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Liu JW, Luangharn T, Yang SM, Yu FQ. The complete mitochondrial genome of Polyozellus multiplex (Thelephorales). Mitochondrial DNA B Resour 2022; 7:1066-1068. [PMID: 35801138 PMCID: PMC9255120 DOI: 10.1080/23802359.2022.2086077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The complete mitogenome of Polyozellus multiplex (Underw.) Murrill 1910, was first sequenced, assembled, and annotated in the present study. The mitogenome length was 47,054 bp with a GC content of 23.35%, including 14 conserved protein-coding genes, one ribosomal protein (RPS3), two DNA polymerases (DPO), two rRNA genes (RNS and RNL), and 24 transfer RNA (tRNA) genes. Phylogenetic analysis, based on a combined mitochondrial gene dataset from 17 taxa of four orders within the class Agaricomycetes, was conducted using maximum-likelihood (ML) and Bayesian inference (BI) methods. It is revealed that P. multiplex is closely related to Thelephora aurantiotincta Corner 1968, both of them have been clustered into Thelephorales.
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Affiliation(s)
- Jian-Wei Liu
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Thatsanee Luangharn
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
| | - Shi-Mei Yang
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Fu-Qiang Yu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Svantesson S, Kõljalg U, Wurzbacher C, Saar I, Larsson KH, Larsson E. Polyozellus vs. Pseudotomentella: generic delimitation with a multi-gene dataset. Fungal Syst Evol 2022; 8:143-154. [PMID: 35005578 PMCID: PMC8687065 DOI: 10.3114/fuse.2021.08.11] [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: 07/12/2020] [Accepted: 10/26/2021] [Indexed: 11/07/2022] Open
Abstract
Polyozellus and Pseudotomentella are two genera of closely related, ectomycorrhizal fungi in the order Thelephorales; the former stipitate and the latter corticioid. Both are widespread in the Northern Hemisphere and many species from both genera seem to be restricted to old growth forest. This study aimed to: a) identify genetic regions useful in inferring the phylogenetic relationship between Polyozellus and Pseudotomentella, b) infer this relationship with the regions identified and c) make any taxonomic changes warranted by the result. RPB2, mtSSU and nearly full-length portions of nrLSU and nrSSU were found to be comparatively easy to sequence and provide a strong phylogenetic signal. A STACEY species tree of these three regions revealed that Polyozellus makes Pseudotomentella paraphyletic. As a result, nearly all species currently placed in Pseudotomentella were recombined to Polyozellus. Pseudotomentella larsenii was found to be closer to Tomentellopsis than Polyozellus, but its placement needs further study and it was hence not recombined.
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Affiliation(s)
- S Svantesson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden.,Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, Victoria 3004, Australia
| | - U Kõljalg
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia.,Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia
| | - C Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden.,Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany
| | - I Saar
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia
| | - K-H Larsson
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden.,Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
| | - E Larsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
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Kõljalg U, Nilsson HR, Schigel D, Tedersoo L, Larsson KH, May TW, Taylor AFS, Jeppesen TS, Frøslev TG, Lindahl BD, Põldmaa K, Saar I, Suija A, Savchenko A, Yatsiuk I, Adojaan K, Ivanov F, Piirmann T, Pöhönen R, Zirk A, Abarenkov K. The Taxon Hypothesis Paradigm-On the Unambiguous Detection and Communication of Taxa. Microorganisms 2020; 8:E1910. [PMID: 33266327 PMCID: PMC7760934 DOI: 10.3390/microorganisms8121910] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/24/2020] [Indexed: 12/27/2022] Open
Abstract
Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.
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Affiliation(s)
- Urmas Kõljalg
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Henrik R. Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; (H.R.N.); (K.-H.L.)
| | - Dmitry Schigel
- Global Biodiversity Information Facility, 2100 Copenhagen, Denmark; (D.S.); (T.S.J.)
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Karl-Henrik Larsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; (H.R.N.); (K.-H.L.)
| | - Tom W. May
- Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, Victoria 3004, Australia;
| | - Andy F. S. Taylor
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK;
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
| | | | | | - Björn D. Lindahl
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden;
| | - Kadri Põldmaa
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Irja Saar
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Ave Suija
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Anton Savchenko
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Iryna Yatsiuk
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (L.T.); (I.S.); (A.S.); (I.Y.)
| | - Kristjan Adojaan
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Filipp Ivanov
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Timo Piirmann
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Raivo Pöhönen
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Allan Zirk
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia; (K.P.); (A.S.); (K.A.); (F.I.); (T.P.); (R.P.); (A.Z.); (K.A.)
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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