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DNA degradation in fish: practical solutions and guidelines to improve DNA preservation for genomic research
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  • Tom Oosting,
  • Elena Hilario,
  • Maren Wellenreuther,
  • Peter Ritchie
Tom Oosting
Victoria University of Wellington
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Elena Hilario
New Zealand Institute for Plant and Food Research Ltd
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Maren Wellenreuther
The New Zealand Institute for Plant & Food Research Ltd
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Peter Ritchie
Victoria University of Wellington
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Abstract

1) The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used, or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome-wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. 2) We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25M EDTA, NaCl saturated solution, and 2. ethanol) under a range of storage conditions over a three-month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. 3) We found that the storage solution has a dramatic effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hours, making samples unsuitable for next-generation-sequencing. 4) We recommend DESS as the most promising solution to improve DNA preservation. These results provide practical and economical advice to improve DNA preservation when sampling for genome-wide applications. Keywords: DMSO, DNA preservation, ethanol, fish, next-generation-sequencing, NGS, snapper

Peer review status:ACCEPTED

24 Mar 2020Submitted to Ecology and Evolution
25 Mar 2020Submission Checks Completed
25 Mar 2020Assigned to Editor
07 Apr 2020Reviewer(s) Assigned
17 Apr 2020Review(s) Completed, Editorial Evaluation Pending
04 May 2020Editorial Decision: Revise Minor
22 May 20201st Revision Received
27 May 2020Submission Checks Completed
27 May 2020Assigned to Editor
27 May 2020Review(s) Completed, Editorial Evaluation Pending
10 Jun 2020Editorial Decision: Accept