Publications by authors named "Margarita Dueñas"

9 Publications

  • Page 1 of 1

Linking morphological and molecular sources to disentangle the case of Xylodon australis.

Sci Rep 2020 12 15;10(1):22004. Epub 2020 Dec 15.

Department of Mycology, Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014, Madrid, Spain.

The use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia-New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.
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http://dx.doi.org/10.1038/s41598-020-78399-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7738490PMC
December 2020

Addressing the diversity of complex through integrative taxonomy.

IMA Fungus 2019 2;10. Epub 2019 Jul 2.

1Departamento de Micología, Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014 Madrid, Spain.

In this study, the taxonomic diversity of the species complex (, ) is examined. Specimens were studied using an integrative taxonomic approach that includes molecular phylogenetic and morphological analyses, and environmental niche comparisons. Four different species were found inside the complex, with a biogeographic distribution pattern bound by geographic regions: Europe, North America, Patagonia, and Australia-New Zealand. Molecular, morphological, and environmental evidences delimit two lineages within this complex: a Northern Hemisphere clade with longer basidiospores and wider ranges in temperature and precipitation tolerance, and a Southern Hemisphere clade with smaller and more spherical basidiospores, and an isothermal and more humid climate preference. The integrative taxonomic approach used in this study demonstrates congruence between data sets and shows how morphological and environmental characteristics contribute to the differentiation of fungal species complexes. By combining various sources of taxonomic information, three new species are described: , and .
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http://dx.doi.org/10.1186/s43008-019-0010-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7184894PMC
July 2019

Multilocus phylogeny reveals taxonomic misidentification of the (KUC8140) representative genome.

MycoKeys 2018 28(38):121-127. Epub 2018 Aug 28.

Departmento de Micología, Real Jardín Botánico, RJB-CSIC, Plaza de Murillo 2, 28014 Madrid, Spain Real Jardín Botánico Madrid Spain.

, current name , is a white-rot fungus with certain useful biotechnological properties. The representative genome of strain KUC8140 was published in 2015 as part of the 1000 Fungal Genomes Project. Multilocus phylogenetic analyses, based on three nuclear regions (ITS, LSU and 2), confirmed a misidentification of strain KUC8140 which should be identified as . This wrong identification explains the unexpected geographical distribution of , since this species has a European distribution, whereas the strain KUC8140 was recorded from Korea, Eastern Asia.
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http://dx.doi.org/10.3897/mycokeys.38.28497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160840PMC
August 2018

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
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http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

Towards a unified paradigm for sequence-based identification of fungi.

Mol Ecol 2013 Nov 24;22(21):5271-7. Epub 2013 Sep 24.

Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia; Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia.

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
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http://dx.doi.org/10.1111/mec.12481DOI Listing
November 2013

Molecular analyses confirm Brevicellicium in Trechisporales.

IMA Fungus 2013 Jul 4;4(1):21-8. Epub 2013 Apr 4.

Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014 Madrid, Spain.

The genus Brevicellicium encompasses wood-inhabiting corticioid fungi characterized by isodiametric subhymenial hyphae, short basidia, and smooth, often subangular spores with a distinct apiculus. Eight new LSU nrDNA sequences and 13 new ITS nrDNA of this genus, including the type species, were aligned with 47 and 42 accessions respectively of species of Trechisporales obtained from GenBank, and phylogenetic analyses were performed. The order Trechisporales was confirmed as a monophyletic group; the genera Porpomyces, Sistotremastrum, Subulicystidium and Trechispora form a highly supported clade where all Brevicellicium sequences are included. Our analyses also support that this genus belongs to Hydnodontaceae. A new species, Brevicellicium atlanticum from the Azores Archipelago, is described.
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http://dx.doi.org/10.5598/imafungus.2013.04.01.03DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719203PMC
July 2013

A new species of Hyphoderma (Meruliaceae, Polyporales) and its discrimination from closely related taxa.

Mycologia 2012 Sep-Oct;104(5):1121-32. Epub 2012 Apr 11.

Departamento de Micología, Real Jardín Botánico, CSIC, Madrid, Spain.

Thirty-five corticioid collections from the Canary Islands and Azores Archipelago were examined morphologically and subjected to molecular phylogenetic analysis. These specimens, almost all collected on endemic and/or xerophilic vegetation, were similar in morphological and ecological characteristics to Hypochnicium prosopidis from the Sonoran Desert (Arizona, USA) and Hyphoderma amoenum. Thirty-seven new ITS nrDNA sequences from these specimens, including the nomenclatural type of the above-mentioned species, were obtained and aligned with homologous sequences from GenBank. These collections were distributed in two strongly supported monophyletic clades. However, similar patterns of morphological variability shared by specimens included in both clades and their differences with related species suggest that they should be described as a single new species. Therefore Hyphoderma macaronesicum is proposed. Studies will be required to test, in a more robust multilocus genealogical framework, whether these populations constitute two cryptic species or whether they are the same taxon. The position of Hypochnicium prosopidis in the resolved tree and its morphological characters suggest that it should be included in Hyphoderma and the new combination Hyphoderma prosopidis is proposed.
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http://dx.doi.org/10.3852/11-344DOI Listing
November 2012

A re-evaluation of Hypochnicium (Polyporales) based on morphological and molecular characters.

Mycologia 2010 Nov-Dec;102(6):1426-36. Epub 2010 Jun 16.

Departamento de Micología, Real Jardín Botánico, CSIC, Plaza de Murillo, 2. 28014 Madrid, Spain.

Hypochnicium is a genus of corticioid, wood-inhabiting fungi in the Polyporales with a worldwide distribution. The genus has been characterized by the nature of the spores; they are thick-walled, smooth or ornamented, and cyanophilous. Nine new ITS nrDNA sequences from species of this genus were aligned with 32 sequences from GenBank, and phylogenetic analyses were performed. Six clades were determined within the genus; one contains taxa with smooth spores, and the other three with ornamented spores. Hypochnicium versatum must be included in Gloeohypochnicium, and the new combination Gloeohypochnicium versatum is proposed. Two new species, Hypochnicium michelii from Spain and Hypochnicium guineensis from Equatorial Guinea, are described.
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http://dx.doi.org/10.3852/09-242DOI Listing
December 2010

Gloeodontia xerophila (Aphyllophorales, Basidiomycota), a new species with corticioid basidioma from the Canary Islands.

Mycologia 2008 Jul-Aug;100(4):673-6

Real Jardín Botdnico, CSIC, Plaza de Murillo, 2. 28014 Madrid, España.

Gloeodontia xerophila sp. nov. is described and illustrated from material collected on dead xerophyte debris in the Canary Islands. This species is characterized by the odontioid hymenophore with short aculei, up to 2 mm long, dimitic hyphal system and amyloid, subglobose and verrucose spores, 4-5 x 3-4 microm. The new taxon is compared with other species in the genus and a key to the species of Gloeodontia is provided.
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http://dx.doi.org/10.3852/07-200r1DOI Listing
October 2008
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