DNA Barcoding Protocols


DNA sequences are being captured at multiple genetic loci for all tree species in the ForestGEO network, with nearly 3,000 plant species sequenced to date. Collection of plant samples for DNA barcode data begins with proper taxonomic identification of individual species from which a reference voucher and tissue sample are collected (Kress et al., 2012 for workflow). Ideally, 4-5 individuals are sampled per species. Field collected samples consist of 0.1-0.5 grams of green leaf tissue that are placed in silica gel desiccant. Only 0.01 gram of tissue is used in DNA extraction for plants where PCR and sequencing follows Fazekas et al. (2012; see also http://ccdb.ca/resources.php). Sequence data are cleaned and aligned into a multi-gene sequence matrix using Geneious (version 7.0, Biomatters), and then used in maximum-likelihood based phylogentic reconstruction following Kress et al. (2009) to generate phylogenetic trees. Quantitative assessment of phylogenetic diversity metrics are conducted in R using the Picante package (see Swenson, 2012; picante.r-forge.r-project.org/ ). DNA barcode data are included in the BOLD database (e.g., Wabikon, USA: dx.doi.org/10.5883/DS-WABLK).

Click here for more information about the Plant DNA Barcode Project with the Botany Department at the Smithsonian National Museum of Natural History.