Studies on Authentication of True Source of Honey Using Pollen DNA
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Using RNA-Seq to Characterize Pollen–Stigma Interactions for Pollination
www.nature.com/scientificreports OPEN Using RNA‑seq to characterize pollen–stigma interactions for pollination studies Juan Lobaton1,3*, Rose Andrew1, Jorge Duitama2, Lindsey Kirkland1, Sarina Macfadyen3 & Romina Rader1 Insects are essential for the reproduction of pollinator‑dependent crops and contribute to the pollination of 87% of wild plants and 75% of the world’s food crops. Understanding pollen fow dynamics between plants and pollinators is thus essential to manage and conserve wild plants and ensure yields are maximized in food crops. However, the determination of pollen transfer in the feld is complex and laborious. We developed a feld experiment in a pollinator‑dependent crop and used high throughput RNA sequencing (RNA‑seq) to quantify pollen fow by measuring changes in gene expression between pollination treatments across diferent apple (Malus domestica Borkh.) cultivars. We tested three potential molecular indicators of successful pollination and validated these results with feld data by observing single and multiple visits by honey bees (Apis mellifera) to apple fowers and measured fruit set in a commercial apple orchard. The frst indicator of successful outcrossing was revealed via diferential gene expression in the cross‑pollination treatments after 6 h. The second indicator of successful outcrossing was revealed by the expression of specifc genes related to pollen tube formation and defense response at three diferent time intervals in the stigma and the style following cross‑pollination (i.e. after 6, 24, and 48 h). Finally, genotyping variants specifc to donor pollen could be detected in cross‑pollination treatments, providing a third indicator of successful outcrossing. Field data indicated that one or fve fower visits by honey bees were insufcient and at least 10 honey bee fower visits were required to achieve a 25% probability of fruit set under orchard conditions. -
Fungal Genomes Tell a Story of Ecological Adaptations
Folia Biologica et Oecologica 10: 9–17 (2014) Acta Universitatis Lodziensis Fungal genomes tell a story of ecological adaptations ANNA MUSZEWSKA Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland E-mail: [email protected] ABSTRACT One genome enables a fungus to have various lifestyles and strategies depending on environmental conditions and in the presence of specific counterparts. The nature of their interactions with other living and abiotic elements is a consequence of their osmotrophism. The ability to degrade complex compounds and especially plant biomass makes them a key component of the global carbon circulation cycle. Since the first fungal genomic sequence was published in 1996 mycology has benefited from the technolgical progress. The available data create an unprecedented opportunity to perform massive comparative studies with complex study design variants targeted at all cellular processes. KEY WORDS: fungal genomics, osmotroph, pathogenic fungi, mycorrhiza, symbiotic fungi, HGT Fungal ecology is a consequence of osmotrophy Fungi play a pivotal role both in encountered as leaf endosymbionts industry and human health (Fisher et al. (Spatafora et al. 2007). Since fungi are 2012). They are involved in biomass involved in complex relationships with degradation, plant and animal infections, other organisms, their ecological fermentation and chemical industry etc. repertoire is reflected in their genomes. They can be present in the form of The nature of their interactions with other resting spores, motile spores, amebae (in organisms and environment is defined by Cryptomycota, Blastocladiomycota, their osmotrophic lifestyle. Nutrient Chytrydiomycota), hyphae or fruiting acquisition and communication with bodies. The same fungal species symbionts and hosts are mediated by depending on environmental conditions secreted molecules. -
1 Molecular Analysis of Honey Bee Foraging Ecology Dissertation
Molecular analysis of honey bee foraging ecology Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Rodney Trey Richardson Graduate Program in Entomology The Ohio State University 2018 Dissertation Committee Professor Reed Johnson, Advisor Professor Mary Gardiner Professor John Christman Professor Roman Lanno 1 Copyrighted by Rodney Trey Richardson 2018 2 Abstract While numerous factors currently impact the health of honey bees and other pollinating Hymenoptera, poor floral resource availability due to habitat loss and land conversion is thought to be important. This issue is particularly salient in the upper Midwest, a location which harbors approximately 60 percent of the US honey bee colonies each summer for honey production. This region has experienced a dramatic expansion in the area devoted to crop production over the past decade. Consequently, understanding how changes to landscape composition affect the diversity, quality and quantity of available floral resources has become an important research goal. Here, I developed molecular methods for the identification of bee-collected pollen by adapting and improving upon the existing amplicon sequencing infrastructure used for microbial community ecology. In thoroughly benchmarking our procedures, I show that a simple and cost-effective three-step PCR-based library preparation protocol in combination with Metaxa2-based hierarchical classification yields an accurate and highly quantitative pollen metabarcoding approach when applied across multiple plant markers. In Chapter 1, I conducted one of the first ever proof-of-concept studies applying amplicon sequencing, or metabarcoding, to the identification of bee-collected pollen. -
Experimental Quantification of Pollen with DNA Metabarcoding Using
www.nature.com/scientificreports OPEN Experimental quantifcation of pollen with DNA metabarcoding using ITS1 and trnL Sandra Baksay 1*, André Pornon1, Monique Burrus1, Jérôme Mariette2, Christophe Andalo1 & Nathalie Escaravage1 Although the use of metabarcoding to identify taxa in DNA mixtures is widely approved, its reliability in quantifying taxon abundance is still the subject of debate. In this study we investigated the relationships between the amount of pollen grains in mock solutions and the abundance of high- throughput sequence reads and how the relationship was afected by the pollen counting methodology, the number of PCR cycles, the type of markers and plant species whose pollen grains have diferent characteristics. We found a signifcant positive relationship between the number of DNA sequences and the number of pollen grains in the mock solutions. However, better relationships were obtained with light microscopy as a pollen grain counting method compared with fow cytometry, with the chloroplastic trnL marker compared with ribosomal ITS1 and with 30 when compared with 25 or 35 PCR cycles. We provide a list of recommendations to improve pollen quantifcation. Environmental DNA metabarcoding is a molecular method that consists of investigating environmental DNA samples made of complex mixtures of genomes from numerous organisms1. Due to new sequencing technologies and bioinformatics tools, metabarcoding has been increasingly used to identify taxa in environmental samples1 to monitor biodiversity2–4, to investigate ecosystem functioning5 and interaction networks6–8, in both aquatic and terrestrial ecosystems. Nevertheless, its reliability in quantitative approaches, which depend on the match between counts of high-throughput sequence reads and the amount of sampled biological material2, is still the subject of debate9,10. -
Pollen DNA Barcoding: Current Applications and Future Prospects
Page 1 of 43 Pollen DNA barcoding: current applications and future prospects Authors: Karen L. Bell 1, Natasha de Vere 2, Alexander Keller 3, Rodney T. Richardson 4, Annemarie Gous 5,6 , Kevin S. Burgess 7, Berry J. Brosi 1 1Emory University, School of Environmental Sciences, Atlanta, GA, USA 2National Botanic Garden of Wales, Llanarthne, United Kingdom 3Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany 4Department of Entomology, The Ohio State University, Columbus, OH, USA 5Biotechnology Platform , Agricultural Research Council , Pretoria, South Africa 6School of Life Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa 7Columbus State University, Columbus, GA, USA Keywords (3-6): DNA metabarcoding; metagenomics; pollen; palynology; high-throughput sequencing; next-generation sequencing Genome Downloaded from www.nrcresearchpress.com by MICHIGAN STATE UNIV on 04/18/16 1 For personal use only. This Just-IN manuscript is the accepted prior to copy editing and page composition. It may differ from final official version of record. Page 2 of 43 ABSTRACT (<200 words) Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. -
Applying Pollen DNA Metabarcoding to the Study of Plant-Pollinator Interactions Karen L
Applying Pollen DNA Metabarcoding to the Study of Plant-Pollinator Interactions Karen L. Bell, Emory University Julie Fowler, Emory University Kevin S. Burgess, The University of Western Australia Emily K. Dobbs, Emory University David Gruenewald, Emory University Brice Lawley, Emory University Connor Morozumi, Emory University Berry Brosi, Emory University Journal Title: Applications in Plant Sciences Volume: Volume 5, Number 6 Publisher: Botanical Society of America: APPS | 2017-06-01 Type of Work: Article | Final Publisher PDF Publisher DOI: 10.3732/apps.1600124 Permanent URL: https://pid.emory.edu/ark:/25593/s3w2z Final published version: http://dx.doi.org/10.3732/apps.1600124 Copyright information: © 2017 Bell et al. Published by the Botanical Society of America This is an Open Access work distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License (http://creativecommons.org/licenses/by-nc-sa/4.0/). Accessed September 26, 2021 6:17 AM EDT Applying Pollen DNA Metabarcoding to the Study of Plant–Pollinator Interactions Author(s): Karen L. Bell, Julie Fowler, Kevin S. Burgess, Emily K. Dobbs, David Gruenewald, Brice Lawley, Connor Morozumi, and Berry J. Brosi Source: Applications in Plant Sciences, 5(6) Published By: Botanical Society of America https://doi.org/10.3732/apps.1600124 URL: http://www.bioone.org/doi/full/10.3732/apps.1600124 BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use. -
Pollen DNA Barcoding Bell, Karen
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Aberystwyth Research Portal Aberystwyth University Pollen DNA barcoding Bell, Karen. L.; De Vere, Natasha; Keller, Alexander; Richardson, Rodney; Gous, Annemarie; Burgess, Kevin S.; Brosi, Berry J. Published in: Genome DOI: 10.1139/gen-2015-0200 Publication date: 2016 Citation for published version (APA): Bell, K. L., De Vere, N., Keller, A., Richardson, R., Gous, A., Burgess, K. S., & Brosi, B. J. (2016). Pollen DNA barcoding: Current applications and future prospects. Genome, 59(9), 629-640. https://doi.org/10.1139/gen- 2015-0200 Document License CC BY General rights Copyright and moral rights for the publications made accessible in the Aberystwyth Research Portal (the Institutional Repository) are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the Aberystwyth Research Portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the Aberystwyth Research Portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. tel: +44 1970 62 2400 email: [email protected] Download date: 09. Jul. 2020 629 REVIEW Pollen DNA barcoding: current applications and future prospects1 Karen L. -
Using Pollen DNA Metabarcoding to Profile Nectar Sources of Urban
Tanaka et al. BMC Res Notes (2020) 13:515 https://doi.org/10.1186/s13104-020-05361-2 BMC Research Notes RESEARCH NOTE Open Access Using pollen DNA metabarcoding to profle nectar sources of urban beekeeping in Kōtō-ku, Tokyo Keisuke Tanaka1, Akinobu Nozaki2, Hazuki Nakadai3, Yuh Shiwa4 and Mariko Shimizu‑Kadota5,6* Abstract Objective: Apis mellifera is a species of honeybee that has been introduced around the world as an industrial bee‑ keeping species. Recently, urban beekeeping has attracted attention as a means of ecosystem protection and urban greening. This study aimed to investigate nectar sources of urban beekeeping in Kōtō‑ku, Tokyo using pollen DNA metabarcoding. Results: We extracted DNA from pollen collected by the honeybees of a local urban beekeeping operation. DNA metabarcoding analysis was carried out by sequencing a part of the rbcL region of the chloroplast genome. A total of 31 samples collected between mid‑March, 2018 and mid‑October, 2018 yielded 54 operational taxonomic units (OTUs) comprising 14 families, 32 genera, and 8 species. Whereas 5 OTUs were profled throughout all seasons, 38 OTUs were season‑specifc (spring, summer, or autumn). Therefore, we were able to infer seasonal nectar sources for the beekeeping operation at the family or genus level, as well as at the species level to a lesser extent. Our pollen‑ sampling strategy was efective for profling season‑specifc nectar sources, with the exception of a few anomalies that can be accounted for by out‑of‑season fowering associated with artifcial gardening and/or pollen accumulation over multiple seasons. Keywords: Honeybee, Urban beekeeping, Nectar source, Pollen, DNA metabarcoding, Metagenome, Ribulose 1,5‑bisphosphate carboxylase/oxygenase, Chloroplast, Next generation sequencing Introduction the colony. -
Multi-Marker Metabarcoding Approach to Study Mesozooplankton at Basin
www.nature.com/scientificreports OPEN Multi-marker metabarcoding approach to study mesozooplankton at basin scale Received: 15 March 2018 Sergio Stefanni1, David Stanković 2,3, Diego Borme4, Alessandra de Olazabal4, Tea Juretić4,5, Accepted: 25 July 2018 Alberto Pallavicini2 & Valentina Tirelli 4 Published: xx xx xxxx Zooplankton plays a pivotal role in marine ecosystems and the characterisation of its biodiversity still represents a challenge for marine ecologists. In this study, mesozooplankton composition from 46 samples collected in summer along the western Adriatic Sea, was retrieved by DNA metabarcoding analysis. For the frst time, the highly variable fragments of the mtDNA COI and the V9 region of 18S rRNA genes were used in a combined matrix to compile an inventory of mesozooplankton at basin scale. The number of sequences retrieved after quality fltering were 824,148 and 223,273 for COI and 18S (V9), respectively. The taxonomical assignment against reference sequences, using 95% (for COI) and 97% (for 18S) similarity thresholds, recovered 234 taxa. NMDS plots and cluster analysis divided coastal from ofshore samples and the most representative species of these clusters were distributed according to the dominant surface current pattern of the Adriatic for the summer period. For selected sampling sites, mesozooplankton species were also identifed under a stereo microscope providing insights on the strength and weakness of the two approaches. In addition, DNA metabarcoding was shown to be helpful for the monitoring of non-indigenous marine metazoans and spawning areas of commercial fsh species. We defned pros and cons of applying this approach at basin scale and the benefts of combining the datasets from two genetic markers. -
2019-Jones-Phd-Papers-Removed
Bangor University DOCTOR OF PHILOSOPHY Investigating the foraging preferences of the honeybee, Apis mellifera L., using DNA metabarcoding Jones, Laura Award date: 2020 Awarding institution: Bangor University Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 11. Oct. 2021 Investigating the foraging preferences of the honeybee, Apis mellifera L., using DNA metabarcoding Laura Jones 2019 A thesis submitted for the degree of Doctor of Philosophy Bangor University 1 2 Declaration and Consent Details of the Work I hereby agree to deposit the following item in the digital repository maintained by Bangor University and/or in any other repository authorized for use by Bangor University. Author Name: ………………………………………………………………………………………………….. Title: ………………………………………………………………………………………..………………………. Supervisor/Department: .................................................................................................................. Funding body (if any): ........................................................................................................................ Qualification/Degree obtained: ………………………………………………………………………. This item is a product of my own research endeavours and is covered by the agreement below in which the item is referred to as “the Work”. -
A Natural Systems Glossary
A NATURAL SYSTEMS GLOSSARY A Glossary of Environmental, Biological, Zoological, Botanical, Ecological, Biogeographical, Evolutionary, Taxonomic, Hydrologic, Geographic, Geomorphologic, Geophysical and Meteorological Terms March 2006 (last revised May 2008) INTRODUCTION This glossary is the outgrowth of the InkaNatura guide training workshop held at Sandoval Lake Lodge and the Heath River Wildlife Center in southeastern Peru and adjacent Bolivia in January and February 2006. It began with the list of approximately 300 vocabulary words and terms generated during the workshop as well as many additional words and terms generated during the January and February 2008 guide training workshop held at Cock-of-the-Rock Lodge and Manu Wildlife Center in southeastern Peru. While originally intended for the use of the InkaNatura guides, it has expanded into a reasonably comprehensive glossary in excess of 2700 terms and useful throughout North and South America. This version of the glossary should only be considered a draft. It has been compiled from many books and online sources. Some entries I wrote myself but the vast majority were cut and pasted from the many online and printed sources. In future versions the definitions will be edited down, but in this version, in the interest of time, for a large number of the entries several definitions from multiple sources have been included. Throughout the glossary, words and terms in boldface type indicate other entries in the glossary. GLOSSARY abdomen - The part of the body that generally contains the intestines; also called the belly; in organisms, such as insects and spiders, is the last body section…In entomology, the part of an insect’s body that contains the digestive system and the organs of reproduction. -
Pollen DNA Barcoding: Current Applications and Future Prospects
Aberystwyth University Pollen DNA barcoding Bell, Karen. L.; De Vere, Natasha; Keller, Alexander; Richardson, Rodney; Gous, Annemarie; Burgess, Kevin S.; Brosi, Berry J. Published in: Genome DOI: 10.1139/gen-2015-0200 Publication date: 2016 Citation for published version (APA): Bell, K. L., De Vere, N., Keller, A., Richardson, R., Gous, A., Burgess, K. S., & Brosi, B. J. (2016). Pollen DNA barcoding: Current applications and future prospects. Genome, 59(9), 629-640. https://doi.org/10.1139/gen- 2015-0200 Document License CC BY General rights Copyright and moral rights for the publications made accessible in the Aberystwyth Research Portal (the Institutional Repository) are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the Aberystwyth Research Portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the Aberystwyth Research Portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. tel: +44 1970 62 2400 email: [email protected] Download date: 24. Sep. 2021 629 REVIEW Pollen DNA barcoding: current applications and future prospects1 Karen L. Bell, Natasha de Vere, Alexander Keller, Rodney T. Richardson, Annemarie Gous, Kevin S. Burgess, and Berry J.