Improving sustainable use of genetic resources in biodiversity archives
- Published
- Accepted
- Subject Areas
- Biodiversity, Bioinformatics, Genetics
- Keywords
- tissue sampling, genetic resources, biodiversity, sustainability , herpetology, biological collections, DNA extraction
- Copyright
- © 2019 Tuschhoff et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. Improving sustainable use of genetic resources in biodiversity archives. PeerJ Preprints 7:e27894v1 https://doi.org/10.7287/peerj.preprints.27894v1
Abstract
Tissue sample databases housed in biodiversity archives represent a vast trove of genetic resources, and these tissues are frequently destructively subsampled and provided to researchers for DNA extractions and subsequent sequencing. While obtaining a sufficient quantity of DNA for downstream applications is vital for these researchers, it is also important to preserve tissue resources for future use given that the original material is destructively and consumptively sampled with each use. It is therefore necessary to develop standardized tissue subsampling and loaning procedures to ensure that tissues are being used efficiently. In this study, we specifically focus on the efficiency of DNA extraction methods by using anuran liver and muscle tissues maintained at a biodiversity archive. We conducted a series of experiments to test whether current practices involving coarse visual assessments of tissue size are effective, how tissue mass correlates with DNA yield and concentration, and whether the amount of DNA recovered is correlated with sample age. We found that tissue samples between 2 mg and 8 mg resulted in the most efficient extractions, with tissues at the lower end of this range providing more DNA per unit mass and tissues at the higher end of this range providing more total DNA. Additionally, we found no correlation between tissue age and DNA yield. Because we find that even very small tissue subsamples tend to yield far more DNA than is required by researchers for modern sequencing applications (including whole genome shotgun sequencing), we recommend that biodiversity archives consider dramatically improving sustainable use of their archived material by providing researchers with set quantities of extracted DNA rather than with the subsampled tissues themselves.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Tissue sample raw data for all experiments
This document includes data on each tissue subsample used in the experiment. This information includes the tissue identity, age, tissue type, mass, and DNA yield as well as the experiment/trial in which it was used.
R code used to run analyses for all experiments
This text document includes the complete R code used to run analyses for all experiments run in this study.