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Cazabonne J, Walker AK, Lesven J, Haelewaters D. Singleton-based species names and fungal rarity: Does the number really matter? IMA Fungus 2024; 15:7. [PMID: 38504339 PMCID: PMC10953280 DOI: 10.1186/s43008-023-00137-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/13/2023] [Indexed: 03/21/2024] Open
Abstract
Fungi are among the least known organisms on earth, with an estimated number of species between 1.5 and 10 million. This number is expected to be refined, especially with increasing knowledge about microfungi in undersampled habitats and increasing amounts of data derived from environmental DNA sequencing. A significant proportion of newly generated sequences fail to match with already named species, and thus represent what has been referred to as fungal "dark taxa". Due to the challenges associated with observing, identifying, and preserving sporophores, many macro- and microfungal species are only known from a single collection, specimen, isolate, and/or sequence-a singleton. Mycologists are consequently used to working with "rare" sequences and specimens. However, rarity and singleton phenomena lack consideration and valorization in fungal studies. In particular, the practice of publishing new fungal species names based on a single specimen remains a cause of debate. Here, we provide some elements of reflection on this issue in the light of the specificities of the fungal kingdom and global change context. If multiple independent sources of data support the existence of a new taxon, we encourage mycologists to proceed with formal description, irrespective of the number of specimens at hand. Although the description of singleton-based species may not be considered best practice, it does represent responsible science in the light of closing the Linnean biodiversity shortfall.
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Affiliation(s)
- Jonathan Cazabonne
- Ecology Research Group of Abitibi RCM, Forest Research Institute, Université du Québec en Abitibi-Témiscamingue, Amos, QC, J9T 2L8, Canada.
- Centre for Forest Research, Université du Québec à Montréal, Montreal, QC, H3C 3P8, Canada.
| | - Allison K Walker
- Department of Biology, Acadia University, Wolfville, NS, B4P 2R6, Canada
| | - Jonathan Lesven
- Laboratoire Chrono-Environnement, UMR 6249 CNRS, Université de Bourgogne Franche-Comté, 25000, Besançon, France
- Forest Research Institute, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, J9X 5E4, Canada
| | - Danny Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, 9000, Ghent, Belgium.
- Faculty of Science, University of South Bohemia, 370 05, Ceske Budejovice, Czech Republic.
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, 80309, USA.
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic.
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Wei F, Wang D, Fan S, Shi J, Cai X, Li Y, Ma Y, Wen Y, Feng J. Complete Genome Sequence Resource for Xanthomonas fragariae Causing Crown Infection Pockets in Strawberry. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:170-173. [PMID: 34645282 DOI: 10.1094/mpmi-05-21-0123-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Xanthomonas fragariae is a global quarantine pathogen, which typically inflicts angular leaf spots. In the present study, we report a new 4.11-Mb high-quality genome sequence of X. fragariae YL19. YL19 can cause the typical angular leaf spot symptoms on strawberry plants in China as well as crown infection pocket symptoms. This new symptom has not been reported in other X. fragariae. Compared with typical X. fragariae strains, including PD885, NBC2815, PD5205, Fap21, and Fap29, the genome and plasmid in YL19 were smaller in size, lacking 109 coding genes, and have more carbohydrate-active enzyme and secondary metabolism genes. The YL19 genome ought to clarify the molecular mechanisms of genome evolution, host adaptation, and pathological process of X. fragariae and help improve strawberry management strategies.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Feng Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Danjuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Sihao Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Jiancheng Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Xiaolin Cai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Yulian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Yangyang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Yingqiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiayue Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
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Olagunju O, Mchunu N, Venter S, Guibert B, Durand N, Métayer I, Montet D, Ijabadeniyi O. Fungal contamination of food commodities in Durban, South Africa. J Food Saf 2018. [DOI: 10.1111/jfs.12515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Omotola Olagunju
- Faculty of Applied Sciences, Department of Biotechnology and Food TechnologyDurban University of Technology Durban South Africa
- Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementUMR Qualisud Montpellier France
| | - Nokuthula Mchunu
- Faculty of Applied Sciences, Department of Biotechnology and Food TechnologyDurban University of Technology Durban South Africa
| | - Sonja Venter
- Agricultural Research Council, Roodeplaat‐Vegetable and Ornamental Plant Institute Pretoria South Africa
| | - Benjamin Guibert
- Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementUMR Qualisud Montpellier France
| | - Noel Durand
- Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementUMR Qualisud Montpellier France
| | - Isabelle Métayer
- Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementUMR Qualisud Montpellier France
| | - Didier Montet
- Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementUMR Qualisud Montpellier France
| | - Oluwatosin Ijabadeniyi
- Faculty of Applied Sciences, Department of Biotechnology and Food TechnologyDurban University of Technology Durban South Africa
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Chan CL, Yew SM, Ngeow YF, Na SL, Lee KW, Hoh CC, Yee WY, Ng KP. Genome analysis of Daldinia eschscholtzii strains UM 1400 and UM 1020, wood-decaying fungi isolated from human hosts. BMC Genomics 2015; 16:966. [PMID: 26581579 PMCID: PMC4650942 DOI: 10.1186/s12864-015-2200-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/10/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Daldinia eschscholtzii is a wood-inhabiting fungus that causes wood decay under certain conditions. It has a broad host range and produces a large repertoire of potentially bioactive compounds. However, there is no extensive genome analysis on this fungal species. RESULTS Two fungal isolates (UM 1400 and UM 1020) from human specimens were identified as Daldinia eschscholtzii by morphological features and ITS-based phylogenetic analysis. Both genomes were similar in size with 10,822 predicted genes in UM 1400 (35.8 Mb) and 11,120 predicted genes in UM 1020 (35.5 Mb). A total of 751 gene families were shared among both UM isolates, including gene families associated with fungus-host interactions. In the CAZyme comparative analysis, both genomes were found to contain arrays of CAZyme related to plant cell wall degradation. Genes encoding secreted peptidases were found in the genomes, which encode for the peptidases involved in the degradation of structural proteins in plant cell wall. In addition, arrays of secondary metabolite backbone genes were identified in both genomes, indicating of their potential to produce bioactive secondary metabolites. Both genomes also contained an abundance of gene encoding signaling components, with three proposed MAPK cascades involved in cell wall integrity, osmoregulation, and mating/filamentation. Besides genomic evidence for degrading capability, both isolates also harbored an array of genes encoding stress response proteins that are potentially significant for adaptation to living in the hostile environments. CONCLUSIONS Our genomic studies provide further information for the biological understanding of the D. eschscholtzii and suggest that these wood-decaying fungi are also equipped for adaptation to adverse environments in the human host.
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Affiliation(s)
- Chai Ling Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Su Mei Yew
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yun Fong Ngeow
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, University Tunku Abdul Rahman, Bandar Sungai Long, 43000, Kajang, Selangor Darul Ehsan, Malaysia.
| | - Shiang Ling Na
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kok Wei Lee
- Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, Seri Kembangan, 43200, Selangor Darul Ehsan, Malaysia.
| | - Chee-Choong Hoh
- Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, Seri Kembangan, 43200, Selangor Darul Ehsan, Malaysia.
| | - Wai-Yan Yee
- Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, Seri Kembangan, 43200, Selangor Darul Ehsan, Malaysia.
| | - Kee Peng Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Kuan CS, Yew SM, Toh YF, Chan CL, Ngeow YF, Lee KW, Na SL, Yee WY, Hoh CC, Ng KP. Dissecting the fungal biology of Bipolaris papendorfii: from phylogenetic to comparative genomic analysis. DNA Res 2015; 22:219-32. [PMID: 25922537 PMCID: PMC4463846 DOI: 10.1093/dnares/dsv007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/28/2015] [Indexed: 01/21/2023] Open
Abstract
Bipolaris papendorfii has been reported as a fungal plant pathogen that rarely causes opportunistic infection in humans. Secondary metabolites isolated from this fungus possess medicinal and anticancer properties. However, its genetic fundamental and basic biology are largely unknown. In this study, we report the first draft genome sequence of B. papendorfii UM 226 isolated from the skin scraping of a patient. The assembled 33.4 Mb genome encodes 11,015 putative coding DNA sequences, of which, 2.49% are predicted transposable elements. Multilocus phylogenetic and phylogenomic analyses showed B. papendorfii UM 226 clustering with Curvularia species, apart from other plant pathogenic Bipolaris species. Its genomic features suggest that it is a heterothallic fungus with a putative unique gene encoding the LysM-containing protein which might be involved in fungal virulence on host plants, as well as a wide array of enzymes involved in carbohydrate metabolism, degradation of polysaccharides and lignin in the plant cell wall, secondary metabolite biosynthesis (including dimethylallyl tryptophan synthase, non-ribosomal peptide synthetase, polyketide synthase), the terpenoid pathway and the caffeine metabolism. This first genomic characterization of B. papendorfii provides the basis for further studies on its biology, pathogenicity and medicinal potential.
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Affiliation(s)
- Chee Sian Kuan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Su Mei Yew
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yue Fen Toh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Chai Ling Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yun Fong Ngeow
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Kok Wei Lee
- Codon Genomics SB, Jalan Bandar Lapan Belas, Selangor Darul Ehsan 47160, Malaysia
| | - Shiang Ling Na
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Wai-Yan Yee
- Codon Genomics SB, Jalan Bandar Lapan Belas, Selangor Darul Ehsan 47160, Malaysia
| | - Chee-Choong Hoh
- Codon Genomics SB, Jalan Bandar Lapan Belas, Selangor Darul Ehsan 47160, Malaysia
| | - Kee Peng Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
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Patulin assessment and fungi identification in organic and conventional fruits and derived products. Food Control 2014. [DOI: 10.1016/j.foodcont.2014.03.043] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lago M, Aguiar A, Natário A, Fernandes C, Faria M, Pinto E. Does fungicide application in vineyards induce resistance to medical azoles in Aspergillus species? ENVIRONMENTAL MONITORING AND ASSESSMENT 2014; 186:5581-5593. [PMID: 24833021 DOI: 10.1007/s10661-014-3804-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 04/30/2014] [Indexed: 06/03/2023]
Abstract
This study assessed if the use of sterol demethylase inhibitor fungicides in vineyard production can induce resistance to azoles in Aspergillus strains and if it can induce selection of resistant species. We also tried to identify the Aspergillus species most prevalent in the vineyards. Two vineyards from northern Portugal were selected from "Vinhos Verdes" and "Douro" regions. The vineyards were divided into plots that were treated or not with penconazole (PEN). In each vineyard, air, soil, and plant samples were collected at three different times. The strains of Aspergillus spp. were isolated and identified by morphological and molecular techniques. We identified 46 Aspergillus section Nigri, eight Aspergillus fumigatus, seven Aspergillus lentulus, four Aspergillus wentii, two Aspergillus flavus, two Aspergillus terreus, one Aspergillus calidoustus, one Aspergillus westerdijkiae, one Aspergillus tamarii, and one Eurotium amstelodami. Aspergillus strains were evaluated for their susceptibility to medical azoles used in human therapy (itraconazole, posaconazole, and voriconazole) and to agricultural azoles (PEN) used in the prevention and treatment of plant diseases. The isolates showed moderate susceptibility to voriconazole. We did not observe any decrease of susceptibility to the medical azoles tested throughout the testing period in any of the treated plots, although some of the resistant species were isolated from there.
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Affiliation(s)
- Magali Lago
- CEQUIMED-UP/Serviço de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
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Kotikalapudi R, Patel RK, Katragadda S. Standardization of DNA extraction from methanol acetic acid fixed cytogenetic cells of cattle and buffalo. Pak J Biol Sci 2013; 16:1823-5. [PMID: 24506057 DOI: 10.3923/pjbs.2013.1823.1825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aim of the study is to standardize the simple method for extracting DNA from cells fixed in fixative (3:1 ratio of methanol and acetic acid glacial) mostly used for chromosomal studies in cattle and buffaloes. These fixed cells were stored for more than 6 months at refrigerated temperature. The fixed cells were washed 2-3 times by the ice cold 1x Phosphate Buffer Saline (PBS) with pH 7.4, so that effect of fixative may be eliminated. The genomic DNA was extracted by adding cell lysis and nucleus lysis buffers. The quality and quantity of DNA were estimated. The readings of nano drop and agarose gel electrophoresis indicate good quality DNA isolated with a rapid and simple protocol routinely using in our laboratory. The method enables us to study the DNA of a cattle and buffaloes after completing cytogenetic investigation or in cases where DNA samples are otherwise not available. This protocol may be useful for molecular analysis of DNA from fixed cells palettes.
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Affiliation(s)
| | - Rajesh K Patel
- Sandor Proteomics Pvt. Ltd., Banjara Hills, Hyderabad-500 034, India
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Involvement of an efflux transporter in prochloraz resistance of Fusarium fujikuroi CF245 causing rice bakanae disease. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s13765-012-2126-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Alatar AA, Mahmoud MA, Al-Sohaibani SA, Abd-Elsalam KA. Simple and rapid protocol for the isolation of PCR-amplifiable DNA from medicinal plants. GENETICS AND MOLECULAR RESEARCH 2012; 11:348-54. [PMID: 22370937 DOI: 10.4238/2012.february.13.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Medicinal plant species has a valuable economic importance because of its usage as pharmaceuticals, nutritional, as well as its use in popular medication. For DNA-based techniques, nanogram quantities of the purified DNA are requisite to amplify and yield sufficient amounts of PCR products. SDS-based DNA isolation method was used to extract DNA from 11 species of different aromatic and medicinal plants collected from Saudi Arabia. Three hundred milligrams of fresh shredded plant material was necessary. The DNA purity was further confirmed by agarose gel, restriction endonuclease digestion and microsatellite primed-polymerase chain reaction (MP-PCR). DNA yields ranged from 10-20 μg (in 100-μL elution volumes) from all plant material evaluated. The DNA obtained was free of any contaminating proteins, polysaccharides and colored pigments. The extracted genomic DNA was found suitable for restriction digestion and PCR amplification. Our experimental procedure provides an easy, suitable, non-toxic, cheap, and quick process for the amplification of DNA from medical plant tissue.
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Affiliation(s)
- A A Alatar
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
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An optimized protocol for DNA extraction from wheat seeds and Loop-Mediated Isothermal Amplification (LAMP) to detect Fusarium graminearum contamination of wheat grain. Int J Mol Sci 2011; 12:3459-72. [PMID: 21747688 PMCID: PMC3131572 DOI: 10.3390/ijms12063459] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 04/28/2011] [Accepted: 05/18/2011] [Indexed: 01/14/2023] Open
Abstract
A simple, rapid, and efficient method for isolating genomic DNA from germinated seeds of wheat that is free from polysaccharides and polyphenols is reported. DNA was extracted, treated with RNase, measured and tested for completeness using agarose gel electrophoresis. DNA purification from wheat grains yielded abundant, amplifiable DNA with yields typically between 100 and 200 ng DNA/mg. The effectiveness and reliability of the method was tested by assessing quantity and quality of the isolated DNA using three PCR-based markers. Inter-simple sequence repeats (ISSRs) were used to assess the genetic diversity between different wheat varieties. Specific PCR primer pair Tox5-1/Tox5-2 and a loop-mediated isothermal amplification (LAMP) procedure were used to detect genomic DNA of Fusarium graminearum in contaminated wheat seeds. In this method there is no need to use liquid nitrogen for crushing germinated seedlings. The protocol takes approximately one hour to prepare high quality DNA. In combination with the LAMP assay it is a fast and cost-effective alternative to traditional diagnostic methods for the early detection of toxigenic fusaria in cereals.
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