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Robin-Soriano A, Maurice K, Boivin S, Bourceret A, Laurent-Webb L, Youssef S, Nespoulous J, Boussière I, Berder J, Damasio C, Vincent B, Boukcim H, Ducousso M, Gros-Balthazard M. Absence of Gigasporales and rarity of spores in a hot desert revealed by a multimethod approach. MYCORRHIZA 2024; 34:251-270. [PMID: 39023766 DOI: 10.1007/s00572-024-01160-w] [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: 03/14/2024] [Accepted: 06/29/2024] [Indexed: 07/20/2024]
Abstract
Hot deserts impose extreme conditions on plants growing in arid soils. Deserts are expanding due to climate change, thereby increasing the vulnerability of ecosystems and the need to preserve them. Arbuscular mycorrhizal fungi (AMF) improve plant fitness by enhancing plant water/nutrient uptake and stress tolerance. However, few studies have focused on AMF diversity and community composition in deserts, and the soil and land use parameters affecting them. This study aimed to comprehensively describe AMF ecological features in a 5,000 km2 arid hyperalkaline region in AlUla, Saudi Arabia. We used a multimethod approach to analyse over 1,000 soil and 300 plant root samples of various species encompassing agricultural, old agricultural, urban and natural ecosystems. Our method involved metabarcoding using 18S and ITS2 markers, histological techniques for direct AMF colonization observation and soil spore extraction and observation. Our findings revealed a predominance of AMF taxa assigned to Glomeraceae, regardless of the local conditions, and an almost complete absence of Gigasporales taxa. Land use had little effect on the AMF richness, diversity and community composition, while soil texture, pH and substantial unexplained stochastic variance drove these compositions in AlUla soils. Mycorrhization was frequently observed in the studied plant species, even in usually non-mycorrhizal plant taxa (e.g. Amaranthaceae, Urticaceae). Date palms and Citrus trees, representing two major crops in the region, however, displayed a very low mycorrhizal frequency and intensity. AlUla soils had a very low concentration of spores, which were mostly small. This study generated new insight on AMF and specific behavioral features of these fungi in arid environments.
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Affiliation(s)
| | - Kenji Maurice
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier, France
| | - Stéphane Boivin
- Department of Research and Development, VALORHIZ, Montferrier sur Lez, France
| | - Amelia Bourceret
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, Paris, France
| | - Liam Laurent-Webb
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, Paris, France
| | - Sami Youssef
- Department of Research and Development, VALORHIZ, Montferrier sur Lez, France
| | - Jérôme Nespoulous
- Department of Research and Development, VALORHIZ, Montferrier sur Lez, France
| | - Inès Boussière
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier, France
| | - Julie Berder
- Department of Research and Development, VALORHIZ, Montferrier sur Lez, France
| | | | - Bryan Vincent
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier, France
| | - Hassan Boukcim
- Department of Research and Development, VALORHIZ, Montferrier sur Lez, France
- ASARI, Mohammed VI Polytechnic University, Laâyoune, Morocco
| | - Marc Ducousso
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier, France
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Cho Y, Kim D, Lee Y, Jeong J, Hussain S, Lim YW. Validation of Fuscoporia (Hymenochaetales, Basidiomycota) ITS sequences and five new species based on multi-marker phylogenetic and morphological analyses. IMA Fungus 2023; 14:12. [PMID: 37381063 DOI: 10.1186/s43008-023-00117-6] [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: 07/15/2022] [Accepted: 05/30/2023] [Indexed: 06/30/2023] Open
Abstract
Although there is a continuous increase in available molecular data, not all sequence identities in public databases are always properly verified and managed. Here, the sequences available in GenBank for Fuscoporia (Hymenochaetales) were validated. Many morphological characters of Fuscoporia overlap among the species, emphasizing the role of molecular identification for accuracy. The identities of 658 Fuscoporia GenBank internal transcribed spacer (ITS) sequences were assessed using ITS phylogeny, revealing 109 (16.6%) misidentified and 196 (29.8%) unspecified sequences. They were validated and re-identified based on the research articles they were published in and, if unpublished, based on sequences from the type, type locality-derived sequences, or otherwise reliable sequences. To enhance the resolution of species delimitation, a phylogenetic assessment of a multi-marker dataset (ITS + nrLSU + rpb2 + tef1) was conducted. The multi-marker phylogeny resolved five of the twelve species complexes found in the ITS phylogeny and uncovered five new Fuscoporia species: F. dolichoseta, F. gilvoides, F. koreana, F. reticulata, and F. semicephala. The validated ITS sequences in this study may prevent further accumulation of misidentified sequences in public databases and contribute to a more accurate taxonomic evaluation of Fuscoporia species.
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Affiliation(s)
- Yoonhee Cho
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Dohye Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Yoongil Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Juhwan Jeong
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Shahid Hussain
- Centre for Plant Sciences and Biodiversity, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea.
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Reason A, Bulgarella M, Lester PJ. Identity, Prevalence, and Pathogenicity of Entomopathogenic Fungi Infecting Invasive Polistes (Vespidae: Polistinae) Paper Wasps in New Zealand. INSECTS 2022; 13:922. [PMID: 36292870 PMCID: PMC9604194 DOI: 10.3390/insects13100922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Two species of entomogenous fungi were discovered infecting the invasive paper wasp Polistes chinensis during an ecological study on Farewell Spit, New Zealand. We sequenced two nuclear ribosomal RDNA genes, the internal transcribed spacer (ITS) and the small ribosomal subunit 18S, and one protein-coding gene, the translation elongation factor 1-alpha (ef1 α). Combining sequence information with morphological examination, we identified these species as Beauveria malawiensis and Ophiocordyceps humbertii. We estimated that these fungi produce infection in approximately 3.3% of colonies in our study population. In bioassays, we successfully infected P. chinensis individuals from healthy colonies with B. malawiensis, with significant effects on adult mortality. This is the first record of both B. malawiensis and O. humbertii from Polistine hosts in New Zealand, and the first investigation into disease causality by these pathogens in P. chinensis. Our findings may contribute to the future development of biological control agents for paper wasps in New Zealand and elsewhere around the world.
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Cottrell MT. A Search for Diastatic Enzymes Endogenous to Humulus lupulus and Produced by Microbes Associated with Pellet Hops Driving “Hop Creep” of Dry Hopped Beer. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2022. [DOI: 10.1080/03610470.2022.2084327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Botnen SS, Mundra S, Kauserud H, Eidesen PB. Glacier retreat in the High Arctic: opportunity or threat for ectomycorrhizal diversity? FEMS Microbiol Ecol 2021; 96:5894921. [PMID: 32816005 DOI: 10.1093/femsec/fiaa171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
Climate change causes Arctic glaciers to retreat faster, exposing new areas for colonization. Several pioneer plants likely to colonize recent deglaciated, nutrient-poor areas depend on fungal partners for successful establishment. Little is known about general patterns or characteristics of facilitating fungal pioneers and how they vary with regional climate in the Arctic. The High Arctic Archipelago Svalbard represents an excellent study system to address these questions, as glaciers cover ∼60% of the land surface and recent estimations suggest at least 7% reduction of glacier area since 1960s. Roots of two ectomycorrhizal (ECM) plants (Salix polaris and Bistorta vivipara) were sampled in eight glacier forelands. Associated ECM fungi were assessed using DNA metabarcoding. About 25% of the diversity was unknown at family level, indicating presence of undescribed species. Seven genera dominated based on richness and abundance, but their relative importance varied with local factors. The genus Geopora showed surprisingly high richness and abundance, particularly in dry, nutrient-poor forelands. Such forelands will diminish along with increasing temperature and precipitation, and faster succession. Our results support a taxonomical shift in pioneer ECM diversity with climate change, and we are likely to lose unknown fungal diversity, without knowing their identity or ecological importance.
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Affiliation(s)
- S S Botnen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316 Oslo, Norway.,The University Centre in Svalbard, PO Box 156, NO-9171 Longyearbyen, Norway
| | - S Mundra
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316 Oslo, Norway.,The University Centre in Svalbard, PO Box 156, NO-9171 Longyearbyen, Norway.,Department of Biology, College of Science, United Arab Emirates University, PO Box 15551, Al-Ain, Abu Dhabi, UAE
| | - H Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316 Oslo, Norway
| | - P B Eidesen
- The University Centre in Svalbard, PO Box 156, NO-9171 Longyearbyen, Norway
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Patocka J, Wu R, Nepovimova E, Valis M, Wu W, Kuca K. Chemistry and Toxicology of Major Bioactive Substances in Inocybe Mushrooms. Int J Mol Sci 2021; 22:ijms22042218. [PMID: 33672330 PMCID: PMC7926736 DOI: 10.3390/ijms22042218] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/14/2021] [Accepted: 02/19/2021] [Indexed: 11/16/2022] Open
Abstract
Mushroom poisoning has always been a threat to human health. There are a large number of reports about ingestion of poisonous mushrooms every year around the world. It attracts the attention of researchers, especially in the aspects of toxin composition, toxic mechanism and toxin application in poisonous mushroom. Inocybe is a large genus of mushrooms and contains toxic substances including muscarine, psilocybin, psilocin, aeruginascin, lectins and baeocystin. In order to prevent and remedy mushroom poisoning, it is significant to clarify the toxic effects and mechanisms of these bioactive substances. In this review article, we summarize the chemistry, most known toxic effects and mechanisms of major toxic substances in Inocybe mushrooms, especially muscarine, psilocybin and psilocin. Their available toxicity data (different species, different administration routes) published formerly are also summarized. In addition, the treatment and medical application of these toxic substances in Inocybe mushrooms are also discussed. We hope that this review will help understanding of the chemistry and toxicology of Inocybe mushrooms as well as the potential clinical application of its bioactive substances to benefit human beings.
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Affiliation(s)
- Jiri Patocka
- Department of Radiology, Toxicology and Civil Protection, Faculty of Health and Social Studies, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic;
- Biomedical Research Centre, University Hospital, 50003 Hradec Kralove, Czech Republic
| | - Ran Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Rokitanského 62, 500 03 Hradec Kralove, Czech Republic;
| | - Martin Valis
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Kralove, Sokolska 581, 50005 Hradec Kralove, Czech Republic;
| | - Wenda Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Rokitanského 62, 500 03 Hradec Kralove, Czech Republic;
- Correspondence: (W.W.); (K.K.); Tel.: +86-152-5185-0173 (W.W.); +420-439-332-509 (K.K.)
| | - Kamil Kuca
- Biomedical Research Centre, University Hospital, 50003 Hradec Kralove, Czech Republic
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Rokitanského 62, 500 03 Hradec Kralove, Czech Republic;
- Correspondence: (W.W.); (K.K.); Tel.: +86-152-5185-0173 (W.W.); +420-439-332-509 (K.K.)
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Baturo-Cieśniewska A, Pusz W, Patejuk K. Problems, Limitations, and Challenges in Species Identification of Ascomycota Members on the Basis of ITS Regions. ACTA MYCOLOGICA 2020. [DOI: 10.5586/am.5512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The internal transcribed spacer (ITS) region is regarded as a formal fungal primary barcode with a high probability of the correct identification for a broad group of fungi. ITS sequences have been widely used to determine many fungal species and analysis of rDNA ITS is still one of the most popular tools used in mycology. However, this region is not equally variable in all groups of fungi; therefore, identification may be problematic and result in ambiguous data, especially in some species-rich genera of Ascomycota. For these reasons, identification based on rDNA ITS is usually complemented by morphological observations and analysis of additional genes. Reliable species identification of Ascomycota members is essential in diagnosing plant diseases, verifying air quality and the effectiveness of agronomic practices, or analyzing relationships between microorganisms. Therefore, the present study aimed to verify, using specific examples, the extent to which ITS sequence analysis is useful in species identification of pathogens and saprobionts from Ascomycota and demonstrate problems related to such identification in practice. We analyzed 105 ITS sequences of isolates originating from air and plant material. Basic local alignment search tool (BLASTn) significantly contributed to the reliable species identification of nearly 80% of isolates such as <em>Arthrinium arundinis</em>, <em>Beauveria bassiana</em>, <em>Boeremia exigua</em>, <em>Cladosporium cladosporioides</em>, <em>Epicoccum nigrum</em>, <em>Nigrospora oryzae</em>, <em>Sclerotinia sclerotiorum</em>, or <em>Sordaria fimicola </em>and members of the genera <em>Alternaria </em>and <em>Trichoderma</em>. However, for most isolates, additional morphological observations, information regarding the isolate origin and, where possible, a PCR with species-specific primers were helpful and complementary. Using our practical approach, we determined that ITS-based species identification and comparative analysis with GenBank sequences significantly helps identifying Ascomycota members. However, in many cases, this should be regarded as suggestive of a taxon because the data usually require the use of additional tools to verify the results of such analysis.
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David AS, Bell-Dereske LP, Emery SM, McCormick BM, Seabloom EW, Rudgers JA. Testing for loss of Epichloë and non-epichloid symbionts under altered rainfall regimes. AMERICAN JOURNAL OF BOTANY 2019; 106:1081-1089. [PMID: 31386172 DOI: 10.1002/ajb2.1340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/19/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Microbial symbionts can buffer plant hosts from environmental change. Therefore, understanding how global change factors alter the associations between hosts and their microbial symbionts may improve predictions of future changes in host population dynamics and microbial diversity. Here, we investigated how one global change factor, precipitation, affected the maintenance or loss of symbiotic fungal endophytes in a C3 grass host. Specifically, we examined the distinct responses of Epichloë (vertically transmitted and systemic) and non-epichloid endophytes (typically horizontally transmitted and localized) by considering (1) how precipitation altered associations with Epichloë and non-epichloid endophytic taxa across host ontogeny, and (2) interactive effects of water availability and Epichloë on early seedling life history stages. METHODS We manipulated the presence of Epichloë amarillans in American beachgrass (Ammophila breviligulata) in a multiyear field experiment that imposed three precipitation regimes (ambient or ±30% rainfall). In laboratory assays, we investigated the interactive effects of water availability and Epichloë on seed viability and germination. RESULTS Reduced precipitation decreased the incidence of Epichloë in leaves in the final sampling period, but had no effect on associations with non-epichloid taxa. Epichloë reduced the incidence of non-epichloid endophytes, including systemic p-endophytes, in seeds. Laboratory assays suggested that association with Epichloë is likely maintained, in part, due to increased seed viability and germination regardless of water availability. CONCLUSIONS Our study empirically demonstrates several pathways for plant symbionts to be lost or maintained across host ontogeny and suggests that reductions in precipitation can drive the loss of a plant's microbial symbionts.
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Affiliation(s)
- Aaron S David
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Lukas P Bell-Dereske
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, 49060, USA
| | - Sarah M Emery
- Department of Biology, University of Louisville, Louisville, KY, 40292, USA
| | - Brandon M McCormick
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Eric W Seabloom
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jennifer A Rudgers
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
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Meiklejohn KA, Damaso N, Robertson JM. Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials. PLoS One 2019; 14:e0217084. [PMID: 31216285 PMCID: PMC6584008 DOI: 10.1371/journal.pone.0217084] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/04/2019] [Indexed: 11/19/2022] Open
Abstract
Taxonomic identification of biological materials can be achieved through DNA barcoding, where an unknown "barcode" sequence is compared to a reference database. In many disciplines, obtaining accurate taxonomic identifications can be imperative (e.g., evolutionary biology, food regulatory compliance, forensics). The Barcode of Life DataSystems (BOLD) and GenBank are the main public repositories of DNA barcode sequences. In this study, an assessment of the accuracy and reliability of sequences in these databases was performed. To achieve this, 1) curated reference materials for plants, macro-fungi and insects were obtained from national collections, 2) relevant barcode sequences (rbcL, matK, trnH-psbA, ITS and COI) from these reference samples were generated and used for searching against both databases, and 3) optimal search parameters were determined that ensure the best match to the known species in either database. While GenBank outperformed BOLD for species-level identification of insect taxa (53% and 35%, respectively), both databases performed comparably for plants and macro-fungi (~81% and ~57%, respectively). Results illustrated that using a multi-locus barcode approach increased identification success. This study outlines the utility of the BLAST search tool in GenBank and the BOLD identification engine for taxonomic identifications and identifies some precautions needed when using public sequence repositories in applied scientific disciplines.
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Affiliation(s)
- Kelly A. Meiklejohn
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, Virginia, United States of America
| | - Natalie Damaso
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, Virginia, United States of America
| | - James M. Robertson
- Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division, Quantico, Virginia, United States of America
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Yang RH, Su JH, Shang JJ, Wu YY, Li Y, Bao DP, Yao YJ. Evaluation of the ribosomal DNA internal transcribed spacer (ITS), specifically ITS1 and ITS2, for the analysis of fungal diversity by deep sequencing. PLoS One 2018; 13:e0206428. [PMID: 30359454 PMCID: PMC6201957 DOI: 10.1371/journal.pone.0206428] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/12/2018] [Indexed: 12/17/2022] Open
Abstract
The nuclear ribosomal DNA internal transcribed spacer (ITS) has been widely used to assess the fungal composition in different environments by deep sequencing. To evaluate the ITS in the analysis of fungal diversity, comparisons of the clustering and taxonomy generated by sequencing with different portions of the whole fragment were conducted in this study. For a total of 83,120 full-length ITS sequences obtained from the UNITE database, it was found that, on average, ITS1 varied more than ITS2 within the kingdom Fungi; this variation included length and GC content variations and polymorphisms, with some polymorphisms specific to particular fungal groups. The taxonomic accuracy for ITS was higher than that for ITS1 or ITS2. The commonly used operational taxonomic unit (OTU) for evaluating fungal diversity and richness assigned several species to a single OTU even with clustering at 99.00% sequence similarity. The clustering and taxonomic capacities did not differ between ITS1 and ITS2. However, the OTU commonality between ITS1 and ITS2 was very low. To test this observation further, 219,741 pyrosequencing reads, including 39,840 full-length ITS sequences, were obtained from 10 soil samples and were clustered into OTUs. The pyrosequencing results agreed with the results of the in silico analysis. ITS1 might overestimate the fungal diversity and richness. Analyses using ITS, ITS1 and ITS2 yielded several different taxa, and the taxonomic preferences for ITS and ITS2 were similar. The results demonstrated that ITS2 alone might be a more suitable marker for revealing the operational taxonomic richness and taxonomy specifics of fungal communities when the full-length ITS is not available.
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Affiliation(s)
- Rui-Heng Yang
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jin-He Su
- Computer Engineering College, Jimei University, Xiamen, China
| | - Jun-Jun Shang
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ying-Ying Wu
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Li
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Da-Peng Bao
- Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- * E-mail: (YJY); (DPB)
| | - Yi-Jian Yao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (YJY); (DPB)
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Porter TM, Hajibabaei M. Over 2.5 million COI sequences in GenBank and growing. PLoS One 2018; 13:e0200177. [PMID: 30192752 PMCID: PMC6128447 DOI: 10.1371/journal.pone.0200177] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/24/2018] [Indexed: 01/20/2023] Open
Abstract
The increasing popularity of cytochrome c oxidase subunit 1 (COI) DNA metabarcoding warrants a careful look at the underlying reference databases used to make high-throughput taxonomic assignments. The objectives of this study are to document trends and assess the future usability of COI records for metabarcode identification. The number of COI records deposited to the NCBI nucleotide database has increased by a geometric average of 51% per year, from 8,137 records deposited in 2003 to a cumulative total of ~ 2.5 million by the end of 2017. About half of these records are fully identified to the species rank, 92% are at least 500 bp in length, 74% have a country annotation, and 51% have latitude-longitude annotations. To ensure the future usability of COI records in GenBank we suggest: 1) Improving the geographic representation of COI records, 2) Improving the cross-referencing of COI records in the Barcode of Life Data System and GenBank to facilitate consolidation and incorporation into existing bioinformatic pipelines, 3) Adherence to the minimum information about a marker gene sequence guidelines, and 4) Integrating metabarcodes from eDNA and mixed community studies with existing reference sequences. The growth of COI reference records over the past 15 years has been substantial and is likely to be a resource across many fields for years to come.
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Affiliation(s)
- Teresita M. Porter
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Ontario, CANADA
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, CANADA
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Ontario, CANADA
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Scully ED, Geib SM, Mason CJ, Carlson JE, Tien M, Chen HY, Harding S, Tsai CJ, Hoover K. Host-plant induced changes in microbial community structure and midgut gene expression in an invasive polyphage (Anoplophora glabripennis). Sci Rep 2018; 8:9620. [PMID: 29942001 PMCID: PMC6018227 DOI: 10.1038/s41598-018-27476-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/29/2018] [Indexed: 11/08/2022] Open
Abstract
Polyphagous insect herbivores possess diverse mechanisms to overcome challenges of feeding in multiple plant species including, but not limited to, transcriptional plasticity and associations with obligate or facultative symbionts. The Asian longhorned beetle (Anoplophora glabripennis) is a polyphagous wood-feeder capable of developing on over 100 tree species and, like other polyphages, its genome contains amplifications of digestive and detoxification genes. This insect also possesses a diverse gut microbial community, which has the metabolic potential to augment digestive physiology. While the genomic repertoires of A. glabripennis and its microbial community have been studied previously, comparatively less is known about how the gut transcriptome and community change in response to feeding in different hosts. In this study, we show that feeding in two suitable hosts (Acer spp. and Populus nigra) altered the expression levels of multicopy genes linked to digestion and detoxification. However, feeding in a host with documented resistance (Populus tomentosa) induced changes in the transcriptome and community beyond what was observed in insects reared in P. nigra, including the downregulation of numerous β-glucosidases, odorant binding proteins, and juvenile hormone binding proteins, the upregulation of several cuticular genes, and the loss of one major bacterial family from the gut community.
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Affiliation(s)
- Erin D Scully
- Stored Product Insect and Engineering Research Unit, USDA-ARS Center for Grain and Animal Health Research, Manhattan, KS, 66502, USA.
| | - Scott M Geib
- Tropical Crop and Commodity Protection Research Unit, USDA-ARS Daniel K. Inouye Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - Charles J Mason
- Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - John E Carlson
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Bioenergy Science and Technology (World Class University), Chonnam National University, Buk-Gu, Gwangju, 500-757, Korea
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Han-Yi Chen
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602-2152, USA
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA
| | - Scott Harding
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602-2152, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602-7223, USA
| | - Chung-Jui Tsai
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602-2152, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602-7223, USA
| | - Kelli Hoover
- Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
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14
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Porter TM, Hajibabaei M. Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis. Mol Ecol 2018; 27:313-338. [PMID: 29292539 DOI: 10.1111/mec.14478] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 12/19/2022]
Abstract
The purpose of this review is to present the most common and emerging DNA-based methods used to generate data for biodiversity and biomonitoring studies. As environmental assessment and monitoring programmes may require biodiversity information at multiple levels, we pay particular attention to the DNA metabarcoding method and discuss a number of bioinformatic tools and considerations for producing DNA-based indicators using operational taxonomic units (OTUs), taxa at a variety of ranks and community composition. By developing the capacity to harness the advantages provided by the newest technologies, investigators can "scale up" by increasing the number of samples and replicates processed, the frequency of sampling over time and space, and even the depth of sampling such as by sequencing more reads per sample or more markers per sample. The ability to scale up is made possible by the reduced hands-on time and cost per sample provided by the newest kits, platforms and software tools. Results gleaned from broad-scale monitoring will provide opportunities to address key scientific questions linked to biodiversity and its dynamics across time and space as well as being more relevant for policymakers, enabling science-based decision-making, and provide a greater socio-economic impact. As genomic approaches are continually evolving, we provide this guide to methods used in biodiversity genomics.
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Affiliation(s)
- Teresita M Porter
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.,Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, ON, Canada
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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15
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Terhonen E, Kovalchuk A, Zarsav A, Asiegbu FO. Biocontrol Potential of Forest Tree Endophytes. ENDOPHYTES OF FOREST TREES 2018. [DOI: 10.1007/978-3-319-89833-9_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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16
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Šandová M, Nilsson RH, Kolařík M. Relationships within Capitotricha bicolor (Lachnaceae, Ascomycota) as inferred from ITS rDNA sequences, including some notes on the Brunnipila and Erioscyphella clades. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1346-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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David AS, Seabloom EW, May G. Disentangling environmental and host sources of fungal endophyte communities in an experimental beachgrass study. Mol Ecol 2017; 26:6157-6169. [DOI: 10.1111/mec.14354] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/15/2017] [Accepted: 09/05/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Aaron S. David
- Department of Ecology, Evolution, and Behavior University of Minnesota Saint Paul MN USA
| | - Eric W. Seabloom
- Department of Ecology, Evolution, and Behavior University of Minnesota Saint Paul MN USA
| | - Georgiana May
- Department of Ecology, Evolution, and Behavior University of Minnesota Saint Paul MN USA
- Department of Plant Biology University of Minnesota Saint Paul MN USA
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18
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Badotti F, de Oliveira FS, Garcia CF, Vaz ABM, Fonseca PLC, Nahum LA, Oliveira G, Góes-Neto A. Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi). BMC Microbiol 2017; 17:42. [PMID: 28228107 PMCID: PMC5322588 DOI: 10.1186/s12866-017-0958-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/14/2017] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Fungi are among the most abundant and diverse organisms on Earth. However, a substantial amount of the species diversity, relationships, habitats, and life strategies of these microorganisms remain to be discovered and characterized. One important factor hindering progress is the difficulty in correctly identifying fungi. Morphological and molecular characteristics have been applied in such tasks. Later, DNA barcoding has emerged as a new method for the rapid and reliable identification of species. The nrITS region is considered the universal barcode of Fungi, and the ITS1 and ITS2 sub-regions have been applied as metabarcoding markers. In this study, we performed a large-scale analysis of all the available Basidiomycota sequences from GenBank. We carried out a rigorous trimming of the initial dataset based in methodological principals of DNA Barcoding. Two different approaches (PCI and barcode gap) were used to determine the performance of the complete ITS region and sub-regions. RESULTS For most of the Basidiomycota genera, the three genomic markers performed similarly, i.e., when one was considered a good marker for the identification of a genus, the others were also; the same results were observed when the performance was insufficient. However, based on barcode gap analyses, we identified genomic markers that had a superior identification performance than the others and genomic markers that were not indicated for the identification of some genera. Notably, neither the complete ITS nor the sub-regions were useful in identifying 11 of the 113 Basidiomycota genera. The complex phylogenetic relationships and the presence of cryptic species in some genera are possible explanations of this limitation and are discussed. CONCLUSIONS Knowledge regarding the efficiency and limitations of the barcode markers that are currently used for the identification of organisms is crucial because it benefits research in many areas. Our study provides information that may guide researchers in choosing the most suitable genomic markers for identifying Basidiomycota species.
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Affiliation(s)
- Fernanda Badotti
- Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Departamento de Química, 30.421-169 Belo Horizonte, MG Brazil
| | | | - Cleverson Fernando Garcia
- Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Departamento de Química, 30.421-169 Belo Horizonte, MG Brazil
| | - Aline Bruna Martins Vaz
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, Av. Antônio Carlos, Belo Horizonte, 6627, 31270-901 MG Brazil
- Faculdade de Minas (FAMINAS), 66055-090 Belo Horizonte, MG Brazil
| | - Paula Luize Camargos Fonseca
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, Av. Antônio Carlos, Belo Horizonte, 6627, 31270-901 MG Brazil
| | - Laila Alves Nahum
- Fundação Oswaldo Cruz (FIOCRUZ), Centro de Pesquisas René Rachou – CPqRR, 30190-002 Belo Horizonte, MG Brazil
- Faculdade Promove de Tecnologia, 30140-061 Belo Horizonte, MG Brazil
| | - Guilherme Oliveira
- Fundação Oswaldo Cruz (FIOCRUZ), Centro de Pesquisas René Rachou – CPqRR, 30190-002 Belo Horizonte, MG Brazil
- Instituto Tecnológico Vale, 66055-090 Belém, PA Brazil
| | - Aristóteles Góes-Neto
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, Av. Antônio Carlos, Belo Horizonte, 6627, 31270-901 MG Brazil
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Birkebak JM, Mayor JR, Ryberg KM, Matheny PB. A systematic, morphological and ecological overview of the Clavariaceae (Agaricales). Mycologia 2017; 105:896-911. [DOI: 10.3852/12-070] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Joshua M. Birkebak
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, Tennessee 37996-1610
| | - Jordan R. Mayor
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panamá, República de Panamá
| | | | - P. Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, Tennessee 37996-1610
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20
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David AS, Quiram GL, Sirota JI, Seabloom EW. Quantifying the associations between fungal endophytes and biocontrol-induced herbivory of invasive purple loosestrife (Lythrum salicariaL.). Mycologia 2017; 108:625-37. [DOI: 10.3852/15-207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 04/04/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Aaron S. David
- University of Minnesota, Department of Ecology, Evolution and Behavior, 1479 Gortner Avenue, Saint Paul, Minnesota 55108
| | - Gina L. Quiram
- University of Minnesota, College of Continuing Education, 1994 Buford Ave, Saint Paul, Minnesota 55108
| | - Jennie I. Sirota
- University of Minnesota, Natural Resources, Science and Management Program, 1530 Cleveland Avenue, Saint Paul, Minnesota 55108
| | - Eric W. Seabloom
- University of Minnesota, Department of Ecology, Evolution and Behavior, 1479 Gortner Avenue, Saint Paul, Minnesota 55108
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21
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DNA barcoding for identification of consumer-relevant mushrooms: A partial solution for product certification? Food Chem 2016; 214:383-392. [PMID: 27507489 DOI: 10.1016/j.foodchem.2016.07.052] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 06/03/2016] [Accepted: 07/09/2016] [Indexed: 02/06/2023]
Abstract
One challenge in the dietary supplement industry is confirmation of species identity for processed raw materials, i.e. those modified by milling, drying, or extraction, which move through a multilevel supply chain before reaching the finished product. This is particularly difficult for samples containing fungal mycelia, where processing removes morphological characteristics, such that they do not present sufficient variation to differentiate species by traditional techniques. To address this issue, we have demonstrated the utility of DNA barcoding to verify the taxonomic identity of fungi found commonly in the food and dietary supplement industry; such data are critical for protecting consumer health, by assuring both safety and quality. By using DNA barcoding of nuclear ribosomal internal transcribed spacer (ITS) of the rRNA gene with fungal specific ITS primers, ITS barcodes were generated for 33 representative fungal samples, all of which could be used by consumers for food and/or dietary supplement purposes. In the majority of cases, we were able to sequence the ITS region from powdered mycelium samples, grocery store mushrooms, and capsules from commercial dietary supplements. After generating ITS barcodes utilizing standard procedures accepted by the Consortium for the Barcode of Life, we tested their utility by performing a BLAST search against authenticate published ITS sequences in GenBank. In some cases, we also downloaded published, homologous sequences of the ITS region of fungi inspected in this study and examined the phylogenetic relationships of barcoded fungal species in light of modern taxonomic and phylogenetic studies. We anticipate that these data will motivate discussions on DNA barcoding based species identification as applied to the verification/certification of mushroom-containing dietary supplements.
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22
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Nilsson RH, Wurzbacher C, Bahram M, R. M. Coimbra V, Larsson E, Tedersoo L, Eriksson J, Duarte C, Svantesson S, Sánchez-García M, Ryberg MK, Kristiansson E, Abarenkov K. Top 50 most wanted fungi. MycoKeys 2016. [DOI: 10.3897/mycokeys.12.7553] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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23
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Garnica S, Schön ME, Abarenkov K, Riess K, Liimatainen K, Niskanen T, Dima B, Soop K, Frøslev TG, Jeppesen TS, Peintner U, Kuhnert-Finkernagel R, Brandrud TE, Saar G, Oertel B, Ammirati JF. Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus. FEMS Microbiol Ecol 2016; 92:fiw045. [PMID: 26929438 DOI: 10.1093/femsec/fiw045] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/14/2022] Open
Abstract
Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by >3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and lineage based-alignments. Our study indicates that 1%-2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 regions alone. Optimal threshold values for different picking approaches and genetic marker lengths inferred from a subset of species containing major lineages ranged from 97.0% to 99.5% sequence similarity using clustering optimization and UNITE SH, and from 1% to 2% sequence dissimilarity with CROP. Errors for the optimal cutoff ranged from 0% to 70%, and these can be reduced to a maximum of 22% when excluding species lacking a barcode gap. A threshold value of 99% is suitable for distinguishing species in the majority of lineages in the genus using the entire ITS region but only 90% of the species could be identified using just the ITS1 or ITS2 region. Prior identification of species, lacking barcode gaps and their subsequent separate analyses, maximized the accuracy of threshold approaches.
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Affiliation(s)
- Sigisfredo Garnica
- Institute of Evolution and Ecology, Plant Evolutionary Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany
| | - Max Emil Schön
- Institute of Evolution and Ecology, Plant Evolutionary Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany
| | - Kessy Abarenkov
- Institute of Ecology and Earth Sciences, University of Tartu, 51005 Tartu, Estonia
| | - Kai Riess
- Institute of Evolution and Ecology, Plant Evolutionary Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany
| | - Kare Liimatainen
- Department of Biosciences, Plant Biology, University of Helsinki, PO Box 65, 00014 Lahti, Finland
| | - Tuula Niskanen
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS, UK
| | - Bálint Dima
- Department of Biosciences, Plant Biology, University of Helsinki, PO Box 65, 00014 Lahti, Finland
| | - Karl Soop
- Honorary Research Associate, Swedish Museum of Natural History, Department of Cryptogamic Botany, Naturhistoriska riksmuseet, 104 05 Stockholm, Sweden
| | - Tobias Guldberg Frøslev
- Natural History Museum of Denmark, Center for Geogenetics, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Thomas Stjernegaard Jeppesen
- Natural History Museum of Denmark, Collections, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Ursula Peintner
- Institute of Microbiology, University Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | | | - Tor Erik Brandrud
- Department of Landscape Ecology (Oslo), Norwegian Institute for Nature Research, N-Oslo 5, Norway
| | | | - Bernhard Oertel
- INRES, University of Bonn, Auf dem Hügel 6, D-53121 Bonn, Germany
| | - Joseph F Ammirati
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
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24
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Looney BP, Ryberg M, Hampe F, Sánchez-García M, Matheny PB. Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi. Mol Ecol 2016; 25:630-47. [PMID: 26642189 DOI: 10.1111/mec.13506] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/10/2015] [Accepted: 11/22/2015] [Indexed: 01/30/2023]
Abstract
Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyperdiverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from molecular operational taxonomic unit cluster sets were examined to infer the distribution and plant association of the genus. This allowed us to test for differences in patterns of diversification between tropical and extratropical taxa, as well as how their associations with different plant lineages may be a driver of diversification. Results show that Russula is most species-rich at temperate latitudes and ancestral state reconstruction shows that the genus initially diversified in temperate areas. Migration into and out of the tropics characterizes the early evolution of the genus, and these transitions have been frequent since this time. We propose the 'generalized diversification rate' hypothesis to explain the reversed latitudinal diversity gradient pattern in Russula as we detect a higher net diversification rate in extratropical lineages. Patterns of diversification with plant associates support host switching and host expansion as driving diversification, with a higher diversification rate in lineages associated with Pinaceae and frequent transitions to association with angiosperms.
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Affiliation(s)
- Brian P Looney
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, TN, 37996-1610, USA
| | - Martin Ryberg
- Department of Organismal Biology, Uppsala University, Evolutionsbiologiskt Centrum, Norbyv. 18D, 75236, Uppsala, Sweden
| | - Felix Hampe
- Department of Biology, Gent University, K.L. Ledeganckstraat 35, 9000, Gent, Belgium
| | - Marisol Sánchez-García
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, TN, 37996-1610, USA
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, TN, 37996-1610, USA
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25
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Nilsson RH, Abarenkov K, Kõljalg U. Molecular Techniques in Mycological Studies and Sequence Data Curating: Quality Control and Challenges. BIOLOGY OF MICROFUNGI 2016. [DOI: 10.1007/978-3-319-29137-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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26
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Ectomycorrhizal fungal communities in Nothofagus nervosa ( Raulí ): A comparison between domesticated and naturally established specimens in a native forest of Patagonia, Argentina. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2015.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Hwang J, Zhao Q, Yang ZL, Wang Z, Townsend JP. Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples - an example of saddle fungi. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:658-667. [PMID: 26033481 DOI: 10.1111/1758-2229.12303] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/26/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
Abstract
The relation between ecological and genetic divergence of Helvella species (saddle fungi) has been perplexing. While a few species have been clearly demonstrated to be ectomycorrhizal fungi, ecological roles of many other species have been controversial, alternately considered as either saprotrophic or mycorrhizal. We applied SATé to build an inclusive deoxyribonucleic acid sequence alignment for the internal transcribed spacers (ITS) of annotated Helvella species and related environmental sequences. Phylogenetic informativeness of ITS and its regions were assessed using PhyDesign. Mycorrhizal lineages present a diversity of ecology, host type and geographic distribution. In two Helvella clades, no Helvella ITS sequences were recovered from root tips. Inclusion of environmental sequences in the ITS phylogeny from these sequences has the potential to link these data and reveal Helvella ecology. This study can serve as a model for revealing the diversity of relationships between unculturable fungi and their potential plant hosts. How non-mycorrhizal life styles within Helvella evolved will require expanded metagenomic investigation of soil and other environmental samples along with study of Helvella genomes.
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Affiliation(s)
- Jonathan Hwang
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
| | - Qi Zhao
- Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zhu L Yang
- Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zheng Wang
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
- Program in Microbiology, Yale University, New Haven, CT 06520, USA
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28
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Scully ED, Geib SM, Carlson JE, Tien M, McKenna D, Hoover K. Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles. BMC Genomics 2014; 15:1096. [PMID: 25495900 PMCID: PMC4299006 DOI: 10.1186/1471-2164-15-1096] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/24/2014] [Indexed: 12/05/2022] Open
Abstract
Background Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the contributions of these apparent symbionts to digestive physiology and nutritional ecology remain uncharacterized in most beetle lineages. Results Through parallel transcriptome profiling of beetle- and microbial- derived mRNAs, we demonstrate that the midgut microbiome of the Asian longhorned beetle (Anoplophora glabripennis), a member of the beetle family Cerambycidae, is enriched in biosynthetic pathways for the synthesis of essential amino acids, vitamins, and sterols. Consequently, the midgut microbiome of A. glabripennis can provide essential nutrients that the beetle cannot obtain from its woody diet or synthesize itself. The beetle gut microbiota also produce their own suite of transcripts that can enhance lignin degradation, degrade hemicellulose, and ferment xylose and wood sugars. An abundance of cellulases from several glycoside hydrolase families are expressed endogenously by A. glabripennis, as well as transcripts that allow the beetle to convert microbe-synthesized essential amino acids into non-essential amino acids. A. glabripennis and its gut microbes likely collaborate to digest carbohydrates and convert released sugars and amino acid intermediates into essential nutrients otherwise lacking from their woody host plants. Conclusions The nutritional provisioning capabilities of the A. glabripennis gut microbiome may contribute to the beetles’ unusually broad host range. The presence of some of the same microbes in the guts of other Cerambycidae and other wood-feeding beetles suggests that partnerships with microbes may be a facilitator of evolutionary radiations in beetles, as in certain other groups of insects, allowing access to novel food sources through enhanced nutritional provisioning. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1096) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Kelli Hoover
- Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, 501 ASI Building, University Park, PA 16802, USA.
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29
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Yew SM, Chan CL, Lee KW, Na SL, Tan R, Hoh CC, Yee WY, Ngeow YF, Ng KP. A five-year survey of dematiaceous fungi in a tropical hospital reveals potential opportunistic species. PLoS One 2014; 9:e104352. [PMID: 25098697 PMCID: PMC4123927 DOI: 10.1371/journal.pone.0104352] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 07/11/2014] [Indexed: 01/06/2023] Open
Abstract
Dematiaceous fungi (black fungi) are a heterogeneous group of fungi present in diverse environments worldwide. Many species in this group are known to cause allergic reactions and potentially fatal diseases in humans and animals, especially in tropical and subtropical climates. This study represents the first survey of dematiaceous fungi in Malaysia and provides observations on their diversity as well as in vitro response to antifungal drugs. Seventy-five strains isolated from various clinical specimens were identified by morphology as well as an internal transcribed spacer (ITS)-based phylogenetic analysis. The combined molecular and conventional approach enabled the identification of three classes of the Ascomycota phylum and 16 genera, the most common being Cladosporium, Cochliobolus and Neoscytalidium. Several of the species identified have not been associated before with human infections. Among 8 antifungal agents tested, the azoles posaconazole (96%), voriconazole (90.7%), ketoconazole (86.7%) and itraconazole (85.3%) showed in vitro activity (MIC ≤1 µg/mL) to the largest number of strains, followed by anidulafungin (89.3%), caspofungin (74.7%) and amphotericin B (70.7%). Fluconazole appeared to be the least effective with only 10.7% of isolates showing in vitro susceptibility. Overall, almost half (45.3%) of the isolates showed reduced susceptibility (MIC >1 µg/mL) to at least one antifungal agent, and three strains (one Pyrenochaeta unguis-hominis and two Nigrospora oryzae) showed potential multidrug resistance.
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Affiliation(s)
- Su Mei Yew
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chai Ling Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Wei Lee
- Codon Genomics SB, Jalan Bandar Lapan Belas, Pusat Bandar Puchong, Selangor Darul Ehsan, Malaysia
| | - Shiang Ling Na
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ruixin Tan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chee-Choong Hoh
- Codon Genomics SB, Jalan Bandar Lapan Belas, Pusat Bandar Puchong, Selangor Darul Ehsan, Malaysia
| | - Wai-Yan Yee
- Codon Genomics SB, Jalan Bandar Lapan Belas, Pusat Bandar Puchong, Selangor Darul Ehsan, Malaysia
| | - Yun Fong Ngeow
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kee Peng Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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Gazis R, Skaltsas D, Chaverri P. Novel endophytic lineages of Tolypocladium provide new insights into the ecology and evolution of Cordyceps-like fungi. Mycologia 2014; 106:1090-105. [PMID: 24987126 DOI: 10.3852/13-346] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The objective of this study was to identify a group of unknown endophytic fungal isolates from the living sapwood of wild and planted Hevea (rubber tree) populations. Three novel lineages of Tolypocladium are described based on molecular and morphological data. Findings from this study open a window for novel hypotheses regarding the ecology and role of endophytes within plant communities as well as trait evolution and potential forces driving diversification of Cordyceps-like fungi. This study stresses the importance of integrating asexual and sexual fungal states for a more complete understanding of the natural history of this diverse group. In addition, it highlights the study of fungi in the sapwood of tropical trees as habitat for the discovery of novel fungal lineages and substrate associations.
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Affiliation(s)
- Romina Gazis
- Clark University, Biology Department, 950 Main Street, Worcester, Massachusetts 01610
| | - Demetra Skaltsas
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland 20742
| | - Priscila Chaverri
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland 20742, and Universidad de Costa Rica, Escuela de Biología, Apdo. 11501-2060, San Pedro, San José, Costa Rica
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31
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Buscardo E, Rodríguez-Echeverría S, Freitas H, De Angelis P, Pereira JS, Muller LAH. Contrasting soil fungal communities in Mediterranean pine forests subjected to different wildfire frequencies. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0294-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Nilsson RH, Hyde KD, Pawłowska J, Ryberg M, Tedersoo L, Aas AB, Alias SA, Alves A, Anderson CL, Antonelli A, Arnold AE, Bahnmann B, Bahram M, Bengtsson-Palme J, Berlin A, Branco S, Chomnunti P, Dissanayake A, Drenkhan R, Friberg H, Frøslev TG, Halwachs B, Hartmann M, Henricot B, Jayawardena R, Jumpponen A, Kauserud H, Koskela S, Kulik T, Liimatainen K, Lindahl BD, Lindner D, Liu JK, Maharachchikumbura S, Manamgoda D, Martinsson S, Neves MA, Niskanen T, Nylinder S, Pereira OL, Pinho DB, Porter TM, Queloz V, Riit T, Sánchez-García M, de Sousa F, Stefańczyk E, Tadych M, Takamatsu S, Tian Q, Udayanga D, Unterseher M, Wang Z, Wikee S, Yan J, Larsson E, Larsson KH, Kõljalg U, Abarenkov K. Improving ITS sequence data for identification of plant pathogenic fungi. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0291-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sjökvist E, Pfeil BE, Larsson E, Larsson KH. Stereopsidales--a new order of mushroom-forming fungi. PLoS One 2014; 9:e95227. [PMID: 24777067 PMCID: PMC4002437 DOI: 10.1371/journal.pone.0095227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 03/14/2014] [Indexed: 11/18/2022] Open
Abstract
One new order, one new family, and one new combination are presented, as the result of molecular phylogenetic analyses. The new order Stereopsidales and the new family Stereopsidaceae are described incorporating Stereopsis radicans and S. globosa, formerly Clavulicium globosum. We show that not only do these species represent an old overlooked lineage, but both species harbor cryptic diversity. In addition, a third species, C. macounii, appears as a plausible sister to the new lineage, but there is conflict in the data. All specimens of S. radicans and S. globosa analysed here are from the South and Central Americas; several records of S. radicans have been made also from tropical Asia. We expect the true diversity in this group to be a lot higher than presented in this paper. Stereopsis radicans was formerly included in Polyporales, but a placement within that order is rejected by our data through SH tests. The dataset consisted of four nuclear markers: rpb2, tef1, LSU and SSU, each of which was analysed separately using maximum likelihood and Bayesian inference. Recombination detection tests indicate no plausible recombinations. The potential of S. radicans, S. globosa and C. macounii being amphitallic is briefly discussed.
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Affiliation(s)
- Elisabet Sjökvist
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Bernard E. Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Ellen Larsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
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U'Ren JM, Riddle JM, Monacell JT, Carbone I, Miadlikowska J, Arnold AE. Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi. Mol Ecol Resour 2014; 14:1032-48. [PMID: 24628864 DOI: 10.1111/1755-0998.12252] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 02/14/2014] [Indexed: 12/23/2022]
Abstract
Next-generation sequencing technologies have provided unprecedented insights into fungal diversity and ecology. However, intrinsic biases and insufficient quality control in next-generation methods can lead to difficult-to-detect errors in estimating fungal community richness, distributions and composition. The aim of this study was to examine how tissue storage prior to DNA extraction, primer design and various quality-control approaches commonly used in 454 amplicon pyrosequencing might influence ecological inferences in studies of endophytic and endolichenic fungi. We first contrast 454 data sets generated contemporaneously from subsets of the same plant and lichen tissues that were stored in CTAB buffer, dried in silica gel or freshly frozen prior to DNA extraction. We show that storage in silica gel markedly limits the recovery of sequence data and yields a small fraction of the diversity observed by the other two methods. Using lichen mycobiont sequences as internal positive controls, we next show that despite careful filtering of raw reads and utilization of current best-practice OTU clustering methods, homopolymer errors in sequences representing rare taxa artificially increased estimates of richness c. 15-fold in a model data set. Third, we show that inferences regarding endolichenic diversity can be improved using a novel primer that reduces amplification of the mycobiont. Together, our results provide a rationale for selecting tissue treatment regimes prior to DNA extraction, demonstrate the efficacy of reducing mycobiont amplification in studies of the fungal microbiomes of lichen thalli and highlight the difficulties in differentiating true information about fungal biodiversity from methodological artefacts.
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Affiliation(s)
- Jana M U'Ren
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
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35
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Waud M, Busschaert P, Ruyters S, Jacquemyn H, Lievens B. Impact of primer choice on characterization of orchid mycorrhizal communities using 454 pyrosequencing. Mol Ecol Resour 2014; 14:679-99. [PMID: 24460947 DOI: 10.1111/1755-0998.12229] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 01/07/2014] [Accepted: 01/08/2014] [Indexed: 01/24/2023]
Abstract
Although the number of studies investigating mycorrhizal associations in orchids has increased in recent years, the fungal communities associating with orchids and how they differ between species and sites remain unclear. Recent research has indicated that individual orchid plants may associate with several fungi concurrently, implying that to study mycorrhizal associations in orchids the fungal community should be assessed, rather than the presence of individual dominant fungal species or strains. High-throughput sequencing methods, such as 454 pyrosequencing, are increasingly used as the primary tool for such analyses. However, many studies combine universal primers from previous phylogenetic or ecological studies to generate amplicons suitable for 454 pyrosequencing without first critically evaluating their performance, potentially resulting in biased fungal community descriptions. Here, following in silico primer analysis we evaluated the performance of different combinations of existing PCR primers to characterize orchid mycorrhizal communities using 454 pyrosequencing by analysis of both an artificially assembled community of mycorrhizal fungi isolated from diverse orchid species and root samples from three different orchid species (Anacamptis morio, Ophrys tenthredinifera and Serapias lingua). Our results indicate that primer pairs ITS3/ITS4OF and ITS86F/ITS4, targeting the internal transcribed spacer-2 (ITS-2) region, outperformed other tested primer pairs in terms of number of reads, number of operational taxonomic units recovered from the artificial community and number of different orchid mycorrhizal associating families detected in the orchid samples. Additionally, we show the complementary specificity of both primer pairs, making them highly suitable for tandem use when studying the diversity of orchid mycorrhizal communities.
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Affiliation(s)
- Michael Waud
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Campus De Nayer, B-2860, Sint-Katelijne-Waver, Belgium; Division of Plant Ecology and Systematics, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001, Heverlee, Belgium
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Multiple ITS copies reveal extensive hybridization within Rheum (Polygonaceae), a genus that has undergone rapid radiation. PLoS One 2014; 9:e89769. [PMID: 24587023 PMCID: PMC3937351 DOI: 10.1371/journal.pone.0089769] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 01/25/2014] [Indexed: 11/24/2022] Open
Abstract
Background During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual. Methodology/Principal Findings In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively. Conclusions These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation.
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37
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Metagenomic Approach Yields Insights into Fungal Diversity and Functioning. SPRINGERBRIEFS IN BIOLOGY 2014. [DOI: 10.1007/978-4-431-54261-2_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Penton CR, StLouis D, Cole JR, Luo Y, Wu L, Schuur EAG, Zhou J, Tiedje JM. Fungal diversity in permafrost and tallgrass prairie soils under experimental warming conditions. Appl Environ Microbiol 2013; 79:7063-72. [PMID: 24014534 PMCID: PMC3811548 DOI: 10.1128/aem.01702-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 09/03/2013] [Indexed: 12/15/2022] Open
Abstract
Soil fungi play a major role in terrestrial ecosystem functioning through interactions with soil structure, plants, micro- and mesofauna, and nutrient cycling through predation, pathogenesis, mutualistic, and saprotrophic roles. The diversity of soil fungi was assessed by sequencing their 28S rRNA gene in Alaskan permafrost and Oklahoma tallgrass prairie soils at experimental sites where the effect of climate warming is under investigation. A total of 226,695 reads were classified into 1,063 genera, covering 62% of the reference data set. Using the Bayesian Classifier offered by the Ribosomal Database Project (RDP) with 50% bootstrapping classification confidence, approximately 70% of sequences were returned as "unclassified" at the genus level, although the majority (∼65%) were classified at the class level, which provided insight into these lesser-known fungal lineages. Those unclassified at the genus level were subjected to BLAST analysis against the ARB-SILVA database, where ∼50% most closely matched nonfungal taxa. Compared to the more abundant sequences, a higher proportion of rare operational taxonomic units (OTU) were successfully classified to genera at 50% bootstrap confidence, indicating that the fungal rare biosphere in these sites is not composed of sequencing artifacts. There was no significant effect after 1 year of warming on the fungal community structure at both sites, except perhaps for a few minor members, but there was a significant effect of sample depth in the permafrost soils. Despite overall significant community structure differences driven by variations in OTU dominance, the prairie and permafrost soils shared 90% and 63% of all fungal sequences, respectively, indicating a fungal "seed bank" common between both sites.
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Affiliation(s)
- C. Ryan Penton
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
| | - Derek StLouis
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
| | - James R. Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Liyou Wu
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - E. A. G Schuur
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
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Nilsson RH, Abarenkov K, Veldre V, Nylinder S, DE Wit P, Brosché S, Alfredsson JF, Ryberg M, Kristiansson E. An open source chimera checker for the fungal ITS region. Mol Ecol Resour 2013; 10:1076-81. [PMID: 21565119 DOI: 10.1111/j.1755-0998.2010.02850.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit holds a central position in the pursuit of the taxonomic affiliation of fungi recovered through environmental sampling. Newly generated fungal ITS sequences are typically compared against the International Nucleotide Sequence Databases for a species or genus name using the sequence similarity software suite blast. Such searches are not without complications however, and one of them is the presence of chimeric entries among the query or reference sequences. Chimeras are artificial sequences, generated unintentionally during the polymerase chain reaction step, that feature sequence data from two (or possibly more) distinct species. Available software solutions for chimera control do not readily target the fungal ITS region, but the present study introduces a blast-based open source software package (available at http://www.emerencia.org/chimerachecker.html) to examine newly generated fungal ITS sequences for the presence of potentially chimeric elements in batch mode. We used the software package on a random set of 12 300 environmental fungal ITS sequences in the public sequence databases and found 1.5% of the entries to be chimeric at the ordinal level after manual verification of the results. The proportion of chimeras in the sequence databases can be hypothesized to increase as emerging sequencing technologies drawing from pooled DNA samples are becoming important tools in molecular ecology research.
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Affiliation(s)
- R H Nilsson
- Department of Plant and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
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40
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Osmundson TW, Robert VA, Schoch CL, Baker LJ, Smith A, Robich G, Mizzan L, Garbelotto MM. Filling gaps in biodiversity knowledge for macrofungi: contributions and assessment of an herbarium collection DNA barcode sequencing project. PLoS One 2013; 8:e62419. [PMID: 23638077 PMCID: PMC3640088 DOI: 10.1371/journal.pone.0062419] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 03/22/2013] [Indexed: 11/19/2022] Open
Abstract
Despite recent advances spearheaded by molecular approaches and novel technologies, species description and DNA sequence information are significantly lagging for fungi compared to many other groups of organisms. Large scale sequencing of vouchered herbarium material can aid in closing this gap. Here, we describe an effort to obtain broad ITS sequence coverage of the approximately 6000 macrofungal-species-rich herbarium of the Museum of Natural History in Venice, Italy. Our goals were to investigate issues related to large sequencing projects, develop heuristic methods for assessing the overall performance of such a project, and evaluate the prospects of such efforts to reduce the current gap in fungal biodiversity knowledge. The effort generated 1107 sequences submitted to GenBank, including 416 previously unrepresented taxa and 398 sequences exhibiting a best BLAST match to an unidentified environmental sequence. Specimen age and taxon affected sequencing success, and subsequent work on failed specimens showed that an ITS1 mini-barcode greatly increased sequencing success without greatly reducing the discriminating power of the barcode. Similarity comparisons and nonmetric multidimensional scaling ordinations based on pairwise distance matrices proved to be useful heuristic tools for validating the overall accuracy of specimen identifications, flagging potential misidentifications, and identifying taxa in need of additional species-level revision. Comparison of within- and among-species nucleotide variation showed a strong increase in species discriminating power at 1-2% dissimilarity, and identified potential barcoding issues (same sequence for different species and vice-versa). All sequences are linked to a vouchered specimen, and results from this study have already prompted revisions of species-sequence assignments in several taxa.
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Affiliation(s)
- Todd W. Osmundson
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
| | - Vincent A. Robert
- Centraalbureau voor Schimmelcultures, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Conrad L. Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lydia J. Baker
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
| | - Amy Smith
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
| | | | - Luca Mizzan
- Venice Museum of Natural History, Venice, Italy
| | - Matteo M. Garbelotto
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
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41
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Glass DJ, Takebayashi N, Olson LE, Taylor DL. Evaluation of the authenticity of a highly novel environmental sequence from boreal forest soil using ribosomal RNA secondary structure modeling. Mol Phylogenet Evol 2013; 67:234-45. [PMID: 23403224 DOI: 10.1016/j.ympev.2013.01.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 01/09/2013] [Accepted: 01/29/2013] [Indexed: 01/31/2023]
Abstract
The number of sequences from both formally described taxa and uncultured environmental DNA deposited in the International Nucleotide Sequence Databases has increased substantially over the last two decades. Although the majority of these sequences represent authentic gene copies, there is evidence of DNA artifacts in these databases as well. These include lab artifacts, such as PCR chimeras, and biological artifacts such as pseudogenes or other paralogous sequences. Sequences that fall in basal positions in phylogenetic trees and appear distant from known sequences are particularly suspect. Phylogenetic analyses suggest that a novel sequence type (NS1) found in two boreal forest soil clone libraries belongs to the fungal kingdom but does not fall unambiguously within any known phylum. We have evaluated this sequence type using an array of secondary-structure analyses. To our knowledge, such analyses have never been used on environmental ribosomal sequences. Ribosomal secondary structure was modeled for four rRNA loci (ITS1, 5.8S, ITS2, 5' LSU). These models were analyzed for the presence of conserved domains, conserved nucleotide motifs, and compensatory base changes. Minimal free energy (MFE) foldings and GC contents of sequences representing the major fungal clades, as well as NS1, were also compared. NS1 displays secondary rRNA structures consistent with other fungi and many, but not all, conserved nucleotide motifs found across eukaryotes. However, our analyses show that many other authentic sequences from basal fungi lack more of these conserved motifs than does NS1. Together our findings suggest that NS1 represents an authentic gene copy. The methods described here can be used on any rRNA-coding sequence, not just environmental fungal sequences. As new-generation sequencing methods that yield shorter sequences become more widely implemented, methods that evaluate sequence authenticity should also be more widely implemented. For fungi, the adjacent 5.8S and ITS2 loci should be prioritized. This region is not only suited to distinguishing between closely related species, but it is also more informative in terms of expected secondary structure.
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Affiliation(s)
- Daniel J Glass
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
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42
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Blaalid R, Kumar S, Nilsson RH, Abarenkov K, Kirk PM, Kauserud H. ITS1 versus ITS2 as DNA metabarcodes for fungi. Mol Ecol Resour 2013; 13:218-24. [PMID: 23350562 DOI: 10.1111/1755-0998.12065] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 11/15/2012] [Accepted: 11/20/2012] [Indexed: 11/28/2022]
Abstract
The nuclear ribosomal Internal Transcribed Spacer ITS region is widely used as a DNA metabarcoding marker to characterize the diversity and composition of fungal communities. In amplicon pyrosequencing studies of fungal diversity, one of the spacers ITS1 or ITS2 of the ITS region is normally used. In this methodological study we evaluate the usability of ITS1 vs. ITS2 as a DNA metabarcoding marker for fungi. We analyse three data sets: two comprising ITS1 and ITS2 sequences of known taxonomic affiliations and a third comprising ITS1 and ITS2 environmental amplicon pyrosequencing data. Clustering analyses of sequences with known taxonomy using the bioinformatics pipeline ClustEx revealed that a 97% similarity cut-off represent a reasonable threshold for estimating the number of known species in the data sets for both ITS1 and ITS2. However, no single threshold value worked well for all fungi at the same time within the curated UNITE database, and we found that the Operational Taxonomic Unit (OTU) concept is not easily translated into the level of species because many species are distributed over several clusters. Clustering analyses of the 134 692 ITS1 and ITS2 pyrosequences using a 97% similarity cut-off revealed a high similarity between the two data sets when it comes to taxonomic coverage. Although some groups are under- or unrepresented in the two data sets due to, e.g. primer mismatches, our results indicate that ITS1 and ITS2 to a large extent yield similar results when used as DNA metabarcodes for fungi.
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Affiliation(s)
- R Blaalid
- Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, PO Box 1066 Blindern, Oslo, NO-0316, Norway
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Healy RA, Smith ME, Bonito GM, Pfister DH, Ge ZW, Guevara GG, Williams G, Stafford K, Kumar L, Lee T, Hobart C, Trappe J, Vilgalys R, McLaughlin DJ. High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizalPezizales. Mol Ecol 2012. [DOI: 10.1111/mec.12135] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. A. Healy
- Department of Plant Biology; University of Minnesota; St. Paul MN 55108 USA
| | - M. E. Smith
- Department of Plant Pathology; University of Florida; Gainesville FL 32611-0680 USA
| | - G. M. Bonito
- Department of Biology; Duke University; Durham NC 27708 USA
| | - D. H. Pfister
- Farlow Herbarium of Cryptogamic Botany; Harvard University; Cambridge MA 02143 USA
| | - Z. -W. Ge
- Department of Plant Pathology; University of Florida; Gainesville FL 32611-0680 USA
- Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650204 China
| | - G. G. Guevara
- Instituto Tecnológico de Cd. Victoria; Tamaulipas 87010 Mexico
| | - G. Williams
- Department of Biology; Duke University; Durham NC 27708 USA
| | - K. Stafford
- Department of Biology; Duke University; Durham NC 27708 USA
| | - L. Kumar
- Department of Plant Biology; University of Minnesota; St. Paul MN 55108 USA
| | - T. Lee
- Department of Plant Biology; University of Minnesota; St. Paul MN 55108 USA
| | - C. Hobart
- University of Sheffield; Sheffield UK
| | - J. Trappe
- Department of Forest Ecosystems and Society; Oregon State University; Corvalis 97331-2106 OR USA
| | - R. Vilgalys
- Department of Biology; Duke University; Durham NC 27708 USA
| | - D. J. McLaughlin
- Department of Plant Biology; University of Minnesota; St. Paul MN 55108 USA
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Nagy LG, Kocsubé S, Csanádi Z, Kovács GM, Petkovits T, Vágvölgyi C, Papp T. Re-mind the gap! Insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi. PLoS One 2012; 7:e49794. [PMID: 23185439 PMCID: PMC3501463 DOI: 10.1371/journal.pone.0049794] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/12/2012] [Indexed: 01/09/2023] Open
Abstract
Rapidly evolving, indel-rich phylogenetic markers play a pivotal role in our understanding of the relationships at multiple levels of the tree of life. There is extensive evidence that indels provide conserved phylogenetic signal, however, the range of phylogenetic depths for which gaps retain tree signal has not been investigated in detail. Here we address this question using the fungal internal transcribed spacer (ITS), which is central in many phylogenetic studies, molecular ecology, detection and identification of pathogenic and non-pathogenic species. ITS is repeatedly criticized for indel-induced alignment problems and the lack of phylogenetic resolution above species level, although these have not been critically investigated. In this study, we examined whether the inclusion of gap characters in the analyses shifts the phylogenetic utility of ITS alignments towards earlier divergences. By re-analyzing 115 published fungal ITS alignments, we found that indels are slightly more conserved than nucleotide substitutions, and when included in phylogenetic analyses, improved the resolution and branch support of phylogenies across an array of taxonomic ranges and extended the resolving power of ITS towards earlier nodes of phylogenetic trees. Our results reconcile previous contradicting evidence for the effects of data exclusion: in the case of more sophisticated indel placement, the exclusion of indel-rich regions from the analyses results in a loss of tree resolution, whereas in the case of simpler alignment methods, the exclusion of gapped sites improves it. Although the empirical datasets do not provide to measure alignment accuracy objectively, our results for the ITS region are consistent with previous simulations studies alignment algorithms. We suggest that sophisticated alignment algorithms and the inclusion of indels make the ITS region and potentially other rapidly evolving indel-rich loci valuable sources of phylogenetic information, which can be exploited at multiple taxonomic levels.
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Affiliation(s)
- László G Nagy
- University of Szeged, Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary.
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Sato H, Tsujino R, Kurita K, Yokoyama K, Agata K. Modelling the global distribution of fungal species: new insights into microbial cosmopolitanism. Mol Ecol 2012; 21:5599-612. [DOI: 10.1111/mec.12053] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 08/09/2012] [Accepted: 08/17/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Hirotoshi Sato
- Graduate School of Global Environmental Studies; Kyoto University; Sakyo-ku; Kyoto; 606-8501; Japan
| | - Riyou Tsujino
- Primate Research Institute; Kyoto University; Sakyo-ku; Kyoto; 606-8501; Japan
| | - Kazuki Kurita
- Laboratory of Systematic Zoology; Graduate School of Science; Kyoto University; Sakyo-ku; Kyoto; 606-8501; Japan
| | | | - Kiyokazu Agata
- Laboratory for Molecular Developmental Biology; Graduate School of Science; Kyoto University; Sakyo-ku; Kyoto; 606-8501; Japan
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Uehling JK, Henkel TW, Vilgalys R, Smith ME. Membranomyces species are common ectomycorrhizal symbionts in Northern Hemisphere forests. MYCORRHIZA 2012; 22:577-581. [PMID: 22847636 DOI: 10.1007/s00572-012-0457-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 07/16/2012] [Indexed: 06/01/2023]
Abstract
Membranomyces (Clavulinaceae, Cantharellales) Jülich consists of two described species of resupinate (crust-like) basidiomycetes. Previous studies indicated that Membranomyces falls within the Clavulinaceae, but the phylogenetic position of the genus has not been fully resolved. Membranomyces species were thought to be saprotrophic until 2003 when Tedersoo et al. detected Membranomyces delectabilis on ectomycorrhizal roots of Populus and Picea. Membranomyces was previously known only from collections made in eastern Canada and Europe. We recently sequenced the ITS rDNA barcode region from Scandinavian herbarium specimens identified as M. delectabilis and Membranomyces spurius. Phylogenetic analyses of these sporocarp sequences and similar environmental sequences indicated that Membranomyces is more diverse than previously thought and forms ectomycorrhizas with hosts from a diverse range of plant families in many north temperate ecosystems.
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47
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Thessen AE, Patterson DJ, Murray SA. The taxonomic significance of species that have only been observed once: the genus Gymnodinium (Dinoflagellata) as an example. PLoS One 2012; 7:e44015. [PMID: 22952856 PMCID: PMC3431360 DOI: 10.1371/journal.pone.0044015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 07/27/2012] [Indexed: 11/19/2022] Open
Abstract
Taxonomists have been tasked with cataloguing and quantifying the Earth's biodiversity. Their progress is measured in code-compliant species descriptions that include text, images, type material and molecular sequences. It is from this material that other researchers are to identify individuals of the same species in future observations. It has been estimated that 13% to 22% (depending on taxonomic group) of described species have only ever been observed once. Species that have only been observed at the time and place of their original description are referred to as oncers. Oncers are important to our current understanding of biodiversity. They may be validly described species that are members of a rare biosphere, or they may indicate endemism, or that these species are limited to very constrained niches. Alternatively, they may reflect that taxonomic practices are too poor to allow the organism to be re-identified or that the descriptions are unknown to other researchers. If the latter are true, our current tally of species will not be an accurate indication of what we know. In order to investigate this phenomenon and its potential causes, we examined the microbial eukaryote genus Gymnodinium. This genus contains 268 extant species, 103 (38%) of which have not been observed since their original description. We report traits of the original descriptions and interpret them in respect to the status of the species. We conclude that the majority of oncers were poorly described and their identity is ambiguous. As a result, we argue that the genus Gymnodinium contains only 234 identifiable species. Species that have been observed multiple times tend to have longer descriptions, written in English. The styles of individual authors have a major effect, with a few authors describing a disproportionate number of oncers. The information about the taxonomy of Gymnodinium that is available via the internet is incomplete, and reliance on it will not give access to all necessary knowledge. Six new names are presented - Gymnodinium campbelli for the homonymous name Gymnodinium translucens Campbell 1973, Gymnodinium antarcticum for the homonymous name Gymnodinium frigidum Balech 1965, Gymnodinium manchuriensis for the homonymous name Gymnodinium autumnale Skvortzov 1968, Gymnodinium christenum for the homonymous name Gymnodinium irregulare Christen 1959, Gymnodinium conkufferi for the homonymous name Gymnodinium irregulare Conrad & Kufferath 1954 and Gymnodinium chinensis for the homonymous name Gymnodinium frigidum Skvortzov 1968.
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Affiliation(s)
- Anne E Thessen
- Center for Library and Informatics, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America.
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48
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Du XH, Zhao Q, Yang ZL, Hansen K, Taskin H, Büyükalaca S, Dewsbury D, Moncalvo JM, Douhan GW, Robert VARG, Crous PW, Rehner SA, Rooney AP, Sink S, O'Donnell K. How well do ITS rDNA sequences differentiate species of true morels (Morchella)? Mycologia 2012; 104:1351-68. [PMID: 22802394 DOI: 10.3852/12-056] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Arguably more mycophiles hunt true morels (Morchella) during their brief fruiting season each spring in the northern hemisphere than any other wild edible fungus. Concerns about overharvesting by individual collectors and commercial enterprises make it essential that science-based management practices and conservation policies are developed to ensure the sustainability of commercial harvests and to protect and preserve morel species diversity. Therefore, the primary objectives of the present study were to: (i) investigate the utility of the ITS rDNA locus for identifying Morchella species, using phylogenetic species previously inferred from multilocus DNA sequence data as a reference; and (ii) clarify insufficiently identified sequences and determine whether the named sequences in GenBank were identified correctly. To this end, we generated 553 Morchella ITS rDNA sequences and downloaded 312 additional ones generated by other researchers from GenBank using emerencia and analyzed them phylogenetically. Three major findings emerged: (i) ITS rDNA sequences were useful in identifying 48/62 (77.4%) of the known phylospecies; however, they failed to identify 12 of the 22 species within the species-rich Elata Subclade and two closely related species in the Esculenta Clade; (ii) at least 66% of the named Morchella sequences in GenBank are misidentified; and (iii) ITS rDNA sequences of up to six putatively novel Morchella species were represented in GenBank. Recognizing the need for a dedicated Web-accessible reference database to facilitate the rapid identification of known and novel species, we constructed Morchella MLST (http://www.cbs.knaw.nl/morchella/), which can be queried with ITS rDNA sequences and those of the four other genes used in our prior multilocus molecular systematic studies of this charismatic genus.
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Affiliation(s)
- Xi-Hui Du
- Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Province, People's Republic of China
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Ryberg M, Matheny PB. Asynchronous origins of ectomycorrhizal clades of Agaricales. Proc Biol Sci 2012; 279:2003-11. [PMID: 22171078 PMCID: PMC3311903 DOI: 10.1098/rspb.2011.2428] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 11/24/2011] [Indexed: 11/12/2022] Open
Abstract
The ectomycorrhizal (ECM) symbiosis is the most widespread biotrophic nutritional mode in mushroom-forming fungi. ECM fungi include, though are not limited to, about 5000 described species of Agaricales from numerous, independently evolved lineages. Two central hypotheses suggest different explanations for the origin of ECM fungal diversity: (i) dual origins, initially with the Pinaceae in the Jurassic and later with angiosperms during the Late Cretaceous, and (ii) a simultaneous and convergent radiation of ECM lineages in response to cooling climate during the Palaeogene and advancing temperate ECM plant communities. Neither of these hypotheses is supported here. While we demonstrate support for asynchronous origins of ECM Agaricales, the timing of such events appears to have occurred more recently than suggested by the first hypothesis, first during the Cretaceous and later during the Palaeogene. We are also unable to reject models of rate constancy, which suggests that the diversity of ECM Agaricales is not a consequence of convergent rapid radiations following evolutionary transitions from saprotrophic to ECM habits. ECM lineages of Agaricales differ not only in age, but also in rates of diversification and rate of substitution at nuclear ribosomal RNA loci. These results question the biological uniformity of the ECM guild.
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Affiliation(s)
- Martin Ryberg
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler, Knoxville, TN 37996, USA.
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DNA sequence analyses reveal abundant diversity, endemism and evidence for Asian origin of the porcini mushrooms. PLoS One 2012; 7:e37567. [PMID: 22629418 PMCID: PMC3356339 DOI: 10.1371/journal.pone.0037567] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 04/20/2012] [Indexed: 11/19/2022] Open
Abstract
The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species) and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions.
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