Data Paper |
Corresponding author: Jose D. Zúñiga ( zunigaj@si.edu ) Academic editor: Yasen Mutafchiev
© 2017 Jose D. Zúñiga, Morgan R. Gostel, Daniel G. Mulcahy, Katharine Barker, Asia Hill, Maryam Sedaghatpour, Samantha Q. Vo, Vicki A. Funk, Jonathan A. Coddington.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Zúñiga JD, Gostel MR, Mulcahy DG, Barker K, Hill A, Sedaghatpour M, Vo SQ, Funk VA, Coddington JA (2017) Data Release: DNA barcodes of plant species collected for the Global Genome Initiative for Gardens Program, National Museum of Natural History, Smithsonian Institution. PhytoKeys 88: 119-122. https://doi.org/10.3897/phytokeys.88.14607
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The Global Genome Initiative has sequenced and released 1961 DNA barcodes for genetic samples obtained as part of the Global Genome Initiative for Gardens Program. The dataset includes barcodes for 29 plant families and 309 genera that did not have sequences flagged as barcodes in GenBank and sequences from officially recognized barcoding genetic markers meet the data standard of the Consortium for the Barcode of Life. The genetic samples were deposited in the Smithsonian Institution’s National Museum of Natural History Biorepository and their records were made public through the Global Genome Biodiversity Network’s portal. The DNA barcodes are now available on GenBank.
DNA barcoding, GenBank, land plants
The Global Genome Initiative (GGI) is a Smithsonian Institution program to collect, organize, share, and study genomic samples of non-human species. The mission of GGI is to preserve and understand Earth’s genomic biodiversity. In pursuit of this mission, GGI aims to collect and preserve genome-quality tissue samples from all major lineages of life on Earth; foster biodiversity genomics research by generating DNA barcodes for dark taxa (i.e., those with no genetic data in online repositories); and promote the use of new technologies to study genomics across the tree of life. GGI supports the Global Genome Biodiversity Network (GGBN), an international network of institutions interested in the preservation of non-human genomic samples (
The Global Genome Initiative for Gardens Program (GGI-Gardens) is a GGI-funded effort to collect and preserve genetic material from the plant Tree of Life that is not yet represented in any of GGBN’s partner institutions, and that are currently found in living collections around the globe. In its first phase, the program targeted living plant collections in the Washington, DC area and collected more than 1,800 genome-quality tissues from 209 families, 1007 genera and 1631 species. Moving forward, GGI-Gardens is focused on expanding its partnerships internationally to continue sample and preserve genomic biodiversity from all families and genera, and, potentially, species of plants on Earth.
The genetic samples collected to date have been deposited in the Smithsonian Institution’s National Museum of Natural History Biorepository (http://naturalhistory.si.edu/rc/biorepository) and are available upon request to researchers across the globe (regulations on sampling leaf material can be found here). All corresponding specimen vouchers have been accessioned in the United States National Herbarium (US) or other recognized, partner herbaria. The GGI-Gardens protocol (
GGI’s barcoding strategy data-mines GenBank to detect taxonomic groups that do not have sequences flagged as barcodes, thus allowing GGI to focus sequencing efforts on lineages that are not represented in this repository. Using this method, GGI selected more than 500 plant genera from GGI-Gardens collections and generated sequences for four genetic markers according to the DNA barcode data standard (
Data are deposited in GenBank under accession numbers MF348326-MF350286 (see supplementary file 1 for the full list of accession numbers). A total of 1961 sequences have been submitted to GenBank representing 160 families and 521 plant genera, including 29 families and 309 genera that previously did not have sequences flagged as barcodes in this data repository. Two of the four genetic markers sequenced, rbcL and matK, have been officially recognized as barcoding regions for land plants (
All laboratory procedures and computer work were conducted in the Laboratories for Analytical Biology facilities at the National Museum of Natural History in Washington, DC and at the Museum Support Center in Suitland, MD. The authors wish to thank Natalia Agudelo and Gabriel Johnson for their continuous support in the lab, Kathryn Faulconer, Sarah Gabler, Kadiera Ingram, Carol Kelloff, Monica Marcelli, Jacob Suissa and Kristen Van Nest for their participation in the collection and curation of the genetic samples and the associated voucher specimens, and Niamh Redmond and Michael Trizna for their advice on post-sequencing data management. This material is based upon work supported by the Global Genome Initiative and Smithsonian Institution Barcoding Network. Any paper(s) resulting directly from this specimen-processing project should reference support from the Smithsonian Institution’s DNA Barcode Network and the Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution.
List of samples collected for the Global Genome Initiative for Gardens project selected for DNA barcoding, with GenBank accession numbers and genetic sample identification numbers. All the sequences are included in the GGI-Gardens BioProject.
Data type: Microsoft Word Document (.docx)
Explanation note: List of samples collected for the Global Genome Initiative for Gardens project selected for DNA barcoding, with GenBank accession numbers and genetic sample identification numbers.