| 1. |
- Abarenkov, Kessy, et al.
(författare)
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The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered
- 2024
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Ingår i: Nucleic Acids Research. - 0305-1048 .- 1362-4962. ; 52:D1, s. D791-D797
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Tidskriftsartikel (refereegranskat)abstract
- UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into similar to 2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms. Graphical Abstract
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| 2. |
- Kõljalg, Urmas, et al.
(författare)
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Towards a unified paradigm for sequence-based identification of fungi.
- 2013
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Ingår i: Molecular ecology. - : Wiley. - 1365-294X .- 0962-1083. ; 22:21, s. 5271-7
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Tidskriftsartikel (refereegranskat)abstract
- 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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| 3. |
- Kondratiuk, Serhii, et al.
(författare)
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Lichenicolous fungi associated with southern Scandinavian Xanthoria calcicola s.lat.
- 2023
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Eleven species of lichenicolous fungi associated with Xanthoria calcicola s.lat. are found in southernmost Scandinavia, i.e., Skåne, the southernmost province in Sweden and southern Denmark. Two species, Didymocyrtis slaptoensis and Pyrenochaeta xanthoriae, are reported as new for the Nordic countries, whereas three species, Didymocyrtis cf. consimilis, Erythricium aurantiacum, and Illosporiopsis christiansenii are new for Skåne.
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| 4. |
- Motiejunaite, Jurga, et al.
(författare)
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Lichens, lichenicolous and allied fungi in Asveja Regional Park (Lithuania)
- 2012
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Ingår i: Botanica Lithuanica. - 1392-1665. ; 18:2, s. 85-100
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Tidskriftsartikel (refereegranskat)abstract
- The paper reports the results of lichenological investigations in Asveja Regional Park (eastern Lithuania). A large part of the study was performed during the joint 18th Symposium of Baltic Mycologists and Lichenologists (BMLS) and Nordic Lichen Society meeting (NLF), September 19–23, 2011. A list of 259 species is presented, 30 of them are new to Lithuania. Arthonia helvola, Bacidina sulphurella, Candelariella lutella, Catillaria croatica, Cladonia conista, Gyalecta derivata, Lecanora quercicola, Leptosphaeria ramalinae, Strigula jamesii, Trichonectria rubefaciens, Verrucaria banatica, V. boblensis, V. christiansenii, V. illinoisensis, V. inornata, V. nigrofusca, V. trabicola, Zwackhiomyces diederichii are recorded for the first time in the Baltic countries. New lichens for Lithuania are: Bacidia incompta, Caloplaca crenulatella, C. pyracea, Catinaria atropurpurea, Lecanora populicola, L. semipallida, Mycobilimbia epixanthoides, Ramalina dilacerata, Verrucaria inaspecta, and new lichenicolous fungi are: Cladosporium licheniphilum, Stigmidium microspilum, Xenonectriella leptalea. Eighteen species included in the Lithuanian Red Data Book were recorded which is the highest number known for any studied area in Lithuania.
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| 5. |
- Motiejunaite, Jurga, et al.
(författare)
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Ninety-one species of lichens and allied fungi new to Latvia with a list of additional records from Kurzeme
- 2016
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Ingår i: Herzogia. - : Herzogia. - 0018-0971. ; 29:1, s. 143-163
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Tidskriftsartikel (refereegranskat)abstract
- The results of lichenological excursions of the 19th Symposium of Baltic Mycologists and Lichenologists (BMLS) in Latvia, Kurzeme region, 22–26 September 2014, are reported. A list of 290 species is presented, of which 238 are lichenized, 43 lichen-inhabiting, and nine saprotrophic fungi: ninety-one species are new to Latvia, twelve of which (Caloplaca duplicata, Cresporhaphis wienkampii, Ellisembia lichenicola, Gallowayella weberi, Gregorella humida, Lichenochora weillii, Parmelia serrana, Polycauliona phlogina, Reconditella physconiarum, Stictis brunnescens, Thelocarpon superellum, and Verrucaria tectorum) are also new for the Baltic States. Athallia alnetorum is reported here for the first time in northern Europe. The presence of Ochrolechia androgyna s. str., Athallia holocarpa and A. pyracea is confirmed for Latvia, and Parmelia submontana is reported as a new host for Homostegia piggotii.
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| 6. |
- Tedersoo, Leho, et al.
(författare)
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Global diversity and geography of soil fungi
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6213, s. artikel nr 1256688-
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Tidskriftsartikel (refereegranskat)abstract
- Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.
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| 10. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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