DNA degradation in fish: practical solutions and guidelines to improve
DNA preservation for genomic research
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