Herbarium genomics is a promising field, as next generation sequencing approaches are well-suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of plastome sequences from herbarium specimens is feasible, from total DNA extracts and apparently only weakly depending on specimen age. We use genome skimming and an automated bioinformatics pipeline, comprising Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on assembly likelihood estimation. Using a range of herbarium specimens, from 12 different Angiosperm families and some of which up to 146 years old, we show that routine plastome sequencing from herbarium specimens using genome skimming is feasible and cost-effective, and can be performed with highly limited sample destruction. Comparison of fresh DNA with both old and young herbarium from the same tree individuals shows that post-mortem damage in herbarium DNA is negligible.
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invited by Sigrid Liede-Schumann and Ulrich Meve, Plant Systematics
Datum | Vortragender | Titel |
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14.04.2016 | Prof. Otmar Urban Division of Impact Studies and Ecophysiological Analyses, CzechGlobe, Czech Academy of Sciences, Brno, CZ | Plant responses to climate change: impacts and adaptation [Abstract] |
21.04.2016 | Dr. Florian R.Storck DVGW-Technologiezentrum Wasser, Karlsruhe | Mikroplastik in Wasserressourcen – Anforderungen an die Analytik und erste Ergebnisse [Abstract] |
S 21, GEO-Gebäude 14:00-16:00 21.04.2016 | Dr. Jana Bürger Department Crop Health, Rostock University | Arable weeds under climate and land-use change – how ecological methods help agricultural researchers [Abstract] |
28.04.2016 | Dr. Michael Sander Environmental Chemistry, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Switzerland | Fate of biodegradable polyesters in agricultural soils - from enzymatic hydrolysis to microbial uptake and mineralization [Abstract] |
12.05.2016 | Prof. Jon Petter Gustafsson Soil and Groundwater Chemistry, KTH Stockholm / SLU Uppsala | Speciation and bioavailability of trace metals and phosphorus in soil systems [Abstract] |
02.06.2016 | Dr. Christine M. Klapeer Entwicklungssoziologie, Universität Bayreuth | Ist Natur politisch? Zum Zusammenhang von Naturkonzeptionen, Geschlechterverhältnissen und kolonialer Gewalt [Abstract] |
09.06.2016 | Dr. Julian Klaus Catchment and Eco-Hydrology Research Group, Luxembourg Institute of Science and Technology | Stable Isotopes in Hydrology: Progress in concepts and process understanding [Abstract] |
16.06.2016 | Freek T. Bakker (PhD) Biosystematics Group, Wageningen University, NL | Herbarium genomics, skimming & plastomics [Abstract] |
Mittwoch 22.06.2016 | Symposium zur Besetzung der W3-Professur Bodenphysik [Abstract] | |
13:00-14:00 23.06.2016 | PD Dr. Karsten Wesche Dept. of Botany, Senckenberg Museum of Natural History Görlitz | Climate controls override grazing effects under extreme conditions of Central Asia [Abstract] |
30.06.2016 | Prof. Dr. Andreas Lang Geomorphology and Environmental Systems, University of Salzburg, AT | The Anthropocene - is there a case for a new geological epoch? [Abstract] |
21.07.2016 | Dr. Marie Spohn Soil Biogeochemistry, Soil Ecology, BayCEER, University of Bayreuth | Biogenic Weathering [Abstract] |
BayCEER-Kolloquium: |
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Do. 21.01.2021 The impact of trees on soil organic carbon dynamics in the Subarctic - Priming effects and microbial N mining |
Do. 28.01.2021 BayCEER Mitgliederversammlung |
Do. 04.02.2021 Investigating communal pathogen defense and its role in social evolution |
Do. 15.04.2021 - folgt - |
Do. 22.04.2021 - folgt - |
13.01.2020 Why Science Communication? |
24.05.2019 Stoichiometric controls of C and N cycling |
07.05.2019 Flying halfway across the globe to dig in the dirt – a research stay in Bloomington, USA |
16.04.2019 Picky carnivorous plants? |