Mining museums for historical DNA: advances and challenges in museomics. Available online 26 August 2021 Highlights The study of historical DNA (hDNA), utilizing museum specimens, has emerged as a sub-discipline distinct from ancient DNA.
Recent advances in hDNA extraction and sequencing support minimally destructive sampling requests for well-represented specimens, and can now be considered routine/low risk. Availability of reference genomes, improved mapping techniques, and decreased costs make whole genome resequencing an attractive option for future hDNA studies.
New research is needed to describe and correct for hDNA degradation over decadal-scales, and across diverse tissues and voucher types. Together, modern and hDNA have the potential to accelerate comparative biological research on a scale not seen since museum collections were first established. The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success. Introduction Herbarium specimens and short-read Next-Generation Sequencing (NGS) are natural partners.
Phylogenetic projects at the largest scales often cannot be reasonably assembled through field collections. Herbaria provide a way to overcome such limitations because they contain centuries of accumulated genetic material that covers vast stretches of space and time. However, because previous-generation sequencing approaches, such as Sanger sequencing, could not be easily optimized for degraded material (Staats et al., 2013; Jones and Good, 2016), the utility of herbaria for large-scale phylogenetics studies was limited.
The burgeoning spectrum of NGS methods has dramatically lowered technical barriers to sequencing degraded materials. Science Forum: The critical importance of vouchers in genomics. Thank you for submitting your manuscript "Vouchers are critical (but often overlooked) in studies of genome biology" to eLife for consideration as a Feature Article.
Your article has been reviewed by three peer reviewers, and their comments have been combined to produce this decision letter. On the basis of the comments from the reviewers, we invite you to submit a revised version of your manuscript that addresses the points below. Summary: Buckner et al. surveyed the available vertebrate genomes on GenBank and discovered that most of them had no "voucher" specimen reference noted in the record or associated publications. In fact, only 11% of the GenBank genomes referenced a voucher specimen (varying from a high in birds of 15% to a low in mammals of 3%). This is a well-written and timely article that addresses a topic that has received some discussion in museum circles, but not often in the world of genomics. Essential Revisions: 1. 2. 3. 4. 5. Completing the tree of life for plants and fungi. The Plant and Fungal Trees of Life Project at Kew As a flagship project of our Science Strategy, Kew is completing the Plant and Fungal Trees of Life Project (PAFTOL).
To achieve this ambitious goal, we will generate and compile genome-scale data for at least one species of all 14,000 flowering plant genera and all 8,200 fungal genera. PAFTOL Plants is well underway, with a 15-strong team of dedicated researchers. More than half of the samples we need are available in our living collections, seed bank and DNA bank. These are the collections that yield the best quality DNA for our labwork. Gaps that exist in these ideal collections can be plugged thanks to Kew’s amazing herbarium collection. Our Victorian founders could not have imagined that their specimens would become an invaluable resource for deciphering the blueprint of life. By the end of this year, we expect to have sequenced a full 25% of all flowering plant genera.
The genomic era is dawning and Kew is embracing it. References. Open: Using historical herbarium specimens to elucidate the evolutionary genomics of plant invasion. The DNA of a 500-year-old tomato. Herbaria are an under-used resource for large phylogenies. New research in Applications in Plant Sciences might change that. □Story □Full paper. Ggi botany expedition protocols 16june2016. Ae81a87a3b3281694f1f449a6bdc5701da3d. On the potential of Angiosperms353 for population genomics. Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes.
Coming up next in the Angiosperms-353 symposium: @funauntlaura talking about the "artisanal" approach to maximizing herbarium data with data curation #botany2020.
Evolution. Genomes. History. Methods. Uses. DNA Banks and Genetic Resources Repositories in the United States. iDigBio is actively compiling a list of DNA banking facilities and genetic resources repositories in the United States that maintain collections of nucleic acid extracts (DNA or RNA) or preserved tissues suitable for genetic and genomic studies of biodiversity.
The following resources (listed alphabetically by institution) represent collections currently known by or reported to iDigBio. Each entry includes the name of the institution, a brief description, and institutional link. To report the availability of genetic resources at your institution, or to revise or update an existing entry, please contact Grant Godden. iDigBio thanks the participants of the DNA Banking Workshop hosted by the Missouri Botanical Garden (January 2013) and Breda Zimkus (Museum of Comparative Zoology, Harvard University), in particular, for assistance in compiling these resources.
NCBI BioCollections Database to connect DNA seq to voucher specimens. Skip to Main Content Sign In Register Close Advanced Search Online ISSN 1758-0463 Copyright © 2018 Oxford University Press Connect Resources Explore Oxford University Press is a department of the University of Oxford.
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