title: Greater thanXkb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA.
abstract: Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples-and their quantifiable metadata-preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall "genome-quality" DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA "greater thanXkb" as a standard of comparison, whereXis a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards ("DNA Threshold" and "Percent above Threshold") introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally usedHindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.
authors.affiliation: Global Genome Initiative, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Mulcahy
authors.affiliation: Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA.
authors.forename: Kenneth S
authors.initials: KS
authors.lastname: Macdonald
authors.affiliation: Department of Entomology, National Museum of Natural History, Smithsonian Institution , Washingtion, DC , USA.
authors.forename: Seán G
authors.identifier: 0000-0003-0468-940X
authors.initials: SG
authors.lastname: Brady
authors.affiliation: Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Meyer
authors.affiliation: Global Genome Initiative, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA.
authors.forename: Katharine B
authors.initials: KB
authors.lastname: Barker
authors.affiliation: Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washingtion, DC, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Coddington
keywords: Agarose gels; DNA extractions; Genomic DNA; Tissue preservation