Abstract
Phylogenetic and barcoding studies usually use fresh plant tissues as sources of DNA and have successfully amplified DNA for various loci. The use of dried samples, however, is often necessary due to the frequent inaccessibility of fresh rare plants or their parts for genetic analyses or barcoding. The difficulty in obtaining amplifiable DNA is a major restriction of the use of herbarium specimens for DNA analyses. Recent study has highlighted the crucial issues for comparing herbarium and fresh plants for barcoding. We analysed the performance of samples of the family Juncaceae from various herbarium specimens of different ages with fresh plant material in PCRs and the sequences of seven loci (rbcL, rpoC1, trnL-F intergenic spacer, trnL intron, and psbA-trnH from chloroplast DNA; atp1 from mitochondrial DNA; and ITS1-5.8S-ITS2 from nuclear DNA) using a combination of 28 primers. The herbarium specimens amplified well and may thus be successfully applied for both phylogenetic analyses and barcoding for the Juncaceae family. Amplifying DNA was more difficult from dried herbarium specimens than fresh samples but could be successful in most cases when appropriate internal primers were designed or methods were optimised. Using the set of universal primers recommended by the Consortium for the Barcode of Life and designing specific primers for a particular group of interest were both useful. Specimen age and amplicon length had limited detrimental effects on amplification success for most of the Juncaceae loci tested.
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Acknowledgements
We are grateful to the herbarium keepers for the opportunity to study and collect plant material in their collections and to Čestmír Vlček for help with sequence editing.
Funding
This study was conducted in the laboratories of the Center for Integrated Genomics, Institute of Molecular Genetics ASCR, Institute of Botany ASCR, and was supported in part by Grants to LZD: SYNTHESYS DK-TAF 1295, SYNTHESYS GB-TAF 2052 and GAČR 206/07/P147, P506/11/0774, and 16-14649S. The study was also supported by a long-term research developmental project of the Institute of Botany ASCR, No. RVO 67985939.
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Handling Editor: Daniel C. Thomas.
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Záveská Drábková_ESM_1.pdf
Online Resource 1 Organisation of the primers used for the rbcL, rpoC1, trnL-F, psbA-trnH, atp1, ITS1-5.8S-ITS2, rpoB, psbK-I, and atpF-H loci. Arrows indicate orientation and approximate position of the primer sites. (PDF 680 kb)
Záveská Drábková_ESM_2.pdf
Online Resource 2 GenBank accession numbers for the loci used in this study (rbcL, rpoC1, trnL-F, psbA-trnH, atp1, and ITS1-5.8S-ITS2). (PDF 366 kb)
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Online Resource 1. Organisation of the primers used for the rbcL, rpoC1, trnL-F, psbA-trnH, atp1, ITS1-5.8S-ITS2, rpoB, psbK-I, and atpF-H loci.
Online Resource 2. GenBank accession numbers for the loci used in this study (rbcL, rpoC1, trnL-F, psbA-trnH, atp1, and ITS1-5.8S-ITS2).
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Do, D., Záveská Drábková, L. Herbarium tale: the utility of dry specimens for DNA barcoding Juncaceae. Plant Syst Evol 304, 281–294 (2018). https://doi.org/10.1007/s00606-017-1476-x
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DOI: https://doi.org/10.1007/s00606-017-1476-x