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1,998 results for “Herbarium specimen”
Data from: Next-generation sampling: pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae)
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Spatiotemporal monitoring of the rare Northern dragonhead, Dracocephalum ruyschiana (Lamiaceae): SNP genotyping and environmental niche modelling herbarium specimens
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Data from: Robust DNA isolation and high-throughput sequencing library construction for herbarium specimens
Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 hours, with only 8 hours of active hands-on time with minimal modifications.
Figure 1 from: Gueidan C, Li L (2022) A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys 86: 195-212. https://doi.org/10.3897/mycokeys.86.77431
Figure 1 Examples of lichen herbarium specimens used for this study AParmotrema perlatum, specimen J.A. Elix 43686 (CANB790817) BEndocarpon pusillum, specimen H. Streiman 45100 (CBG9011273) CBuellia albula, specimen J.A. Elix 45138 (CANB810791) DCatillaria sp., specimen J.A Elix 37142 (CANB872684). Scale bar: 1 cm. Photos C. Gueidan.
Figure 2 from: Gueidan C, Li L (2022) A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys 86: 195-212. https://doi.org/10.3897/mycokeys.86.77431
Figure 2 Sequencing success for different morphological groups of taxa included in this study. Specimens were grouped into three main morphological categories: 1Buellia, Catillaria and other crustose saxicolous taxa 2Endocarpon and other squamulose terricolous taxa 3 the foliose corticolous genus Parmotrema. In the graph, stalked columns show successful samples (sequence generated for the target species) in dark grey and unsuccessful samples (no sequence generated or generated sequences not from the target species) in light grey. The total number of samples (N) is indicated below each corresponding column.
Figure 3 from: Gueidan C, Li L (2022) A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys 86: 195-212. https://doi.org/10.3897/mycokeys.86.77431
Figure 3 Sequencing success for different ages of specimens included in this study. Specimens were grouped in five categories: 1966–1980, 1981–1990, 1991–2000, 2001–2010, 2011–2020. In the graph, stalked columns show successful samples (sequence generated for the target species) in dark grey and unsuccessful samples (no sequence generated or generated sequences not from the target species) in light grey. The total number of samples (N) is indicated below each corresponding column.
Figure 3 from: Nualart N, Ibáñez N, Luque P, Pedrol J, Vilar L, Guàrdia R (2017) Dataset of herbarium specimens of threatened vascular plants in Catalonia. PhytoKeys 77: 41-62. https://doi.org/10.3897/phytokeys.77.11542
Figure 3 - Families with 18 or more specimens (number of the taxa in the upper axis and number of specimens in the lower axis).
Figure 6 from: Nualart N, Ibáñez N, Luque P, Pedrol J, Vilar L, Guàrdia R (2017) Dataset of herbarium specimens of threatened vascular plants in Catalonia. PhytoKeys 77: 41-62. https://doi.org/10.3897/phytokeys.77.11542
Figure 6 - Comparative map of the number of taxa of the dataset and that according to Sáez et al. (2010: 733). Gray color indicates that all the taxa cited in this book have a specimen in the herbaria studied; yellow-red color indicates that the dataset doesn't include all the taxa published in this book and green color indicates that there are more taxa in the dataset that those published in this book.
Fig. 1 in A considerable review on type specimens of Korean vascular plants in the Herbarium of the Komarov Botanical Institute (LE) Addition
Fig. 1. Type specimens of Korean vascular plants in the herbarium of the Komarov Botanical Institute. 1. Selliguea coraiensis Christ (LE01000272), 2. Acer triflorum Kom. (LE01005880), 3. Acer triflorum Kom. f. subcoriacea Kom. (LE01005883), 4. Acer tschonoskii Maxim. var. rubripes Kom. (LE01005892), 5. Dendropanax morbiferum H. Lév. (LE01007511), 6. Artemisia fauriei Nakai (LE01008378), 7. Artemisia feddei H. Lév. & Vaniot (LE01008391), 8. Artemisia hallaisanensis Nakai (LE01008385), 9. Inula taquetii H. Lév. (LE01009281), 10. Saussurea saxatilis Kom. (LE01008657), 11. Adenophora marsupiiflora (Schult.) Fisch. var. jaluensis Kom. (LE01008888), 12. Silene oldhamiana Miq. (LE01013488).
Figure 2 from: Berger A (2018) Rediscovery of Chamisso's type specimens of Hawaiian Psychotria (Rubiaceae, Psychotrieae) in the herbarium of the Natural History Museum, Vienna. PhytoKeys 114: 27-42. https://doi.org/10.3897/phytokeys.114.29426
Figure 2 Lectotype of Psychotriamariniana (Cham. & Schltdl.) Fosberg collected by L.K.A. von Chamisso during the Romanzoffian Expedition in 1817 (L.K.A. von Chamisso s.n., W-Endl. 0066414). The sheet originates from the private herbarium of S.L. Endlicher, now preserved at the Herbarium of the Natural History Museum, Vienna. Photo: Courtesy of the Natural History Museum, Vienna.
Figure 1 from: Berger A (2018) Rediscovery of Chamisso's type specimens of Hawaiian Psychotria (Rubiaceae, Psychotrieae) in the herbarium of the Natural History Museum, Vienna. PhytoKeys 114: 27-42. https://doi.org/10.3897/phytokeys.114.29426
Figure 1 Lectotype of Psychotriakaduana (Cham. & Schltdl.) Fosberg collected by L.K.A. von Chamisso during the Romanzoffian Expedition in 1817 (L.K.A. von Chamisso s.n., W-Endl. 0065914). The sheet originates from the private herbarium of S.L. Endlicher, now preserved at the Herbarium of the Natural History Museum, Vienna. Photo: Courtesy of the Natural History Museum, Vienna.
Supplementary material 1 from: Gueidan C, Elix JA, McCarthy PM, Roux C, Mallen-Cooper M, Kantvilas G (2019) PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens. MycoKeys 53: 73-91. https://doi.org/10.3897/mycokeys.53.34761
: Data type: measurement
Figure 1 in Herbarium specimens reveal the exchange network of British and Irish botanists, 1856-1932
Figure 1 The schema used for cleaning the individual's names in the dataset.
Text-fig. 7. Original material of Peziza sulphurea. A-B. apothecia in the specimen L 910,261-594; C. apothecia which do produce a purple reaction to KOH in the specimen L 910,256-897; D. apothecia which do not produce a purple reaction to KOH in the specimen L 910,256-897. Scale bars = 1 mm. in A Revision Of Trichopeziza Lizonii, T. Sulphurea And T. Violascens (Ascomycota, Helotiales) From The Herbarium Prm With Notes On Type Material Of Peziza Sulphurea
Text-fig. 7. Original material of Peziza sulphurea. A-B. apothecia in the specimen L 910,261-594; C. apothecia which do produce a purple reaction to KOH in the specimen L 910,256-897; D. apothecia which do not produce a purple reaction to KOH in the specimen L 910,256-897. Scale bars = 1 mm.
FIGURE 1 in Revision of herbarium specimens of freshwater Enteromorpha-like Ulva (Ulvaceae, Chlorophyta) collected from Central Europe during the years 1849-1959
FIGURE 1. Distribution of sampling locations of freshwater Ulva.
Linked collectors and determiners for: Herbarium specimens of Herbiers Universitaires de Clermont-Ferrand (CLF).
Natural history specimen data linked to collectors and determiners held within, "Herbarium specimens of Herbiers Universitaires de Clermont-Ferrand (CLF)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/def8d066-e920-42d6-bb67-dfca6980c7f3">https://bionomia.net/dataset/def8d066-e920-42d6-bb67-dfca6980c7f3</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/def8d066-e920-42d6-bb67-dfca6980c7f3">https://gbif.org/dataset/def8d066-e920-42d6-bb67-dfca6980c7f3</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Bryophyte specimens at TAN Herbarium.
Natural history specimen data linked to collectors and determiners held within, "Bryophyte specimens at TAN Herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/d06771c1-2276-49b8-81ba-f7be0887d0bd">https://bionomia.net/dataset/d06771c1-2276-49b8-81ba-f7be0887d0bd</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/d06771c1-2276-49b8-81ba-f7be0887d0bd">https://gbif.org/dataset/d06771c1-2276-49b8-81ba-f7be0887d0bd</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Herbarium specimens, Harmas J.H. Fabre (FABR - Sérignan-du-Comtat) of the Muséum national d'Histoire naturelle (MNHN - Paris).
Natural history specimen data linked to collectors and determiners held within, "Herbarium specimens, Harmas J.H. Fabre (FABR - Sérignan-du-Comtat) of the Muséum national d'Histoire naturelle (MNHN - Paris)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/a578b33b-72f6-4833-a3eb-45d61f79f091">https://bionomia.net/dataset/a578b33b-72f6-4833-a3eb-45d61f79f091</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/a578b33b-72f6-4833-a3eb-45d61f79f091">https://gbif.org/dataset/a578b33b-72f6-4833-a3eb-45d61f79f091</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Visual Plants (144.41.33.158) - Herbarium specimen from "EA", Kenya.
Natural history specimen data linked to collectors and determiners held within, "Visual Plants (144.41.33.158) - Herbarium specimen from "EA", Kenya". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/863844d8-f762-11e1-a439-00145eb45e9a">https://bionomia.net/dataset/863844d8-f762-11e1-a439-00145eb45e9a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/863844d8-f762-11e1-a439-00145eb45e9a">https://gbif.org/dataset/863844d8-f762-11e1-a439-00145eb45e9a</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Visual Plants (144.41.33.158) - Herbarium specimen from "USJ", Costa Rica.
Natural history specimen data linked to collectors and determiners held within, "Visual Plants (144.41.33.158) - Herbarium specimen from "USJ", Costa Rica". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/863a8ee6-f762-11e1-a439-00145eb45e9a">https://bionomia.net/dataset/863a8ee6-f762-11e1-a439-00145eb45e9a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/863a8ee6-f762-11e1-a439-00145eb45e9a">https://gbif.org/dataset/863a8ee6-f762-11e1-a439-00145eb45e9a</a>. Formatted as a Frictionless Data package.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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