Feasibility of using dried plant specimens for DNA barcoding. A case study of the Juncaceae
- Published
- Accepted
- Subject Areas
- Genomics, Plant Science
- Keywords
- DNA barcoding, dry plants, herbarium specimens, Juncaceae
- Copyright
- © 2016 Do 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
- 2016. Feasibility of using dried plant specimens for DNA barcoding. A case study of the Juncaceae. PeerJ Preprints 4:e2293v1 https://doi.org/10.7287/peerj.preprints.2293v1
Abstract
Background. Phylogenetic and barcoding studies usually employ fresh parts of plants as the source of DNA. Successful DNA amplification has been achieved in such investigations for different regions. However, there is need for the utilization of dried samples, due to frequent inaccessibility of fresh precious plants or their parts for genetic analyses or barcoding studies. Difficulties in obtaining amplifiable DNA have appeared as one of the major pitfalls that resulted in slowdown of the use of herbarium specimens for DNA analyses. Methods. Recent study highlights the crucial issues that are being faced by comparison of herbarium and fresh plants for barcoding purposes. We analyzed the performance of samples from herbarium specimens of different age and fresh plants in PCR reaction and sequencing of seven regions (cpDNA: rbcL, rpoC1, trnL-F intergenic spacer, trnL intron, psbA-trnH, mtDNA: atp1 and nrDNA: ITS1-5.8S-ITS2) with a combination of twenty-eight primers. Conclusions. We show that herbarium specimens may be successfully applied both for phylogenetic as well as for barcoding purposes. In comparison with fresh samples, working with dried herbarium specimens is more complicated, but may lead to amplification and sequencing success in almost all cases when appropriate internal primers are designed or optimization methods are used. Both attempts are useful for this aim: using the set of universal primers recommended by CBOL and design specific primers for a particular group of interest. We found limited detrimental effect of specimen age and length of the amplicon on the amplification success in most of the tested regions in the Juncaceae.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Figure S1
Organization of used primers of the rbcL, rpoC1, trnL-F, psbA-trnH, atp1, ITS1-5.8S-ITS2, rpoB, psbK-I and atpF-H regions. Arrows indicate orientation and approximate position of primer sites.
Table S1
Genbank accession numbers for the regions used in this study (rbcL, rpoC1, trnL-F, psbA-trnH, atp1 and ITS1-5.8S-ITS2).