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Prakofjewa J, Sartori M, Kalle R, Łuczaj Ł, Karbarz M, Mattalia G, Šarka P, Prūse B, Stryamets N, Anegg M, Kuznetsova N, Kolosova V, Belichenko O, Aziz MA, Pieroni A, Sõukand R. "But how true that is, I do not know": the influence of written sources on the medicinal use of fungi across the western borderlands of the former Soviet Union. IMA Fungus 2024; 15:22. [PMID: 39103962 PMCID: PMC11299371 DOI: 10.1186/s43008-024-00156-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 07/25/2024] [Indexed: 08/07/2024] Open
Abstract
Fungi have been used for medicinal purposes for many centuries. This study, based on 35 historical written sources and 581 in-depth semi-structured interviews from eight countries in the western borderlands of the former Soviet Union, investigates the medicinal use of fungi by local communities. We compared the taxa and uses obtained from fieldwork and historical sources with works that advocated fungi use within Soviet herbals, representing the centralised medical system. During fieldwork, we identified eight locally used fungi and one lichen. The highest numbers of medicinal uses were documented in Russia, Estonia and Ukraine. Studies published before the Soviet era listed 21 fungal taxa and one lichen species used in the study region. However, only six of these taxa were mentioned as used by people in our field studies (Amanita muscaria, Boletus edulis, Lycoperdon, Morchella, Phallus impudicus and Cetraria islandica). Notably, these same six taxa were consistently endorsed in Soviet herbals. Of the remaining three taxa recorded in the fieldwork, none were mentioned in historical written sources. However, they were promoted either in Soviet herbals (Inonotus obliquus, Kombucha) or later popular publications (Cantharellus cibarius). This highlights the significant influence of written sources on the use of fungi for medicinal purposes within the studied local communities.
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Affiliation(s)
- Julia Prakofjewa
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
| | - Matteo Sartori
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy.
| | - Raivo Kalle
- Estonian Literary Museum, Tartu, Estonia
- University of Gastronomic Sciences, Pollenzo, Italy
| | - Łukasz Łuczaj
- Institute of Biology, University of Rzeszów, Rzeszów, Poland
| | | | - Giulia Mattalia
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
- Institut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona (ICTA-UAB), Barcelona, Spain
| | - Povilas Šarka
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
- Botanical Garden of Vilnius University, Vilnius, Lithuania
| | - Baiba Prūse
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
- Athena Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Nataliya Stryamets
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
- Roztochya Nature Reserve, Ivano-Frankove, Ukraine
- Faculty of Forest Sciences, School of Forest Management, Swedish University of Agricultural Sciences, Skinnskatteberg, Sweden
| | - Martin Anegg
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
- Utz Group, Bremgarten, Switzerland
| | - Natalia Kuznetsova
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
- Università Cattolica del Sacro Cuore, Milan, Italy
| | - Valeria Kolosova
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
| | - Olga Belichenko
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
- Muséum National d'Histoire Naturelle, Paris, France
| | - Muhammad Abdul Aziz
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
| | - Andrea Pieroni
- University of Gastronomic Sciences, Pollenzo, Italy
- Medical Analysis Department, Tishk International University, Erbil, Iraq
| | - Renata Sõukand
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
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Sen K, Llewellyn M, Taheri B, Turner RJ, Berglund T, Maloney K. Mechanism of fungal remediation of wetland water: Stropharia rugosoannulata as promising fungal species for the development of biofilters to remove clinically important pathogenic and antibiotic resistant bacteria in contaminated water. Front Microbiol 2023; 14:1234586. [PMID: 37965549 PMCID: PMC10642173 DOI: 10.3389/fmicb.2023.1234586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/20/2023] [Indexed: 11/16/2023] Open
Abstract
Mycoremediation uses mushroom forming fungi for remediation of sites contaminated with biotic and abiotic contaminants. The root-like hyphae of many fungi, the mycelia, have been used to remediate soil and water. In this study mushroom mycelia biofilters were evaluated for remediation efficacy of wetland water polluted with crow feces containing antibiotic resistant (AMR) bacteria. Three strains of fungi, Pleurotus ostreatus, Stropharia rugosoannulata, and Pleurotus pulmonarius, were allowed to develop dense mycelia for 3-5 weeks on wood chips within cylindrical jars. Biofilter jars were incubated with wetland water (WW) obtained from a crow roost area that was additionally spiked with AMR bacteria isolated from previous crow fecal collections. E. coli, Staphylococcus aureus, Enterococcus faecium, Campylobacter jejuni, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Salmonella enteritidis were added at concentrations of 1,500-3,500 CFU/100 ml. Remediation was calculated from bacterial counts or gene copy numbers (GCN), before and after passage of water through jars. Stropharia and P. pulmonarius biofilters remediated all bacteria, but Klebsiella, in the range of 43-78%, after 1 h. Incubation of water for 24 h showed Stropharia remediation to be superior relative to other tested fungi. Percent remediation varied as follows: S. aureus-100%, E. faecium-97%, C. jejuni-59%, P. aeruginosa-54%, E. coli-65% and S. enteritidis-27%. The mechanism of remediation was tested by removing the mycelium from the biofilter column after passage of water, followed by extraction of DNA. Association of bacterial DNA with the mycelia was demonstrated by qPCR for all bacteria, except S. aureus and Salmonella. Depending on the bacteria, the GCN ranged from 3,500 to 54,000/250 mg of mycelia. Thus, some of the ways in which mycelia biofilters decrease bacteria from water are through bio-filtration and bio-absorption. Active fungal growth and close contact with bacteria appear necessary for removal. Overall these results suggest that mushroom mycelia biofilters have the potential to effectively remediate water contaminated with pathogenic and AMR bacteria.
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Affiliation(s)
- Keya Sen
- Division of Biological Sciences, School of Science, Technology, Engineering and Mathematics (STEM), University of Washington, Bothell, WA, United States
| | - Marina Llewellyn
- Division of Biological Sciences, School of Science, Technology, Engineering and Mathematics (STEM), University of Washington, Bothell, WA, United States
| | - Babak Taheri
- Division of Biological Sciences, School of Science, Technology, Engineering and Mathematics (STEM), University of Washington, Bothell, WA, United States
| | - Robert J. Turner
- School of Interdisciplinary Arts and Sciences, University of Washington, Bothell, WA, United States
| | - Tanner Berglund
- Division of Biological Sciences, School of Science, Technology, Engineering and Mathematics (STEM), University of Washington, Bothell, WA, United States
| | - Kellen Maloney
- School of Interdisciplinary Arts and Sciences, University of Washington, Bothell, WA, United States
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Gemmellaro MD, Lorusso NS, Domke R, Kovalska KM, Hashim A, Arevalo Mojica M, O’Connor AJ, Patel U, Pate O, Raise G, Shumskaya M. Assessment of Fungal Succession in Decomposing Swine Carcasses ( Sus scrofa L.) Using DNA Metabarcoding. J Fungi (Basel) 2023; 9:866. [PMID: 37754974 PMCID: PMC10532525 DOI: 10.3390/jof9090866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
The decomposition of animal bodies is a process defined by specific stages, described by the state of the body and participation of certain guilds of invertebrates and microorganisms. While the participation of invertebrates in decomposing is well-studied and actively used in crime scene investigations, information on bacteria and fungi from the scene is rarely collected or used in the identification of important factors such as estimated time of death. Modern molecular techniques such as DNA metabarcoding allow the identification and quantification of the composition of microbial communities. In this study, we used DNA metabarcoding to monitor fungal succession during the decomposition of juvenile pigs in grasslands of New Jersey, USA. Our findings show that decomposition stages differ in a diversity of fungal communities. In particular, we noted increased fungal species richness in the more advanced stages of decomposition (e.g., bloat and decay stages), with unique fungal taxa becoming active with the progression of decay. Overall, our findings improve knowledge of how fungi contribute to forensically relevant decomposition and could help with the assessment of crime scenes.
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Affiliation(s)
| | | | - Rachel Domke
- Department of Biology, Kean University, Union, NJ 07083, USA
| | | | - Ayesha Hashim
- Department of Biology, Kean University, Union, NJ 07083, USA
| | | | | | - Urvi Patel
- Department of Biology, Kean University, Union, NJ 07083, USA
| | - Olivia Pate
- Department of Biology, Kean University, Union, NJ 07083, USA
| | - Gloria Raise
- Department of Biology, Kean University, Union, NJ 07083, USA
| | - Maria Shumskaya
- Department of Biology, Kean University, Union, NJ 07083, USA
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Guo M, Yuan C, Tao L, Cai Y, Zhang W. Life barcoded by DNA barcodes. CONSERV GENET RESOUR 2022; 14:351-365. [PMID: 35991367 PMCID: PMC9377290 DOI: 10.1007/s12686-022-01291-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.
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Bartlett P, Eberhardt U, Schütz N, Beker HJ. Species determination using AI machine-learning algorithms: Hebeloma as a case study. IMA Fungus 2022; 13:13. [PMID: 35773719 PMCID: PMC9245212 DOI: 10.1186/s43008-022-00099-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
The genus Hebeloma is renowned as difficult when it comes to species determination. Historically, many dichotomous keys have been published and used with varying success rate. Over the last 20 years the authors have built a database of Hebeloma collections containing not only metadata but also parametrized morphological descriptions, where for about a third of the cases micromorphological characters have been analysed and are included, as well as DNA sequences for almost every collection. The database now has about 9000 collections including nearly every type collection worldwide and represents over 120 different taxa. Almost every collection has been analysed and identified to species using a combination of the available molecular and morphological data in addition to locality and habitat information. Based on these data an Artificial Intelligence (AI) machine-learning species identifier has been developed that takes as input locality data and a small number of the morphological parameters. Using a random test set of more than 600 collections from the database, not utilized within the set of collections used to train the identifier, the species identifier was able to identify 77% correctly with its highest probabilistic match, 96% within its three most likely determinations and over 99% of collections within its five most likely determinations.
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Affiliation(s)
- Peter Bartlett
- La Baraka, Gorse Hill Road, Virginia Water, Surrey, GU25 4AP, UK
| | - Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191, Stuttgart, Germany.
| | - Nicole Schütz
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191, Stuttgart, Germany
| | - Henry J Beker
- , Rue Père de Deken 19, 1040, Bruxelles, Belgium.,Royal Holloway College, University of London, Egham, UK.,Plantentuin Meise, Nieuwelaan 38, B-1860, Meise, Belgium
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Eberhardt U, Kong A, Montoya A, Schütz N, Bartlett P, Beker HJ. Not (only) poison pies - Hebeloma (Agaricales, Hymenogastraceae) in Mexico. MycoKeys 2022; 90:163-202. [PMID: 36760422 PMCID: PMC9849069 DOI: 10.3897/mycokeys.90.85267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/07/2022] [Indexed: 11/12/2022] Open
Abstract
The species of Hebeloma have been little studied in Mexico, but have received attention as edibles and in trials to enhance production of edible fungi and tree growth through inoculation of seedlings with ectomycorrhizal fungi. Here we describe three new species of Hebeloma that are currently known only from Mexico. These species belong to separate sections of the genus: H.ambustiterranum is a member of H.sect.Hebeloma, H.cohaerens belongs to H.sect.Theobromina, while H.magnicystidiatum belongs to H.sect.Denudata. All three species were collected from subtropical pine-oak woodland; all records of H.cohaerens came from altitudes above 2500 m. Hebelomaambustiterranum is commonly sold in the local markets of Tlaxcala as a prized edible mushroom. An additional nine species are reported from Mexico, of which eight are new records for the country: H.aanenii, H.eburneum, H.excedens, H.ingratum, H.neurophyllum, H.sordidulum, H.subaustrale and H.velutipes. First modern descriptions of H.neurophyllum and H.subaustrale, originally described from the USA, are given here.
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Affiliation(s)
- Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Alejandro Kong
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Km 10.5 carretera San Martín Texmelucan-Tlaxcala, San Felipe Ixtacuixtla, Tlaxcala, 90120, Mexico
| | - Adriana Montoya
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Km 10.5 carretera San Martín Texmelucan-Tlaxcala, San Felipe Ixtacuixtla, Tlaxcala, 90120, Mexico
| | - Nicole Schütz
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Peter Bartlett
- La Baraka, Gorse Hill Road, Virginia Water, Surrey GU25 4AP, United Kingdom
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Eberhardt U, Schütz N, Bartlett P, Hosaka K, Kasuya T, Beker HJ. Revisiting Hebeloma (Hymenogastraceae, Agaricales) in Japan: four species recombined into other genera but three new species discovered. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01757-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
AbstractHere, we present the results of studies of Japanese Hebeloma collections. The four species described by Imai as Hebeloma (H. fimicola, H. helvolescens, H. humosum, and H. tomoeae) are not from the genus Hebeloma, but are members of Agrocybe, Homophron, or Pholiota. Recombinations are made. Hebelomacrustuliniforme f. microspermum, described by Hongo, is a synonym of H. nanum. Three species of Hebeloma are described as new to science, all currently known only from Japan. Two of these species, H. asperosporum and H. cinnamomeum, are members of H. sect. Denudata while the third species H. citrisporum belongs to H. sect. Velutipes. Japanese records of H. cavipes, H. eburneum, H. hygrophilum, H. subtortum, and H. velutipes are validated. In total, fifteen species of Hebeloma are confirmed from Japan; this is compared with previous checklists.
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Eberhardt U, Schütz N, Bartlett P, Beker HJ. 96 North American taxa sorted - Peck's Hebeloma revisited. Mycologia 2022; 114:337-387. [PMID: 35230235 DOI: 10.1080/00275514.2021.2012063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Charles Horton Peck described some 2700 species of North American fungi in the 19th and early 20th centuries. Among these were 31 species that he described as Hebeloma or that later authors recombined into Hebeloma. These 31 taxa have been analyzed morphologically and molecularly, as far as possible. For six of these species, lectotypes are designated. For twelve species, ITS sequences (some partial) were generated. Thirteen of the species analyzed are Hebeloma, as the genus is delimited today. Of these 13, nine are regarded as 'current', i.e. are names that should be accepted and used. Of the remaining four, three are synonymized with earlier Peck species and one with the generic type H. mesophaeum. Numerous Hebeloma species described from America are synonymized with some of Peck's species, such as H. albidulum, H. album, H. colvinii, H. excedens, H. palustre, H. sordidulum, and H. velatum; Peck's H. album, H. palustre, and H. velatum are earlier names for H. fragilipes, H. clavulipes, and H. dunense, respectively. All three names were in current use and described from Europe. The 18 species that are not Hebeloma belong to a range of genera: Agrocybe, Hemistropharia, Inocybe, Inosperma, Naucoria, and Pholiota; three species that were not previously recombined into their respective genera are here recombined and one species, Hebeloma commune is synonymized with Pholiota lenta. Two taxa, that are not Hebeloma, remain unresolved. Sixty later Hebeloma taxa described from North America are revised and synonymized with Peck species and seven with H. mesophaeum, 36 of these supported by ITS (some partial) sequence data. Updates on two species, H. petrakii and H. remyi, from Europe, are also given, and a lectotype and epitype selected for the latter.
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Affiliation(s)
- Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Nicole Schütz
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Peter Bartlett
- La Baraka, Gorse Hill Road, Virginia Water, Surrey GU25 4AP, United Kingdom
| | - Henry J Beker
- Rue Père de Deken 19, B-1040 Bruxelles, Belgium; Royal Holloway College, University of London, Egham, United Kingdom; Plantentuin Meise, Nieuwelaan 38, B-1860 Meise, Belgium
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Suárez Casanova VM, Shumskaya M. Exploring DNA in biochemistry lab courses: DNA barcoding and phylogenetic analysis. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:789-799. [PMID: 34096689 DOI: 10.1002/bmb.21551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 04/18/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
DNA structure has been leveraged in a variety of facets that allow scientists to perform a range of assays, including ones for identification of species, establishing evolutionary relationships between taxa, or even identifying individuals. Here, we present a DNA barcoding method as practical, hands-on approach that connects several experimental techniques in one sequence to teach the principles behind DNA isolation, purification, PCR, sequencing, and phylogeny analysis. Our set of exercises is designed for a teaching university laboratory setting. The three laboratory class assignments utilize DNA from a mushroom (can be purchased at a supermarket) and provide a pipeline to guide students through the process of identifying an unknown sample, like in many research laboratories. The third assignment can be used as a stand-alone exercise on phylogeny analysis and can be taught remotely. Students explore the theory behind the standard molecular techniques and apply it in a hands-on setting that involves experimental design, sample preparation, and use of hallmark molecular instruments.
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Affiliation(s)
- Víctor Manuel Suárez Casanova
- School of Natural Sciences, Biology, Kean University, New Jersey, USA
- Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Maria Shumskaya
- School of Natural Sciences, Biology, Kean University, New Jersey, USA
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Prahl RE, Khan S, Deo RC. The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces. PLoS One 2021; 16:e0253772. [PMID: 34191835 PMCID: PMC8244850 DOI: 10.1371/journal.pone.0253772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/13/2021] [Indexed: 11/19/2022] Open
Abstract
Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. However, inter- and intra-specific distances in ITS sequences highly vary among some fungal groups; consequently, it is not a solely reliable tool for species delineation. Ampelomyces, mycoparasites of the fungal phytopathogen order Erysiphales, can have ITS genetic differences up to 15%; this may lead to misidentification with other closely related unknown fungi. Indeed, Ampelomyces were initially misidentified as other pycnidial mycoparasites, but subsequent research showed that they differ in pycnidia morphology and culture characteristics. We investigated whether the ITS2 nucleotide content and secondary structure was different between Ampelomyces ITS2 sequences and those unrelated to this genus. To this end, we retrieved all ITS sequences referred to as Ampelomyces from the GenBank database. This analysis revealed that fungal ITS environmental DNA sequences are still being deposited in the database under the name Ampelomyces, but they do not belong to this genus. We also detected variations in the conserved hybridization model of the ITS2 proximal 5.8S and 28S stem from two Ampelomyces strains. Moreover, we suggested for the first time that pseudogenes form in the ITS region of this mycoparasite. A phylogenetic analysis based on ITS2 sequences-structures grouped the environmental sequences of putative Ampelomyces into a different clade from the Ampelomyces-containing clades. Indeed, when conducting ITS2 analysis, resolution of genetic distances between Ampelomyces and those putative Ampelomyces improved. Each clade represented a distinct consensus ITS2 S2, which suggested that different pre-ribosomal RNA (pre-rRNA) processes occur across different lineages. This study recommends the use of ITS2 S2s as an important tool to analyse environmental sequencing and unveiling the underlying evolutionary processes.
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Affiliation(s)
- Rosa E. Prahl
- School of Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia
- * E-mail:
| | - Shahjahan Khan
- School of Sciences, Centre for Health Research, Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Ravinesh C. Deo
- School of Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia
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van Bemmelen van der Plaat A, van Treuren R, van Hintum TJL. Reliable genomic strategies for species classification of plant genetic resources. BMC Bioinformatics 2021; 22:173. [PMID: 33789577 PMCID: PMC8011391 DOI: 10.1186/s12859-021-04018-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 02/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To address the need for easy and reliable species classification in plant genetic resources collections, we assessed the potential of five classifiers (Random Forest, Neighbour-Joining, 1-Nearest Neighbour, a conservative variety of 3-Nearest Neighbours and Naive Bayes) We investigated the effects of the number of accessions per species and misclassification rate on classification success, and validated theirs generic value results with three complete datasets. RESULTS We found the conservative variety of 3-Nearest Neighbours to be the most reliable classifier when varying species representation and misclassification rate. Through the analysis of the three complete datasets, this finding showed generic value. Additionally, we present various options for marker selection for classification taks such as these. CONCLUSIONS Large-scale genomic data are increasingly being produced for genetic resources collections. These data are useful to address species classification issues regarding crop wild relatives, and improve genebank documentation. Implementation of a classification method that can improve the quality of bad datasets without gold standard training data is considered an innovative and efficient method to improve gene bank documentation.
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Affiliation(s)
| | - Rob van Treuren
- Centre for Genetic Resources, Wageningen University and Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Theo J L van Hintum
- Centre for Genetic Resources, Wageningen University and Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
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Łuczaj Ł, Lamxay V, Tongchan K, Xayphakatsa K, Phimmakong K, Radavanh S, Kanyasone V, Pietras M, Karbarz M. Wild food plants and fungi sold in the markets of Luang Prabang, Lao PDR. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2021; 17:6. [PMID: 33499871 PMCID: PMC7835671 DOI: 10.1186/s13002-020-00423-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/28/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Open air markets hold an important position for ethnobiologists. In Southeast Asia, they are seriously understudied, in spite of their incredible biocultural diversity. In order to fill this gap we recorded plants and fungi sold in the open air markets of Luang Prabang, Lao PDR. METHODS The markets were visited 38 times in four seasons: the dry season, early monsoon, mid-monsoon, and end-of-monsoon, at least 8 times per season. All items were photographed and voucher specimens were collected. Fungi were identified using DNA barcoding techniques. RESULTS We recorded 110 species of wild edible plants and 54 species of fungi, including 49 wild-collected species. The sold plants included 86 species of green vegetables, 18 species of fruits and 3 species of flowers. Products from woody species constitute around half of all taxa sold. These include the young shoots of tree leaves, which are used for salads-an interesting feature of Lao cuisine. A large number of extremely rare Russula, with no reference sequences represented in databases or even species unknown to science is present on sale in the markets. CONCLUSIONS Luang Prabang markets are some of the richest in species of wild edible plants and fungi in Asia, and indeed in the whole world. It is worth pointing out the exceptionally long list of wild edible mushrooms which are sold in Luang Prabang (and probably elsewhere in Laos). We view the Morning Market of Luang Prabang as a cultural treasure that unites the traditions of eating a large number of living species with very diverse flora and fauna. Measures should be taken to strike a balance between local foraging traditions and nature conservation priorities.
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Affiliation(s)
- Łukasz Łuczaj
- Institute of Biology and Biotechnology, ul. Pigonia 1, 35-310 Rzeszów, Poland
| | - Vichith Lamxay
- Department of Biology, Faculty of Natural Sciences, National University of Laos, Vientiane, Lao People’s Democratic Republic
| | - Khamphart Tongchan
- Pha Tad Ke Botanical Garden, Ban Wat That, PO Box 959, 06000 Luang Prabang, Lao People’s Democratic Republic
| | - Kosonh Xayphakatsa
- Biotechnology and Ecology Institute, Ministry of Science and Technology, Doon Teaw Village, Km 14 Office, Thangon Road, Xaythany District PO Box 2279, Vientiane, Lao People’s Democratic Republic
| | - Kongchay Phimmakong
- Department of Science, Ministry of Science and Technology, Doon Teaw, Km 14, Thangon Road, Xaythany District PO Box 2279, Vientiane, Lao People’s Democratic Republic
| | - Somphavanh Radavanh
- Biotechnology and Ecology Institute, Ministry of Science and Technology, Doon Teaw Village, Km 14 Office, Thangon Road, Xaythany District PO Box 2279, Vientiane, Lao People’s Democratic Republic
| | - Villapone Kanyasone
- Department of Science and Technology, Luang Prabang, Lao People’s Democratic Republic
| | - Marcin Pietras
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Małgorzata Karbarz
- Institute of Biology and Biotechnology, ul. Pigonia 1, 35-310 Rzeszów, Poland
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Eberhardt U, Beker HJ, Schütz N, Pedersen OS, Sysouphanthong P, Læssøe T. Adventurous cuisine in Laos: Hebeloma parvisporum, a new species in Hebeloma section Porphyrospora. Mycologia 2020; 112:172-184. [PMID: 31900082 DOI: 10.1080/00275514.2019.1680220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Hebeloma parvisporum is described as new and placed within H. sect. Porphyrospora. This mushroom is sold as an edible in markets of Laos under the local name "wai khom." Hebeloma sect. Porphyrospora is discussed and expanded to include the species formerly included in the genus Anamika and recently transferred to Hebeloma. Hebeloma sect. Porphyrospora currently comprises 16 species, 14 of which are known only from the western Pacific and Indian subcontinent. All species in this section share the character of having red-brown spores when fresh, atypical for other sections of Hebeloma, which causes the lamellae to be red-brown. However, this red-brown color fades when the material is dried. The close links, morphologically and molecularly, between H. parvisporum and other members of H. sect. Porphyrospora, particularly H. victoriense, are shown.
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Affiliation(s)
- Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Henry J Beker
- Rue Père de Deken 19, B-1040 Bruxelles, Belgium; Royal Holloway College, University of London, Egham, United Kingdom; Plantentuin Meise, Nieuwelaan 38, B-1860 Meise, Belgium
| | - Nicole Schütz
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | | | - Phongeun Sysouphanthong
- Ecology Division, Biotechnology and Ecology Institute, Ministry of Science and Technology, P.O. Box 2279, Vientiane Capital, Lao People's Democratic Republic
| | - Thomas Læssøe
- Department of Biology/Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
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14
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Caboň M, Li GJ, Saba M, Kolařík M, Jančovičová S, Khalid AN, Moreau PA, Wen HA, Pfister DH, Adamčík S. Phylogenetic study documents different speciation mechanisms within the Russula globispora lineage in boreal and arctic environments of the Northern Hemisphere. IMA Fungus 2019; 10:5. [PMID: 32647614 PMCID: PMC7325667 DOI: 10.1186/s43008-019-0003-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 11/10/2022] Open
Abstract
The Russula globispora lineage is a morphologically and phylogenetically well-defined group of ectomycorrhizal fungi occurring in various climatic areas. In this study we performed a multi-locus phylogenetic study based on collections from boreal, alpine and arctic habitats of Europe and Western North America, subalpine collections from the southeast Himalayas and collections from subtropical coniferous forests of Pakistan. European and North American collections are nearly identical and probably represent a single species named R. dryadicola distributed from the Alps to the Rocky Mountains. Collections from the southeast Himalayas belong to two distinct species: R. abbottabadensis sp. nov. from subtropical monodominant forests of Pinus roxburghii and R. tengii sp. nov. from subalpine mixed forests of Abies and Betula. The results suggest that speciation in this group is driven by a climate disjunction and adaptation rather than a host switch and geographical distance.
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Affiliation(s)
- Miroslav Caboň
- Department of Cryptogams, Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovakia
| | - Guo-Jie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 1st Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Malka Saba
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320 Pakistan
- Department of Botany, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590 Pakistan
- Farlow Reference Library and Herbarium of Cryptogamic Botany, Harvard University, Cambridge, MA 02138 USA
| | - Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Praha, Czech Republic
| | - Soňa Jančovičová
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Révová 39, SK-811 02 Bratislava, Slovakia
| | - Abdul Nasir Khalid
- Department of Botany, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590 Pakistan
| | - Pierre-Arthur Moreau
- Laboratoire IMPECS, Fac. Pharma. Lille, Université de Lille, F-59000 Lille, France
| | - Hua-An Wen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No 3 1st Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Donald H. Pfister
- Farlow Reference Library and Herbarium of Cryptogamic Botany, Harvard University, Cambridge, MA 02138 USA
| | - Slavomír Adamčík
- Department of Cryptogams, Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovakia
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15
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Vu D, Groenewald M, de Vries M, Gehrmann T, Stielow B, Eberhardt U, Al-Hatmi A, Groenewald J, Cardinali G, Houbraken J, Boekhout T, Crous P, Robert V, Verkley G. Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation. Stud Mycol 2019; 92:135-154. [PMID: 29955203 PMCID: PMC6020082 DOI: 10.1016/j.simyco.2018.05.001] [Citation(s) in RCA: 424] [Impact Index Per Article: 84.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Species identification lies at the heart of biodiversity studies that has in recent years favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source for diverse and high-quality reference materials in microbiology, and yet the strains preserved in these biobanks have been exploited only on a limited scale to generate DNA barcodes. As part of a project funded in the Netherlands to barcode specimens of major national biobanks, sequences of two nuclear ribosomal genetic markers, the Internal Transcribed Spaces and 5.8S gene (ITS) and the D1/D2 domain of the 26S Large Subunit (LSU), were generated as DNA barcode data for ca. 100 000 fungal strains originally assigned to ca. 17 000 species in the CBS fungal biobank maintained at the Westerdijk Fungal Biodiversity Institute, Utrecht. Using more than 24 000 DNA barcode sequences of 12 000 ex-type and manually validated filamentous fungal strains of 7 300 accepted species, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. We showed that 17 % and 18 % of the species could not be discriminated by the ITS and LSU genetic markers, respectively. Among them, ∼8 % were indistinguishable using both genetic markers. ITS has been shown to outperform LSU in filamentous fungal species discrimination with a probability of correct identification of 82 % vs. 77.6 %, and a clustering quality value of 84 % vs. 77.7 %. At higher taxonomic classifications, LSU has been shown to have a better discriminatory power than ITS. With a clustering quality value of 80 %, LSU outperformed ITS in identifying filamentous fungi at the ordinal level. At the generic level, the clustering quality values produced by both genetic markers were low, indicating the necessity for taxonomic revisions at genus level and, likely, for applying more conserved genetic markers or even whole genomes. The taxonomic thresholds predicted for filamentous fungal identification at the genus, family, order and class levels were 94.3 %, 88.5 %, 81.2 % and 80.9 % based on ITS barcodes, and 98.2 %, 96.2 %, 94.7 % and 92.7 % based on LSU barcodes. The DNA barcodes used in this study have been deposited to GenBank and will also be publicly available at the Westerdijk Institute's website as reference sequences for fungal identification, marking an unprecedented data release event in global fungal barcoding efforts to date.
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Affiliation(s)
- D. Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - T. Gehrmann
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - B. Stielow
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - U. Eberhardt
- Staatliches Museum f. Naturkunde Stuttgart, Abt. Botanik, Rosenstein 1, D-70191 Stuttgart, Germany
| | - A. Al-Hatmi
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - G. Cardinali
- University of Perugia, Dept. of Pharmaceutical Sciences, Via Borgo 20 Giugno 74, I 06121 Perugia, Italy
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, The Netherlands
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - G.J.M. Verkley
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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16
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Kotowski MA, Pietras M, Łuczaj Ł. Extreme levels of mycophilia documented in Mazovia, a region of Poland. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2019; 15:12. [PMID: 30755235 PMCID: PMC6371552 DOI: 10.1186/s13002-019-0291-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 01/28/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND The paper presents documentation of the traditional use of wild edible mushrooms in Mazovia (33,900 km2), a region of Poland. METHODS A total of 695 semi-structured interviews were carried out among local informants in 38 localities proportionally distributed throughout the study area (one locality approximately every 30 km), asking which mushrooms they collected and how. The species utilized were identified using visual props, morphological identification of voucher specimens, and DNA barcoding. RESULTS Altogether, 92 taxa identified to the species or genus level were recorded, among them 76 species used as food, 21 taxa known as toxic, and 11 taxa used for non-culinary purposes. Out of 76 identified edible fungi species, 47% (36 species) were identified using ITS DNA barcode method. Eleven of them were identified exclusively by molecular analysis. The mean number of edible taxa mentioned per interview was 9.5. Two species new to the mycobiota of Poland, Hydnum ellipsosporum and Paxillus cuprinus, were found. Frequent interaction with mushroom collectors enabled the transcription of local folk taxonomy into proper taxonomic classification and the definition of changes in local preferences concerning wild fungi collection. CONCLUSIONS The list of species utilized is the longest regional list of edible mushrooms ever recorded during ethnomycological field research, putting the inhabitants of the studied region at the top of the mycophilia spectrum.
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Affiliation(s)
- Marcin Andrzej Kotowski
- Department of Botany, Faculty of Biotechnology, University of Rzeszów, Pigonia 1, 35-310 Rzeszów, Poland
| | - Marcin Pietras
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Łukasz Łuczaj
- Department of Botany, Faculty of Biotechnology, University of Rzeszów, Pigonia 1, 35-310 Rzeszów, Poland
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17
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Cripps CL, Eberhardt U, Schütz N, Beker HJ, Vera S Evenson, Horak E. The genus Hebeloma in the Rocky Mountain Alpine Zone. MycoKeys 2019:1-54. [PMID: 30787668 PMCID: PMC6379322 DOI: 10.3897/mycokeys.46.32823] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/17/2019] [Indexed: 11/16/2022] Open
Abstract
Numerous taxa of Hebeloma have been reported in association with Salix, Dryas, and Betula in arctic-alpine habitats. However, species are notoriously difficult to delineate because morphological features overlap, and previously there was little reliable molecular data available. Recent progress in ITS-sequencing within the genus, coupled with an extensive database of parametrically described collections, now allows comparisons between species and their distributions. Here we report 16 species of Hebeloma from the Rocky Mountain alpine zone from some of the lowest latitudes (latitude 36°–45°N) and highest elevations (3000–4000 m) for arctic-alpine fungi in the northern hemisphere. Twelve of these species have been reported from arctic-alpine habitats in Europe and Greenland and are now molecularly confirmed from the Middle and Southern Rockies, greatly expanding their distribution. These are: Hebelomaalpinum, H.aurantioumbrinum, H.dunense, H.hiemale, H.marginatulum, H.mesophaeum, H.nigellum, H.oreophilum, H.subconcolor, H.spetsbergense, H.vaccinum, and H.velutipes. Hebelomahygrophilum is known from subalpine habitats in Europe, but was never recorded in arctic-alpine ecology. Three species recorded from the Rockies, but as yet not reported from Europe, are H.alpinicola, H.avellaneum, and H.excedens. The last two have never previously been reported from an arctic-alpine habitat. For all three of these species, the holotypes have been studied morphologically and molecularly, and have been incorporated into the analysis.
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Affiliation(s)
- Cathy L Cripps
- Plant Sciences and Plant Pathology, 119 Plant Biosciences Bldg, Montana State University, Bozeman, MT 59717, USA
| | - Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, D-70191 Stuttgart, Germany
| | - Nicole Schütz
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, D-70191 Stuttgart, Germany
| | - Henry J Beker
- Rue Père de Deken 19, B-1040 Bruxelles, Belgium; Royal Holloway College, University of London, Egham, United Kingdom; Plantentuin Meise, Nieuwelaan 38, B-1860 Meise, Belgium
| | - Vera S Evenson
- Sam Mitchel Herbarium of Fungi, Denver Botanic Garden, 909 York Street, Denver, CO 80206, USA
| | - Egon Horak
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6th floor, A-6020 Innsbruck, Austria
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18
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Bandini D, Oertel B, Ploch S, Ali T, Vauras J, Schneider A, Scholler M, Eberhardt U, Thines M. Revision of some central European species of Inocybe (Fr.: Fr.) Fr. subgenus Inocybe, with the description of five new species. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1439-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Marizzi C, Florio A, Lee M, Khalfan M, Ghiban C, Nash B, Dorey J, McKenzie S, Mazza C, Cellini F, Baria C, Bepat R, Cosentino L, Dvorak A, Gacevic A, Guzman-Moumtzis C, Heller F, Holt NA, Horenstein J, Joralemon V, Kaur M, Kaur T, Khan A, Kuppan J, Laverty S, Lock C, Pena M, Petrychyn I, Puthenkalam I, Ram D, Ramos A, Scoca N, Sin R, Gonzalez I, Thakur A, Usmanov H, Han K, Wu A, Zhu T, Micklos DA. DNA barcoding Brooklyn (New York): A first assessment of biodiversity in Marine Park by citizen scientists. PLoS One 2018; 13:e0199015. [PMID: 30020927 PMCID: PMC6051577 DOI: 10.1371/journal.pone.0199015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 05/30/2018] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding is both an important research and science education tool. The technique allows for quick and accurate species identification using only minimal amounts of tissue samples taken from any organism at any developmental phase. DNA barcoding has many practical applications including furthering the study of taxonomy and monitoring biodiversity. In addition to these uses, DNA barcoding is a powerful tool to empower, engage, and educate students in the scientific method while conducting productive and creative research. The study presented here provides the first assessment of Marine Park (Brooklyn, New York, USA) biodiversity using DNA barcoding. New York City citizen scientists (high school students and their teachers) were trained to identify species using DNA barcoding during a two-week long institute. By performing NCBI GenBank BLAST searches, students taxonomically identified 187 samples (1 fungus, 70 animals and 116 plants) and also published 12 novel DNA barcodes on GenBank. Students also identified 7 ant species and demonstrated the potential of DNA barcoding for identification of this especially diverse group when coupled with traditional taxonomy using morphology. Here we outline how DNA barcoding allows citizen scientists to make preliminary taxonomic identifications and contribute to modern biodiversity research.
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Affiliation(s)
- Christine Marizzi
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Antonia Florio
- Department of Herpetology, American Museum of Natural History, New York, New York, United States of America
| | - Melissa Lee
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Mohammed Khalfan
- New York University, New York, New York, United States of America
| | - Cornel Ghiban
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Bruce Nash
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jenna Dorey
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- The New York Botanical Garden, Bronx, New York, United States of America
| | - Sean McKenzie
- The Rockefeller University, New York, New York, United States of America
| | - Christine Mazza
- Genovesi Environmental Study Center, New York City Department of Education, Brooklyn, New York, United States of America
| | - Fabiana Cellini
- Genovesi Environmental Study Center, New York City Department of Education, Brooklyn, New York, United States of America
| | - Carlo Baria
- CSI for International Studies, New York City Department of Education, Staten Island, New York, United States of America
| | - Ron Bepat
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Lena Cosentino
- CSI for International Studies, New York City Department of Education, Staten Island, New York, United States of America
| | - Alexander Dvorak
- International High School at Union Square, New York City Department of Education New York, New York, United States of America
| | - Amina Gacevic
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Cristina Guzman-Moumtzis
- Frank McCourt High School, New York City Department of Education, New York, New York, United States of America
| | - Francesca Heller
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Nicholas Alexander Holt
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Jeffrey Horenstein
- Stuyvesant High School, New York City Department of Education, New York, New York, United States of America
| | - Vincent Joralemon
- Frank McCourt High School, New York City Department of Education, New York, New York, United States of America
| | - Manveer Kaur
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Tanveer Kaur
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Armani Khan
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Jessica Kuppan
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Scott Laverty
- CSI for International Studies, New York City Department of Education, Staten Island, New York, United States of America
| | - Camila Lock
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Marianne Pena
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Ilona Petrychyn
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Indu Puthenkalam
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Daval Ram
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Arlene Ramos
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Noelle Scoca
- Brooklyn International High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Rachel Sin
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Izabel Gonzalez
- High School for Health Professions and Human Services, New York City Department of Education, New York, New York, United States of America
| | - Akansha Thakur
- Forest Hills High School, New York City Department of Education, Queens, New York, United States of America
| | - Husan Usmanov
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Karen Han
- High School for Construction Trades, Engineering and Architecture, New York City Department of Education, Queens, New York, United States of America
| | - Andy Wu
- Franklin D. Roosevelt High School, New York City Department of Education, Brooklyn, New York, United States of America
| | - Tiger Zhu
- Stuyvesant High School, New York City Department of Education, New York, New York, United States of America
| | - David Andrew Micklos
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
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DNA Barcoding for Identification of Consumer-Relevant Fungi Sold in New York: A Powerful Tool for Citizen Scientists? Foods 2018; 7:foods7060087. [PMID: 29890621 PMCID: PMC6025134 DOI: 10.3390/foods7060087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/31/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Although significant progress has been made in our understanding of fungal diversity, identification based on phenotype can be difficult, even for trained experts. Fungi typically have a cryptic nature and can have a similar appearance to distantly related species. Moreover, the appearance of industrially processed mushrooms complicates species identification, as they are often sold sliced and dried. Here we present a small-scale citizen science project, wherein the participants generated and analyzed DNA sequences from fruiting bodies of dried and fresh fungi that were sold for commercial use in New York City supermarkets. We report positive outcomes and the limitations of a youth citizen scientist, aiming to identify dried mushrooms, using established DNA barcoding protocols and exclusively open-access data analysis tools for species identification. Our results indicate that the single-locus nuclear ribosomal internal transcribed spacer (ITS) DNA barcoding approach allowed for identification of only a subset of all of the samples at the species level, although the generated high-quality DNA barcodes were submitted to three different databases. Our results highlight the need for a curated, centralized, and open access ITS reference database that allows rapid third-party annotations for the benefit of both traditional research as well as the emerging citizen science community.
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Hill GE. Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap. Ecol Evol 2016; 6:5831-42. [PMID: 27547358 PMCID: PMC4983595 DOI: 10.1002/ece3.2338] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial genes are widely used in taxonomy and systematics because high mutation rates lead to rapid sequence divergence and because such changes have long been assumed to be neutral with respect to function. In particular, the nucleotide sequence of the mitochondrial gene cytochrome c oxidase subunit 1 has been established as a highly effective DNA barcode for diagnosing the species boundaries of animals. Rarely considered in discussions of mitochondrial evolution in the context of systematics, speciation, or DNA barcodes, however, is the genomic architecture of the eukaryotes: Mitochondrial and nuclear genes must function in tight coordination to produce the complexes of the electron transport chain and enable cellular respiration. Coadaptation of these interacting gene products is essential for organism function. I extend the hypothesis that mitonuclear interactions are integral to the process of speciation. To maintain mitonuclear coadaptation, nuclear genes, which code for proteins in mitochondria that cofunction with the products of mitochondrial genes, must coevolve with rapidly changing mitochondrial genes. Mitonuclear coevolution in isolated populations leads to speciation because population-specific mitonuclear coadaptations create between-population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes, particularly in response to climate or altitude, can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. By this model, the defining characteristic of a metazoan species is a coadapted mitonuclear genotype that is incompatible with the coadapted mitochondrial and nuclear genotype of any other population.
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Affiliation(s)
- Geoffrey E. Hill
- Department Biological ScienceAuburn University331 Funchess HallAuburnAlabama36849‐5414
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Adamčík S, Slovák M, Eberhardt U, Ronikier A, Jairus T, Hampe F, Verbeken A. Molecular inference, multivariate morphometrics and ecological assessment are applied in concert to delimit species in the Russula clavipes complex. Mycologia 2016; 108:716-30. [PMID: 27091390 DOI: 10.3852/15-194] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/29/2016] [Indexed: 01/28/2023]
Abstract
Species of Russula subsect. Xerampelinae are notoriously difficult to identify and name and have not been subject to molecular study. A group of species, referred to here as the R. clavipes complex, growing in association with Salix, Betula and Populus as well as coniferous tree species from temperate to arctic and alpine habitats, were examined. Analyses of the nuc rDNA internal transcribed spacer (ITS) region and a numerical analysis of morphological characters were used. The R. clavipes complex is a monophyletic group within Russula subsect. Xerampelinae, according to molecular results. The complex includes three species: R. nuoljae is a phylogenetically and morphologically well-supported species while the other two, R. clavipes and R. pascua, are similar based on ITS data and morphology but separate based on their ecology. Russula pseudoolivascens is conspecific with R. clavipes Several combinations of characters traditionally used in the taxonomy of R. subsect. Xerampelinae are inappropriate for species delimitation in this group and the adequacy of the ITS for species identification in this group is discussed. Detailed microscopic observations on the type collection of R. nuoljae are presented and illustrated, along with a key to the European members of R. subsect. Xerampelinae.
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Affiliation(s)
- Slavomír Adamčík
- Institute of Botany SAS, Dúbravská cesta 14, SK-845 23 Bratislava, Slovakia
| | - Marek Slovák
- Institute of Botany SAS, Dúbravská cesta 14, SK-845 23 Bratislava, Slovakia
| | - Ursula Eberhardt
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, DE-70191 Stuttgart, Germany
| | - Anna Ronikier
- Department of Mycology, W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Cracow, Poland
| | - Teele Jairus
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu 51005, Estonia
| | - Felix Hampe
- Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Abstract
The accumulation of DNA barcode sequences will provide an increasingly useful and comprehensive library for species identification and discovery of marine metazoans. Here we present a summary of protocols designed to obtain DNA barcodes of marine metazoans from diverse phyla.
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Affiliation(s)
- Dirk Steinke
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1.
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
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Grilli E, Beker HJ, Eberhardt U, Schütz N, Leonardi M, Vizzini A. Unexpected species diversity and contrasting evolutionary hypotheses in Hebeloma (Agaricales) sections Sinapizantia and Velutipes in Europe. Mycol Prog 2015. [DOI: 10.1007/s11557-015-1148-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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DNA barcodes for ecology, evolution, and conservation. Trends Ecol Evol 2015; 30:25-35. [DOI: 10.1016/j.tree.2014.10.008] [Citation(s) in RCA: 284] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 10/23/2014] [Accepted: 10/28/2014] [Indexed: 01/28/2023]
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Sorbicillinoid analogs with cytotoxic and selective anti-Aspergillus activities from Scytalidium album. J Antibiot (Tokyo) 2014; 68:191-6. [PMID: 25248727 PMCID: PMC4372511 DOI: 10.1038/ja.2014.125] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/14/2014] [Accepted: 07/18/2014] [Indexed: 11/08/2022]
Abstract
As part of an ongoing project to explore filamentous fungi for anticancer and antibiotic leads, eleven compounds were isolated and identified from an organic extract of the fungus Scytalidium album (MSX51631) using bioactivity-directed fractionation against human cancer cell lines. Of these, eight were a series of sorbicillinoid analogues (1–8), of which four were new [scalbucillin A (2), scalbucillin B (3), scalbucillin C (6), and scalbucillin D (8)], two were phthalides (9–10), and one was naphthalenone (11). Compounds (1–11) were tested in the MDA-MB-435 (melanoma) and SW-620 (colon) cancer cell lines. Compound 1 was the most potent with IC50 values of 1.5 and 0.5 μM, respectively, followed by compound 5, with IC50 values of 2.3 and 2.5 μM at 72 h. Compound 1 showed a 48-h IC50 value of 3.1 μM when tested against the lymphocytic leukemia cell line OSU-CLL, while the nearly identical compound 5 had almost no activity in this assay. Compounds 1 and 5 showed selective and equipotent activity against Aspergillus niger with minimum inhibitory concentration values of 0.05 and 0.04 μg/ml (0.20 and 0.16 μM), respectively. The in vitro hemolytic activity against sheep erythrocytes of compounds 1 and 5 was investigated and were found to provoke 10% hemolysis at 52.5 and 45.0 μg/ml, respectively, indicative of a promising safety factor.
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Wang X, Fu YF, Wang RY, Li L, Cao YH, Chen YQ, Zhao HZ, Zhang QQ, Wu JQ, Weng XH, Cheng XJ, Zhu LP. Identification of clinically relevant fungi and prototheca species by rRNA gene sequencing and multilocus PCR coupled with electrospray ionization mass spectrometry. PLoS One 2014; 9:e98110. [PMID: 24835205 PMCID: PMC4024029 DOI: 10.1371/journal.pone.0098110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 04/28/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Multilocus PCR coupled with electrospray ionization mass spectrometry (PCR/ESI-MS) is a new strategy for pathogen identification, but information about its application in fungal identification remains sparse. METHODS One-hundred and twelve strains and isolates of clinically important fungi and Prototheca species were subjected to both rRNA gene sequencing and PCR/ESI-MS. Three regions of the rRNA gene were used as targets for sequencing: the 5' end of the large subunit rRNA gene (D1/D2 region), and the internal transcribed spacers 1 and 2 (ITS1 and ITS2 regions). Microbial identification (Micro ID), acquired by combining results of phenotypic methods and rRNA gene sequencing, was used to evaluate the results of PCR/ESI-MS. RESULTS For identification of yeasts and filamentous fungi, combined sequencing of the three regions had the best performance (species-level identification rate of 93.8% and 81.8% respectively). The highest species-level identification rate was achieved by sequencing of D1/D2 for yeasts (92.2%) and ITS2 for filamentous fungi (75.8%). The two Prototheca species could be identified to species level by D1/D2 sequencing but not by ITS1 or ITS2. For the 102 strains and isolates within the coverage of PCR/ESI-MS identification, 87.3% (89/102) achieved species-level identification, 100% (89/89) of which were concordant to Micro ID on species/complex level. The species-level identification rates for yeasts and filamentous fungi were 93.9% (62/66) and 75% (27/36) respectively. CONCLUSIONS rRNA gene sequencing provides accurate identification information, with the best results obtained by a combination of ITS1, ITS2 and D1/D2 sequencing. Our preliminary data indicated that PCR/ESI-MS method also provides a rapid and accurate identification for many clinical relevant fungi.
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Affiliation(s)
- Xuan Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yong-Feng Fu
- Department of Medical Microbiology and Parasitology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Rui-Ying Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Li Li
- Mycology Lab, Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Ya-Hui Cao
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yan-Qiong Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Hua-Zhen Zhao
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Qiang-Qiang Zhang
- Mycology Lab, Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Ji-Qin Wu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xin-Hua Weng
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xun-Jia Cheng
- Department of Medical Microbiology and Parasitology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Li-Ping Zhu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
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Fišer Pečnikar Ž, Buzan EV. 20 years since the introduction of DNA barcoding: from theory to application. J Appl Genet 2013; 55:43-52. [PMID: 24203863 DOI: 10.1007/s13353-013-0180-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 10/14/2013] [Accepted: 10/15/2013] [Indexed: 01/29/2023]
Abstract
Traditionally, taxonomic identification has relied upon morphological characters. In the last two decades, molecular tools based on DNA sequences of short standardised gene fragments, termed DNA barcodes, have been developed for species discrimination. The most common DNA barcode used in animals is a fragment of the cytochrome c oxidase (COI) mitochondrial gene, while for plants, two chloroplast gene fragments from the RuBisCo large subunit (rbcL) and maturase K (matK) genes are widely used. Information gathered from DNA barcodes can be used beyond taxonomic studies and will have far-reaching implications across many fields of biology, including ecology (rapid biodiversity assessment and food chain analysis), conservation biology (monitoring of protected species), biosecurity (early identification of invasive pest species), medicine (identification of medically important pathogens and their vectors) and pharmacology (identification of active compounds). However, it is important that the limitations of DNA barcoding are understood and techniques continually adapted and improved as this young science matures.
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Affiliation(s)
- Živa Fišer Pečnikar
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia,
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