-3568(2004)054[0066:TVOMCF]2.0.CO;2 CrossRefGoogle Scholar
  16. Wake DB, Maxson LR, Wurst GZ (1978) Differentiation, albumin evolution, and their biogeographic implications in plethodontid salamanders of California and Southern Europe. Evolution Int J Org Evolution 32:529–539. doi: 10.1111/j.1558-5646.1978.tb04595.x CrossRefGoogle Scholar
  17. Wisely SM, Maldonado JE, Fleische RC (2004) A technique for sampling ancient DNA that minimizes damage to museum specimens. Conserv Genet 5:105–107. doi: 10.1023/B:COGE.0000014061.04963.da CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  • Michael L. Yuan
    • 1
  • Guinevere O. U. Wogan
    • 1
  • Ian J. Wang
    • 1
  1. 1.Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyUSA

Personalised recommendations