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Koch RA, Herr JR. Global Distribution and Richness of Armillaria and Related Species Inferred From Public Databases and Amplicon Sequencing Datasets. Front Microbiol 2021; 12:733159. [PMID: 34803949 PMCID: PMC8602889 DOI: 10.3389/fmicb.2021.733159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/14/2021] [Indexed: 01/30/2023] Open
Abstract
Armillaria is a globally distributed fungal genus most notably composed of economically important plant pathogens that are found predominantly in forest and agronomic systems. The genus sensu lato has more recently received attention for its role in woody plant decomposition and in mycorrhizal symbiosis with specific plants. Previous phylogenetic analyses suggest that around 50 species are recognized globally. Despite this previous work, no studies have analyzed the global species richness and distribution of the genus using data derived from fungal community sequencing datasets or barcoding initiatives. To assess the global diversity and species richness of Armillaria, we mined publicly available sequencing datasets derived from numerous primer regions for the ribosomal operon, as well as ITS sequences deposited on Genbank, and clustered them akin to metabarcoding studies. Our estimates reveal that species richness ranges from 50 to 60 species, depending on whether the ITS1 or ITS2 marker is used. Eastern Asia represents the biogeographic region with the highest species richness. We also assess the overlap of species across geographic regions and propose some hypotheses regarding the drivers of variability in species diversity and richness between different biogeographic regions.
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Affiliation(s)
- Rachel A. Koch
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, United States
| | - Joshua R. Herr
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, United States
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2
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D’Andreano S, Cuscó A, Francino O. Rapid and real-time identification of fungi up to species level with long amplicon nanopore sequencing from clinical samples. Biol Methods Protoc 2021; 6:bpaa026. [PMID: 33506108 PMCID: PMC7820110 DOI: 10.1093/biomethods/bpaa026] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/02/2020] [Accepted: 12/18/2020] [Indexed: 12/21/2022] Open
Abstract
The availability of long-read technologies, like Oxford Nanopore Technologies, provides the opportunity to sequence longer fragments of the fungal ribosomal operon, up to 6 Kb (18S-ITS1-5.8S-ITS2-28S) and to improve the taxonomy assignment of the communities up to species level and in real-time. We assess the applicability for taxonomic assignment of amplicons targeting a 3.5 Kb region (V3 18S-ITS1-5.8S-ITS2-28S D2) and a 6 Kb region (V1 18S-ITS1-5.8S-ITS2-28S D12) with the What's in my pot (WIMP) classifier. We used the ZymoBIOMICSTM mock community and different microbiological fungal cultures as positive controls. Long amplicon sequencing correctly identified Saccharomyces cerevisiae and Cryptococcus neoformans from the mock community and Malassezia pachydermatis, Microsporum canis and Aspergillus fumigatus from the microbiological cultures. Besides, we identified Rhodotorula graminis in a culture mislabelled as Candida spp. We applied the same approach to external otitis in dogs. Malassezia was the dominant fungal genus in dogs' ear skin, whereas Ma. pachydermatis was the main species in the healthy sample. Conversely, we identified a higher representation of Ma. globosa and Ma. sympodialis in otitis affected samples. We demonstrate the suitability of long ribosomal amplicons to characterize the fungal community of complex samples, either healthy or with clinical signs of infection.
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Affiliation(s)
- Sara D’Andreano
- SVGM, Servei Veterinari de Genètica
Molecular, Universitat Autònoma de Barcelona, 08193,
Bellaterra, Barcelona, Spain
- Vetgenomics, Edifici EUREKA, Parc de Recerca de la
UAB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Anna Cuscó
- Vetgenomics, Edifici EUREKA, Parc de Recerca de la
UAB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Olga Francino
- SVGM, Servei Veterinari de Genètica
Molecular, Universitat Autònoma de Barcelona, 08193,
Bellaterra, Barcelona, Spain
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Wurzbacher C, Larsson E, Bengtsson-Palme J, Van den Wyngaert S, Svantesson S, Kristiansson E, Kagami M, Nilsson RH. Introducing ribosomal tandem repeat barcoding for fungi. Mol Ecol Resour 2018; 19:118-127. [PMID: 30240145 DOI: 10.1111/1755-0998.12944] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/29/2018] [Accepted: 09/07/2018] [Indexed: 01/19/2023]
Abstract
Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom in terms of both taxonomy and marker coverage in the reference sequence databases. To facilitate the integration of reference data from all of the ribosomal markers, we present three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats. The primers cover all ribosomal markers: ETS, SSU, ITS1, 5.8S, ITS2, LSU and IGS. We coupled these primers successfully with third-generation sequencing (PacBio and Nanopore sequencing) to showcase our approach on authentic fungal herbarium specimens (Basidiomycota), aquatic chytrids (Chytridiomycota) and a poorly understood lineage of early diverging fungi (Nephridiophagidae). In particular, we were able to generate high-quality reference data with Nanopore sequencing in a high-throughput manner, showing that the generation of reference data can be achieved on a regular desktop computer without the involvement of any large-scale sequencing facility. The quality of the Nanopore generated sequences was 99.85%, which is comparable with the 99.78% accuracy described for Sanger sequencing. With this work, we hope to stimulate the generation of a new comprehensive standard of ribosomal reference data with the ultimate aim to close the huge gaps in our reference datasets.
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Affiliation(s)
- Christian Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany.,Gothenburg Global Biodiversity Centre, Göteborg, Sweden
| | - Ellen Larsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Göteborg, Sweden
| | - Johan Bengtsson-Palme
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin.,Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | | | - Sten Svantesson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Göteborg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | - Maiko Kagami
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin, Stechlin, Germany.,Department of Environmental Science, Faculty of Science, Toho University, Funabashi, Japan.,Graduate School of Environment and Information Sciences, Yokohama National University, Hodogayaku, Yokohama, Japan
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Göteborg, Sweden
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Benítez-Páez A, Sanz Y. Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer. Gigascience 2018; 6:1-12. [PMID: 28605506 PMCID: PMC5534310 DOI: 10.1093/gigascience/gix043] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 06/09/2017] [Indexed: 02/07/2023] Open
Abstract
The miniaturized and portable DNA sequencer MinION™ has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION™ platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION™ device using R9 and R9.4 chemistries were sufficient to study 2 mock microbial communities in a multiplex manner and to almost completely reconstruct the microbial diversity contained in the HM782D and D6305 mock communities. Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, we presented a novel approach consisting of multi-locus and long amplicon sequencing using the MinION™ MkIb DNA sequencer and R9 and R9.4 chemistries that help to overcome the main disadvantage of this portable sequencing platform. Furthermore, the nanopore sequencing library, constructed with the last releases of pore chemistry (R9.4) and sequencing kit (SQK-LSK108), permitted the retrieval of the higher level of 1D read accuracy sufficient to characterize the microbial species present in each mock community analysed. Improvements in nanopore chemistry, such as minimizing base-calling errors and new library protocols able to produce rapid 1D libraries, will provide more reliable information in the near future. Such data will be useful for more comprehensive and faster specific detection of microbial species and strains in complex ecosystems.
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Affiliation(s)
- Alfonso Benítez-Páez
- Microbial Ecology, Nutrition and Health Research Unit. Institute of Agrochemistry and Food Technology (IATA-CSIC). C. Catedràtic Agustín Escardino Benlloch, 7. 46980 Paterna-Valencia, Spain
| | - Yolanda Sanz
- Microbial Ecology, Nutrition and Health Research Unit. Institute of Agrochemistry and Food Technology (IATA-CSIC). C. Catedràtic Agustín Escardino Benlloch, 7. 46980 Paterna-Valencia, Spain
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Malagon F. RNase III is required for localization to the nucleoid of the 5' pre-rRNA leader and for optimal induction of rRNA synthesis in E. coli. RNA 2013; 19:1200-7. [PMID: 23893733 PMCID: PMC3753927 DOI: 10.1261/rna.038588.113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/14/2013] [Indexed: 05/24/2023]
Abstract
It has recently been demonstrated that ribosomes are preferentially localized outside the nucleoid in Escherichia coli, but little is known about the spatial regulation of pre-rRNA processing. In this work, I investigate the cellular distribution of leader pre-rRNAs using RNA-FISH. In contrast to mature rRNA, the 5' proximal leader region associates with the nucleoid, and this association occurs in an RNase III-dependent manner. Moreover, RNase III plays a role in the rapid induction of ribosomal operons during outgrowth and is essential in the absence of the transcriptional regulator Fis, suggesting a linkage of transcription and RNA processing for ribosomal operons in E. coli.
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Affiliation(s)
- Francisco Malagon
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4264, USA.
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