scholarly journals Using herbarium samples for NGS methods – a methodological comparison

2021 ◽  
Author(s):  
Pia Marincek ◽  
Natascha D. Wagner ◽  
Salvatore Tomasello
Keyword(s):  
Plant Material ◽  
Herbarium Specimens ◽  
Target Enrichment ◽  
Dna Yield ◽  
Plant Collections ◽  
Tremendous Amount ◽  
Selected Subset ◽  
Methodological Comparison ◽  
Plant Systematic ◽  
Standard Library

Herbaria harbor a tremendous amount of plant specimens that are rarely used for plant systematic studies. The main reason is the difficulty to extract a decent quantity of good quality DNA from the preserved plant material. While the extraction of ancient DNA in animals is well established, studies including old plant material are still underrepresented. In our study we compared the standard Qiagen DNeasy Plant Mini Kit and a specific PTB-DTT protocol on to two different plant genera (Xanthium L. and Salix L.).  The included herbarium material covered about two centuries of plant collections. A selected subset of samples was used for a standard library preparation as well as a target enrichment approach. The results revealed that PTB-PTT resulted in higher quantity and quality regarding DNA yield. Despite the lower overall yield of DNA, the Qiagen Kit resulted in better sequencing results regarding the number of filtered and mapped reads. We were able to successfully sequence a sample from 1820 and conclude that it is possible to include old herbarium specimens in NGS approaches. This opens a treasure box in phylogenomic research.

Microwave drying of plant material for herbarium specimens and genetic analysis

Taxon ◽  
2013 ◽  
Vol 62 (4) ◽  
pp. 790-797 ◽  
Author(s):  
Tonya A. Lander ◽  
Bernadeta Dadonaite ◽  
Alex K. Monro
Keyword(s):  
Genetic Analysis ◽  
Plant Material ◽  
Microwave Drying ◽  
Herbarium Specimens

scholarly journals Beehives possess their own distinct microbiomes

2021 ◽  
Author(s):  
Lorenzo Santorelli ◽  
Toby Wilkinson ◽  
Ronke Abdulmalik ◽  
Yuma Rai ◽  
Christopher J. Creevey ◽  
...  
Keyword(s):  
16S Rdna ◽  
Honey Bees ◽  
Plant Material ◽  
Surrounding Environment ◽  
Insect Pollinators ◽  
Tremendous Amount ◽  
Environmental Bacteria ◽  
Local Plants ◽  
Bacterial Groups ◽  
Different Parts

AbstractHoney bees use plant material to manufacture their own food. These insect pollinators visit flowers repeatedly to collect nectar and pollen, which are shared with other hive bees to produce honey and beebread. While producing these products, beehives accumulate a tremendous amount of microbes, including bacteria that derive from plants and different parts of the honey bees’ body. In this study, we conducted 16S rDNA metataxonomic analysis on honey and beebread samples that were collected from 15 beehives in the southeast of England in order to quantify the bacteria associated with beehives. The results highlighted that honeybee products carry a significant variety of bacterial groups that comprise bee commensals, environmental bacteria and pathogens of plants and animals. Remarkably, this bacterial diversity differs amongst the beehives, suggesting a defined fingerprint that is affected, not only by the nectar and pollen gathered from local plants, but also from other environmental sources. In summary, our results show that every hive possesses their own distinct microbiome, and that honeybee products are valuable indicators of the bacteria present in the beehives and their surrounding environment.

scholarly journals Occurrence, Composition and Formation of Ruppia, Widgeon Grass, balls in Saskatchewan Lakes

2005 ◽  
Vol 119 (1) ◽  
pp. 114 ◽  
Author(s):  
Randy W. Olson ◽  
Josef K. Schmutz ◽  
Theodore Hammer
Keyword(s):  
Plant Material ◽  
Saline Lake ◽  
Vascular Plant ◽  
Herbarium Specimens ◽  
Ruppia Maritima ◽  
Washing Machine ◽  
Invertebrate Animal ◽  
Turtle Grass ◽  
Aquatic Vascular Plant ◽  
Near Shore

Widgeon Grass (Ruppia maritima) is an aquatic vascular plant (Ruppiaceae) which has been the source for rare balls of plant material found at the shores of lakes on four continents. In North America, the lakes involved were in North Dakota, Oregon, and now northern and southern Saskatchewan. The formation of the balls has not been observed in nature, but similar balls have been produced in other studies with Posidonia or Turtle Grass (Hydrocharitaceae) fibers under the wavelike action in a washing machine. Our samples are from a saline lake in southern Saskatchewan (49°N), and an over 40-year-old sample from an unknown lake north of the boreal transition zone (52°N). Comparisons of the plant material with herbarium specimens confirm that the balls are almost entirely comprised of Ruppia maritima, with minor items including invertebrate animal parts, sand pebbles and feathers. The context in which the material was found is consistent with the proposition that they are formed by Ruppia inflorescences breaking apart, drifting to near shore due to wind and being rolled into balls by wave action.

scholarly journals Engaging Children with Herbarium Specimens at Royal Botanic Gardens Kew’s Science Festival

2018 ◽  
Vol 2 ◽  
pp. e25933
Author(s):  
Melissa Bavington
Keyword(s):  
Plant Material ◽  
Scientific Data ◽  
Lessons Learned ◽  
Specimen Preparation ◽  
Herbarium Specimens ◽  
Full Time ◽  
Plant Parts ◽  
Herbarium Collection ◽  
Herbarium Sheet ◽  
Royal Botanic Gardens

The Kew and Wakehurst Science Festivals consists of five days of activities over two weekends. Workshops and tours allow visitors to engage with the scientists and their research. We designed an interactive experience, so children could understand what a herbarium sheet is and the process of making one. The Herbarium accessions an average of 30,000 specimens per year and because specimens need to have a long life and be able to withstand being handled for hundreds of years they need to be ‘mounted’ according to strict protocols and guidelines. Botanical specimens are vital to research at Kew and beyond, providing key scientific data. Once mounted onto herbarium sheets botanical specimens are added to the Herbarium and made widely available to visiting scientists and researchers. Digitising these specimens increases access further through online portals. To achieve a specimen that can be handled for many years the specimens are mounted onto archival paper, along with their labels, before being added to the collection. There are 6 members in RBG Kew’s Specimen Preparation team who work full time to prepare botanical specimens for accession into the Herbarium collection; which currently stands at 7 million specimens and the oldest dates from the 1700s. We simplified this specimen preparation process down to the basic component parts of paper, glue, plant material and pressing. Using material and tools that visitors would be able to find for themselves; art paper, child friendly glue and plant material used in flower crafts we created a hands-on experience for mounting a herbarium specimen. The Science Festival is now in its 3rd year and each year the activity has been modified based on lessons learned over the course of the festival and each year. The stall is immensely popular going from 300 participants in the first year to over 700 in 2017. In the second year we added a new dimension and allowed visitors to image the specimens they created allowing them to zoom in and see plant parts and structures in further detail to highlight the importance of digitisation. These images can be viewed on the Kew Science Flickr group.

scholarly journals SYSTEMATIC ANALYSIS OF THE SPECIES OF THE GENUS QUERCUS L. IN THE ARBORETUM HERBARIUM OF THE UNIVERSITY

2021 ◽  
Vol 11 (3) ◽  
pp. 5-15
Author(s):  
Svetlana Degtyareva ◽  
Valentina Dorofeeva ◽  
Yuliya Chekmeneva
Keyword(s):  
Life Form ◽  
Educational Institution ◽  
Federal State ◽  
Herbarium Specimens ◽  
State Budget ◽  
Systematic Analysis ◽  
Traditional Classification ◽  
Plant Collections ◽  
The University

The results of the analysis of Quercus L. species stored in the herbarium of the Department of Botany and Plant Physiology of Federal State Budget Educational Institution of Higher Education VSUFT (Voronezh) are presented. This herbarium of historical plant collections of the genus Quercus L. is critical for tracking changes in the genus, including the introduction and distribution of species. We examined the belonging of the species to systematic units – subgenus, section, subsection, row, using the traditional classification and the updated intrageneric classification of oaks. Information about the life form, plant height, date and place of collection of the specimen was recorded. We entered information into the database, which will further simplify the work on registration, revision of the herbarium fund and when replenishing herbarium specimens. Conclusions were drawn based on the results of the workabout changes in the taxonomic nature and phylogenetic relationships of species in Quercus L. genus

Lectotype of Solidago ×niederederi (Asteraceae) selected from a recently rediscovered original material

Phytotaxa ◽  
2020 ◽  
Vol 438 (1) ◽  
pp. 62-64
Author(s):  
KATARÍNA SKOKANOVÁ ◽  
PAVOL MEREĎA Jr. ◽  
BARBORA ŠINGLIAROVÁ ◽  
STANISLAV ŠPANIEL
Keyword(s):  
Plant Material ◽  
Herbarium Specimens ◽  
Solidago Canadensis ◽  
Original Material ◽  
Field Margins ◽  
Forest Edges ◽  
Hybrid Species ◽  
Living Material ◽  
The 19Th Century ◽  
First Time

Solidago ×niederederi Khek (1905: 22) is a hybrid between North-American S. canadensis Linnaeus (1753: 878) and European native S. virgaurea Linnaeus (1753: 880). Solidago canadensis was introduced to Europe in the 17th century (Kowarik 2003). It has spread invasively throughout Europe since the second half of the 19th century (Weber 1998), reaching, besides sites disturbed by human activity, also (semi)natural biotopes, as forest edges, abandoned meadows and field margins which are often inhabited by native S. virgaurea. Their hybrid was discovered for the first time in nature by a local schoolmaster Franz Niedereder in the area of Vorderstoder village (Austria). Niedereder sent a plant material of the assumed hybrid to Eugen Johan Khek (born in 1861, Neuhaus/Jindřichov Hradec; died in 1927, Vienna), the pharmacist and botanist who lived in Vienna since 1889 (Anonymous 1916). Khek described the hybrid species under the name S. ×niederederi in honour of his discoverer (Khek 1905). The protologue indicates that the relevant communication between Niedereder and Khek was going on between July 1900 (when they met for the first time) and February 1905 (when the hybrid’s description was published). Before its description, Khek studied the hybrid for four years and he saw a herbarium material from Niedereder as well as a living material. In the protologue, no particular herbarium specimens or illustrations had been indicated or associated with S. ×niederederi (Khek 1905).

scholarly journals Unmounted Doesn’t Mean Unprocessed: A Case Study of Exporting Australian Herbarium Specimens

2018 ◽  
Vol 2 ◽  
pp. e26284
Author(s):  
Sarah Hirst ◽  
Peter Jobson
Keyword(s):  
Plant Material ◽  
The United States ◽  
Herbarium Specimens ◽  
United States Department ◽  
Department Of Agriculture ◽  
States Department ◽  
The Usa ◽  
Exchange Material ◽  
Herbarium Collections

In 2017, two incoming international herbarium loans were confiscated and destroyed by the Commonwealth Department of Agriculture and Water Resources (DAWR). Following these regrettable incidents, communication has improved between Managers of Australasian Herbarium Collections (MAHC) and Plant Import Operations Branch of DAWR. The outcome is that new protocols now exist for shipment of plant material between herbaria based on the recognition by DAWR that all herbarium specimens are in fact processed (pressed, dried and frozen) even if they are not fully mounted (Brown et al, this conference). Simultaneously, the United States Department of Agriculture (USDA) had been reported to be destroying incoming unmounted specimens, thus making it difficult to send unmounted exchange material overseas, and particularly to the USA. Using the documentation developed for incoming overseas loans by MAHC and, encouraging the receiving institution in the USA to acquire a USDA 588 Importing Permit for unprocessed plant specimens (non-loan, unmounted herbarium specimens), it was possible to export unmounted herbarium specimens and dried DNA samples into the USA. Excluding the USA specific requirements, we were also able to export exchange material and dried DNA samples to Singapore and Sweden.

Floristic Studies in Two Species of Eleocharis R. Brown (Cyperaceae)

2021 ◽  
Vol 4 (6) ◽  
pp. 299-301
Author(s):  
Dr. Shaikh Rafeeque Ishakhoddin
Keyword(s):  
Comparative Study ◽  
Plant Material ◽  
Present Report ◽  
Relevant Information ◽  
Basic Material ◽  
Herbarium Specimens ◽  
Taxonomic Description ◽  
Fresh Plant Material ◽  
Floristic Studies ◽  
Different Parts

Present study is on our own critical observations on fresh plant material collected from the different parts. The observations are also based on herbarium specimens. Relevant data from literature have been referred for comparative study and conclusion including recent nomenclature. The study of Eleocharis R. Brown provides a detailed taxonomic description, illustration and relevant information for its easy identification in the field. Two species are collected and are described. The present report is hoped to provide basic material for further research in Cyperaceae

Tillandsia bandensis (Bromeliaceae): its lectotypification and a new subspecies from Uruguay

Phytotaxa ◽  
2019 ◽  
Vol 405 (1) ◽  
pp. 15 ◽  
Author(s):  
ANDRÉS J. ROSSADO ◽  
SABINA DONADÍO ◽  
JOSÉ M. BONIFACINO
Keyword(s):  
Plant Material ◽  
Conservation Status ◽  
Herbarium Specimens ◽  
Living Plant ◽  
New Subspecies ◽  
Reproductive Structures

A new epilithic subspecies of Tillandsia bandensis (Bromeliaceae) is described based on the analysis of herbarium specimens as well as living plant material in the field and in cultivation. The new subspecies differs from the typical one mainly by its bigger and more lepidote reproductive structures. Detailed morphological descriptions for T. bandensis and its subspecies are provided, as well as images, illustrations and data on distribution, habitat, phenology and conservation status for the new subspecies here described. Lectotypes for T. bandensis, T. bandensis var. intermedia and T. recurvata var. majuscula are designated.

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