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Yang S, Qiao J, Zhang M, Kwok LY, Matijašić BB, Zhang H, Zhang W. Prevention and treatment of antibiotics-associated adverse effects through the use of probiotics: A review. J Adv Res 2024:S2090-1232(24)00230-3. [PMID: 38844120 DOI: 10.1016/j.jare.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/18/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND The human gut hosts a diverse microbial community, essential for maintaining overall health. However, antibiotics, commonly prescribed for infections, can disrupt this delicate balance, leading to antibiotic-associated diarrhea, inflammatory bowel disease, obesity, and even neurological disorders. Recognizing this, probiotics have emerged as a promising strategy to counteract these adverse effects. AIM OF REVIEW This review aims to offer a comprehensive overview of the latest evidence concerning the utilization of probiotics in managing antibiotic-associated side effects. KEY SCIENTIFIC CONCEPTS OF REVIEW Probiotics play a crucial role in preserving gut homeostasis, regulating intestinal function and metabolism, and modulating the host immune system. These mechanisms serve to effectively alleviate antibiotic-associated adverse effects and enhance overall well-being.
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Affiliation(s)
- Shuwei Yang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Jiaqi Qiao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Meng Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | | | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China.
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2
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Prescott TAK, Hill R, Mas-Claret E, Gaya E, Burns E. Fungal Drug Discovery for Chronic Disease: History, New Discoveries and New Approaches. Biomolecules 2023; 13:986. [PMID: 37371566 DOI: 10.3390/biom13060986] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Fungal-derived drugs include some of the most important medicines ever discovered, and have proved pivotal in treating chronic diseases. Not only have they saved millions of lives, but they have in some cases changed perceptions of what is medically possible. However, now the low-hanging fruit have been discovered it has become much harder to make the kind of discoveries that have characterised past eras of fungal drug discovery. This may be about to change with new commercial players entering the market aiming to apply novel genomic tools to streamline the discovery process. This review examines the discovery history of approved fungal-derived drugs, and those currently in clinical trials for chronic diseases. For key molecules, we discuss their possible ecological functions in nature and how this relates to their use in human medicine. We show how the conservation of drug receptors between fungi and humans means that metabolites intended to inhibit competitor fungi often interact with human drug receptors, sometimes with unintended benefits. We also plot the distribution of drugs, antimicrobial compounds and psychoactive mushrooms onto a fungal tree and compare their distribution to those of all fungal metabolites. Finally, we examine the phenomenon of self-resistance and how this can be used to help predict metabolite mechanism of action and aid the drug discovery process.
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Affiliation(s)
| | - Rowena Hill
- Earlham Institute, Norwich NR4 7UZ, Norfolk, UK
| | | | - Ester Gaya
- Royal Botanic Gardens, Kew, Richmond TW9 3AB, Surrey, UK
| | - Edie Burns
- Royal Botanic Gardens, Kew, Richmond TW9 3AB, Surrey, UK
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3
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Segers FJ, Dijksterhuis J, Giesbers M, Debets AJ. Natural folding of airborne fungal spores: a mechanism for dispersal and long-term survival? FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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van den Brule T, Punt M, Seekles SJ, Segers FJ, Houbraken J, Hazeleger WC, Ram AF, Wösten HA, Zwietering MH, Dijksterhuis J, den Besten HM. Intraspecific variability in heat resistance of fungal conidia. Food Res Int 2022; 156:111302. [DOI: 10.1016/j.foodres.2022.111302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 11/29/2022]
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5
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Dunn RR, Burger JR, Carlen EJ, Koltz AM, Light JE, Martin RA, Munshi-South J, Nichols LM, Vargo EL, Yitbarek S, Zhao Y, Cibrián-Jaramillo A. A Theory of City Biogeography and the Origin of Urban Species. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.761449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many of the choices humans make with regard to infrastructure, urban planning and other phenomena have impacts that will last thousands of years. This can readily be seen in modern cities in which contemporary streets run along street grids that were laid out thousands of years prior or even in which ancient viaducts still play a role. However, rarely do evolutionary biologists explicitly consider the future of life likely to be associated with the decisions we are making today. Here, we consider the evolutionary future of species in cities with a focus on the origin of lineages and species. We do so by adjusting evolutionary predictions from the theory of island biogeography so as to correspond to the unique features of cities as islands. Specifically, the species endemic to cities tend to be associated with the gray habitats in cities. Those habitats tend to be dominated by human bodies, pet bodies and stored food. It is among such species where the origin of new lineages is most likely, although most research on evolution in cities has focused on green habitats. We conclude by considering a range of scenarios for the far future and their implications for the origin of lineages and species.
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6
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Fierro F, Vaca I, Castillo NI, García-Rico RO, Chávez R. Penicillium chrysogenum, a Vintage Model with a Cutting-Edge Profile in Biotechnology. Microorganisms 2022; 10:573. [PMID: 35336148 PMCID: PMC8954384 DOI: 10.3390/microorganisms10030573] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/20/2022] Open
Abstract
The discovery of penicillin entailed a decisive breakthrough in medicine. No other medical advance has ever had the same impact in the clinical practise. The fungus Penicillium chrysogenum (reclassified as P. rubens) has been used for industrial production of penicillin ever since the forties of the past century; industrial biotechnology developed hand in hand with it, and currently P. chrysogenum is a thoroughly studied model for secondary metabolite production and regulation. In addition to its role as penicillin producer, recent synthetic biology advances have put P. chrysogenum on the path to become a cell factory for the production of metabolites with biotechnological interest. In this review, we tell the history of P. chrysogenum, from the discovery of penicillin and the first isolation of strains with high production capacity to the most recent research advances with the fungus. We will describe how classical strain improvement programs achieved the goal of increasing production and how the development of different molecular tools allowed further improvements. The discovery of the penicillin gene cluster, the origin of the penicillin genes, the regulation of penicillin production, and a compilation of other P. chrysogenum secondary metabolites will also be covered and updated in this work.
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Affiliation(s)
- Francisco Fierro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Unidad Iztapalapa, Ciudad de México 09340, Mexico
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Nancy I. Castillo
- Grupo de Investigación en Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá 110231, Colombia;
| | - Ramón Ovidio García-Rico
- Grupo de Investigación GIMBIO, Departamento De Microbiología, Facultad de Ciencias Básicas, Universidad de Pamplona, Pamplona 543050, Colombia;
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170020, Chile;
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7
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Shama G. Uninvited Guests: a Chronology of Petri Dish Contaminations. ADVANCES IN APPLIED MICROBIOLOGY 2021; 116:169-200. [PMID: 34353504 DOI: 10.1016/bs.aambs.2021.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Petri dish contaminations are commonplace and personally witnessed by every microbiologist. The vast majority of such contaminations result in nothing more than annoyance following which the Petri dishes are discarded. However, a handful of incidents of contaminations have led to momentous outcomes, the most renowned of which being that perceived by Alexander Fleming on the basis of the immense number of lives saved by penicillin. Petri dish contaminations as reported upon in the literature fall broadly into two categories; those in which the contaminant caused antagonism toward the species being cultured, and those in which the contaminant was established to be a species novum. Accounts of both of these categories of contaminations are set out here.
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Affiliation(s)
- Gilbert Shama
- Department of Chemical Engineering, Loughborough University, Loughborough, United Kingdom.
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8
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Hernández-Hernández T, Miller EC, Román-Palacios C, Wiens JJ. Speciation across the Tree of Life. Biol Rev Camb Philos Soc 2021; 96:1205-1242. [PMID: 33768723 DOI: 10.1111/brv.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.
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Affiliation(s)
- Tania Hernández-Hernández
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A.,Catedrática CONACYT asignada a LANGEBIO-UGA Cinvestav, Libramiento Norte Carretera León Km 9.6, 36821, Irapuato, Guanajuato, Mexico
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
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9
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Pathak A, Nowell RW, Wilson CG, Ryan MJ, Barraclough TG. Comparative genomics of Alexander Fleming's original Penicillium isolate (IMI 15378) reveals sequence divergence of penicillin synthesis genes. Sci Rep 2020; 10:15705. [PMID: 32973216 PMCID: PMC7515868 DOI: 10.1038/s41598-020-72584-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 09/03/2020] [Indexed: 11/18/2022] Open
Abstract
Antibiotics were derived originally from wild organisms and therefore understanding how these compounds evolve among different lineages might help with the design of new antimicrobial drugs. We report the draft genome sequence of Alexander Fleming's original fungal isolate behind the discovery of penicillin, now classified as Penicillium rubens Biourge (1923) (IMI 15378). We compare the structure of the genome and genes involved in penicillin synthesis with those in two 'high producing' industrial strains of P. rubens and the closely related species P. nalgiovense. The main effector genes for producing penicillin G (pcbAB, pcbC and penDE) show amino acid divergence between the Fleming strain and both industrial strains, whereas a suite of regulatory genes are conserved. Homologs of penicillin N effector genes cefD1 and cefD2 were also found and the latter displayed amino acid divergence between the Fleming strain and industrial strains. The draft assemblies contain several partial duplications of penicillin-pathway genes in all three P. rubens strains, to differing degrees, which we hypothesise might be involved in regulation of the pathway. The two industrial strains are identical in sequence across all effector and regulatory genes but differ in duplication of the pcbAB-pcbC-penDE complex and partial duplication of fragments of regulatory genes. We conclude that evolution in the wild encompassed both sequence changes of the effector genes and gene duplication, whereas human-mediated changes through mutagenesis and artificial selection led to duplication of the penicillin pathway genes.
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Affiliation(s)
- Ayush Pathak
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK
| | - Reuben W Nowell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK
| | - Christopher G Wilson
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK
| | | | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK.
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK.
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10
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Mahmoudjanlou Y, Dahlmann TA, Kück U. Molecular analysis of mating type loci from the mycophenolic acid producer Penicillium brevicompactum: Phylogeny and MAT protein characterization suggest a cryptic sexual life cycle. Fungal Biol 2020; 124:821-833. [PMID: 32883432 DOI: 10.1016/j.funbio.2020.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
The mycophenolic acid producing ascomycete Penicillium brevicompactum is considered to be an anamorphic (asexual) species, for which a sexual cycle was never observed. However, since recent reports of otherwise asexually propagating filamentous fungi have demonstrated a sexual cycle controlled by mating type loci, we carried out a molecular analysis of mating type loci from P. brevicompactum. Using data from extensive DNA sequencing analysis, we determined the mating type loci from 22 strains derived from various type culture collections. We found 8 strains carrying a MAT1-1 locus encoding a 362 amino acid alpha domain transcription factor. The other 14 possessed a MAT1-2 locus encoding a 298 amino acid HMG domain transcription factor. cDNA analysis confirmed that both mating type loci are transcriptionally expressed. The karyotype of six selected strains, determined using contour-clamped homogeneous electric field (CHEF) electrophoresis, demonstrated distinct differences in size and numbers of chromosomes between the strains investigated. Interestingly, our phylogenetic survey of 72 strains from 11 different Penicillium species revealed that MAT genes serve as excellent molecular markers to determine phylogenetic relationships among species closely related to P. brevicompactum. Based on our sequencing results, we constructed transformation vectors for site-specific deletion of mating type loci from two selected strains of opposite mating type. Complementation strains were constructed containing both the mating type locus deletion cassette and a MAT-egfp fusion gene. These strains were used for comparative phenotypic analyses between strains containing or lacking the mating type gene. Whereas all MAT1-2 strains were indistinguishable, the MAT1-1 and MAT1-1-1 deletion strains differed distinctly. The MAT1-1-1 deletion strain produced more conidiospores on solid media, but smaller pellets in liquid media. This is probably the consequence of fewer conidial germ tubes than with the wild type mating type strain. Finally, we showed that the MAT-EGPF fusion protein is localized to the nuclei and detectable in protein samples by Western analysis. Together, our results suggest that the asexually propagating fungus P. brevicompactum might be a heterothallic species with a cryptic sexual life cycle.
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Affiliation(s)
| | - Tim A Dahlmann
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Ulrich Kück
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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11
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Martín JF. Insight into the Genome of Diverse Penicillium chrysogenum Strains: Specific Genes, Cluster Duplications and DNA Fragment Translocations. Int J Mol Sci 2020; 21:E3936. [PMID: 32486280 PMCID: PMC7312703 DOI: 10.3390/ijms21113936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND There are eighteen species within the Penicillium genus section chrysogena, including the original penicillin producers Penicillium notatum (Fleming strain) and Penicillium chrysogenum NRRL 1951. Other wild type isolates of the Penicillium genus are relevant for the production of useful proteins and primary or secondary metabolites. The aim of this article is to characterize strain specific genes and those genes which are involved in secondary metabolite biosynthesis, particularly the mutations that have been introduced during the β-lactams strain improvement programs. RESULTS The available genomes of several classical and novel P. chrysogenum strains have been compared. The first genome sequenced was that of the reference strain P. chrysogenum Wis54-1255, which derives from the wild type P. chrysogenum NRRL 1951; its genome size is 32.19 Mb and it encodes 12,943 proteins. Four chromosomes were resolved in P. chrysogenum and P. notatum by pulse field gel electrophoresis. The genomes of three industrial strains have a similar size but contain gene duplications and truncations; the penicillin gene cluster copy number ranges from one in the wild type to twelve in the P. chrysogenum ASP-E1 industrial strain and is organized in head to tail tandem repeats. The genomes of two new strains, P. chrysogenum KF-25, a producer of antifungal proteins isolated from a soil sample, and P. chrysogenum HKF2, a strain with carbohydrate-converting activities isolated from a sludge treatment plant, showed strain specific genes. CONCLUSIONS The overall comparison of all available P. chrysogenum genomes indicates that there are a significant number of strain-specific genes, mutations of structural and regulatory genes, gene cluster duplications and DNA fragment translocations. This information provides important leads to improve the biosynthesis of enzymes, antifungal agents, prebiotics or different types of secondary metabolites.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
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12
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Houbraken J, Kocsubé S, Visagie C, Yilmaz N, Wang XC, Meijer M, Kraak B, Hubka V, Bensch K, Samson R, Frisvad J. Classification of Aspergillus, Penicillium, Talaromyces and related genera ( Eurotiales): An overview of families, genera, subgenera, sections, series and species. Stud Mycol 2020; 95:5-169. [PMID: 32855739 PMCID: PMC7426331 DOI: 10.1016/j.simyco.2020.05.002] [Citation(s) in RCA: 264] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Eurotiales is a relatively large order of Ascomycetes with members frequently having positive and negative impact on human activities. Species within this order gain attention from various research fields such as food, indoor and medical mycology and biotechnology. In this article we give an overview of families and genera present in the Eurotiales and introduce an updated subgeneric, sectional and series classification for Aspergillus and Penicillium. Finally, a comprehensive list of accepted species in the Eurotiales is given. The classification of the Eurotiales at family and genus level is traditionally based on phenotypic characters, and this classification has since been challenged using sequence-based approaches. Here, we re-evaluated the relationships between families and genera of the Eurotiales using a nine-gene sequence dataset. Based on this analysis, the new family Penicillaginaceae is introduced and four known families are accepted: Aspergillaceae, Elaphomycetaceae, Thermoascaceae and Trichocomaceae. The Eurotiales includes 28 genera: 15 genera are accommodated in the Aspergillaceae (Aspergillago, Aspergillus, Evansstolkia, Hamigera, Leiothecium, Monascus, Penicilliopsis, Penicillium, Phialomyces, Pseudohamigera, Pseudopenicillium, Sclerocleista, Warcupiella, Xerochrysium and Xeromyces), eight in the Trichocomaceae (Acidotalaromyces, Ascospirella, Dendrosphaera, Rasamsonia, Sagenomella, Talaromyces, Thermomyces, Trichocoma), two in the Thermoascaceae (Paecilomyces, Thermoascus) and one in the Penicillaginaceae (Penicillago). The classification of the Elaphomycetaceae was not part of this study, but according to literature two genera are present in this family (Elaphomyces and Pseudotulostoma). The use of an infrageneric classification system has a long tradition in Aspergillus and Penicillium. Most recent taxonomic studies focused on the sectional level, resulting in a well-established sectional classification in these genera. In contrast, a series classification in Aspergillus and Penicillium is often outdated or lacking, but is still relevant, e.g., the allocation of a species to a series can be highly predictive in what functional characters the species might have and might be useful when using a phenotype-based identification. The majority of the series in Aspergillus and Penicillium are invalidly described and here we introduce a new series classification. Using a phylogenetic approach, often supported by phenotypic, physiologic and/or extrolite data, Aspergillus is subdivided in six subgenera, 27 sections (five new) and 75 series (73 new, one new combination), and Penicillium in two subgenera, 32 sections (seven new) and 89 series (57 new, six new combinations). Correct identification of species belonging to the Eurotiales is difficult, but crucial, as the species name is the linking pin to information. Lists of accepted species are a helpful aid for researchers to obtain a correct identification using the current taxonomic schemes. In the most recent list from 2014, 339 Aspergillus, 354 Penicillium and 88 Talaromyces species were accepted. These numbers increased significantly, and the current list includes 446 Aspergillus (32 % increase), 483 Penicillium (36 % increase) and 171 Talaromyces (94 % increase) species, showing the large diversity and high interest in these genera. We expanded this list with all genera and species belonging to the Eurotiales (except those belonging to Elaphomycetaceae). The list includes 1 187 species, distributed over 27 genera, and contains MycoBank numbers, collection numbers of type and ex-type cultures, subgenus, section and series classification data, information on the mode of reproduction, and GenBank accession numbers of ITS, beta-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) gene sequences.
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Key Words
- Acidotalaromyces Houbraken, Frisvad & Samson
- Acidotalaromyces lignorum (Stolk) Houbraken, Frisvad & Samson
- Ascospirella Houbraken, Frisvad & Samson
- Ascospirella lutea (Zukal) Houbraken, Frisvad & Samson
- Aspergillus chaetosartoryae Hubka, Kocsubé & Houbraken
- Classification
- Evansstolkia Houbraken, Frisvad & Samson
- Evansstolkia leycettana (H.C. Evans & Stolk) Houbraken, Frisvad & Samson
- Hamigera brevicompacta (H.Z. Kong) Houbraken, Frisvad & Samson
- Infrageneric classification
- New combinations, series
- New combinations, species
- New genera
- New names
- New sections
- New series
- New taxa
- Nomenclature
- Paecilomyces lagunculariae (C. Ram) Houbraken, Frisvad & Samson
- Penicillaginaceae Houbraken, Frisvad & Samson
- Penicillago kabunica (Baghd.) Houbraken, Frisvad & Samson
- Penicillago mirabilis (Beliakova & Milko) Houbraken, Frisvad & Samson
- Penicillago moldavica (Milko & Beliakova) Houbraken, Frisvad & Samson
- Phialomyces arenicola (Chalab.) Houbraken, Frisvad & Samson
- Phialomyces humicoloides (Bills & Heredia) Houbraken, Frisvad & Samson
- Phylogeny
- Polythetic classes
- Pseudohamigera Houbraken, Frisvad & Samson
- Pseudohamigera striata (Raper & Fennell) Houbraken, Frisvad & Samson
- Talaromyces resinae (Z.T. Qi & H.Z. Kong) Houbraken & X.C. Wang
- Talaromyces striatoconidius Houbraken, Frisvad & Samson
- Taxonomic novelties: New family
- Thermoascus verrucosus (Samson & Tansey) Houbraken, Frisvad & Samson
- Thermoascus yaguchii Houbraken, Frisvad & Samson
- in Aspergillus: sect. Bispori S.W. Peterson, Varga, Frisvad, Samson ex Houbraken
- in Aspergillus: ser. Acidohumorum Houbraken & Frisvad
- in Aspergillus: ser. Inflati (Stolk & Samson) Houbraken & Frisvad
- in Penicillium: sect. Alfrediorum Houbraken & Frisvad
- in Penicillium: ser. Adametziorum Houbraken & Frisvad
- in Penicillium: ser. Alutacea (Pitt) Houbraken & Frisvad
- sect. Crypta Houbraken & Frisvad
- sect. Eremophila Houbraken & Frisvad
- sect. Formosana Houbraken & Frisvad
- sect. Griseola Houbraken & Frisvad
- sect. Inusitata Houbraken & Frisvad
- sect. Lasseniorum Houbraken & Frisvad
- sect. Polypaecilum Houbraken & Frisvad
- sect. Raperorum S.W. Peterson, Varga, Frisvad, Samson ex Houbraken
- sect. Silvatici S.W. Peterson, Varga, Frisvad, Samson ex Houbraken
- sect. Vargarum Houbraken & Frisvad
- ser. Alliacei Houbraken & Frisvad
- ser. Ambigui Houbraken & Frisvad
- ser. Angustiporcata Houbraken & Frisvad
- ser. Arxiorum Houbraken & Frisvad
- ser. Atramentosa Houbraken & Frisvad
- ser. Aurantiobrunnei Houbraken & Frisvad
- ser. Avenacei Houbraken & Frisvad
- ser. Bertholletiarum Houbraken & Frisvad
- ser. Biplani Houbraken & Frisvad
- ser. Brevicompacta Houbraken & Frisvad
- ser. Brevipedes Houbraken & Frisvad
- ser. Brunneouniseriati Houbraken & Frisvad
- ser. Buchwaldiorum Houbraken & Frisvad
- ser. Calidousti Houbraken & Frisvad
- ser. Canini Houbraken & Frisvad
- ser. Carbonarii Houbraken & Frisvad
- ser. Cavernicolarum Houbraken & Frisvad
- ser. Cervini Houbraken & Frisvad
- ser. Chevalierorum Houbraken & Frisvad
- ser. Cinnamopurpurea Houbraken & Frisvad
- ser. Circumdati Houbraken & Frisvad
- ser. Clavigera Houbraken & Frisvad
- ser. Conjuncti Houbraken & Frisvad
- ser. Copticolarum Houbraken & Frisvad
- ser. Coremiiformes Houbraken & Frisvad
- ser. Corylophila Houbraken & Frisvad
- ser. Costaricensia Houbraken & Frisvad
- ser. Cremei Houbraken & Frisvad
- ser. Crustacea (Pitt) Houbraken & Frisvad
- ser. Dalearum Houbraken & Frisvad
- ser. Deflecti Houbraken & Frisvad
- ser. Egyptiaci Houbraken & Frisvad
- ser. Erubescentia (Pitt) Houbraken & Frisvad
- ser. Estinogena Houbraken & Frisvad
- ser. Euglauca Houbraken & Frisvad
- ser. Fennelliarum Houbraken & Frisvad
- ser. Flavi Houbraken & Frisvad
- ser. Flavipedes Houbraken & Frisvad
- ser. Fortuita Houbraken & Frisvad
- ser. Fumigati Houbraken & Frisvad
- ser. Funiculosi Houbraken & Frisvad
- ser. Gallaica Houbraken & Frisvad
- ser. Georgiensia Houbraken & Frisvad
- ser. Goetziorum Houbraken & Frisvad
- ser. Gracilenta Houbraken & Frisvad
- ser. Halophilici Houbraken & Frisvad
- ser. Herqueorum Houbraken & Frisvad
- ser. Heteromorphi Houbraken & Frisvad
- ser. Hoeksiorum Houbraken & Frisvad
- ser. Homomorphi Houbraken & Frisvad
- ser. Idahoensia Houbraken & Frisvad
- ser. Implicati Houbraken & Frisvad
- ser. Improvisa Houbraken & Frisvad
- ser. Indica Houbraken & Frisvad
- ser. Japonici Houbraken & Frisvad
- ser. Jiangxiensia Houbraken & Frisvad
- ser. Kalimarum Houbraken & Frisvad
- ser. Kiamaensia Houbraken & Frisvad
- ser. Kitamyces Houbraken & Frisvad
- ser. Lapidosa (Pitt) Houbraken & Frisvad
- ser. Leporum Houbraken & Frisvad
- ser. Leucocarpi Houbraken & Frisvad
- ser. Livida Houbraken & Frisvad
- ser. Longicatenata Houbraken & Frisvad
- ser. Macrosclerotiorum Houbraken & Frisvad
- ser. Monodiorum Houbraken & Frisvad
- ser. Multicolores Houbraken & Frisvad
- ser. Neoglabri Houbraken & Frisvad
- ser. Neonivei Houbraken & Frisvad
- ser. Nidulantes Houbraken & Frisvad
- ser. Nigri Houbraken & Frisvad
- ser. Nivei Houbraken & Frisvad
- ser. Nodula Houbraken & Frisvad
- ser. Nomiarum Houbraken & Frisvad
- ser. Noonimiarum Houbraken & Frisvad
- ser. Ochraceorosei Houbraken & Frisvad
- ser. Olivimuriarum Houbraken & Frisvad
- ser. Osmophila Houbraken & Frisvad
- ser. Paradoxa Houbraken & Frisvad
- ser. Paxillorum Houbraken & Frisvad
- ser. Penicillioides Houbraken & Frisvad
- ser. Phoenicea Houbraken & Frisvad
- ser. Pinetorum (Pitt) Houbraken & Frisvad
- ser. Polypaecilum Houbraken & Frisvad
- ser. Pulvini Houbraken & Frisvad
- ser. Quercetorum Houbraken & Frisvad
- ser. Raistrickiorum Houbraken & Frisvad
- ser. Ramigena Houbraken & Frisvad
- ser. Restricti Houbraken & Frisvad
- ser. Robsamsonia Houbraken & Frisvad
- ser. Rolfsiorum Houbraken & Frisvad
- ser. Roseopurpurea Houbraken & Frisvad
- ser. Rubri Houbraken & Frisvad
- ser. Salinarum Houbraken & Frisvad
- ser. Samsoniorum Houbraken & Frisvad
- ser. Saturniformia Houbraken & Frisvad
- ser. Scabrosa Houbraken & Frisvad
- ser. Sclerotigena Houbraken & Frisvad
- ser. Sclerotiorum Houbraken & Frisvad
- ser. Sheariorum Houbraken & Frisvad
- ser. Simplicissima Houbraken & Frisvad
- ser. Soppiorum Houbraken & Frisvad
- ser. Sparsi Houbraken & Frisvad
- ser. Spathulati Houbraken & Frisvad
- ser. Spelaei Houbraken & Frisvad
- ser. Speluncei Houbraken & Frisvad
- ser. Spinulosa Houbraken & Frisvad
- ser. Stellati Houbraken & Frisvad
- ser. Steyniorum Houbraken & Frisvad
- ser. Sublectatica Houbraken & Frisvad
- ser. Sumatraensia Houbraken & Frisvad
- ser. Tamarindosolorum Houbraken & Frisvad
- ser. Teporium Houbraken & Frisvad
- ser. Terrei Houbraken & Frisvad
- ser. Thermomutati Houbraken & Frisvad
- ser. Thiersiorum Houbraken & Frisvad
- ser. Thomiorum Houbraken & Frisvad
- ser. Unguium Houbraken & Frisvad
- ser. Unilaterales Houbraken & Frisvad
- ser. Usti Houbraken & Frisvad
- ser. Verhageniorum Houbraken & Frisvad
- ser. Versicolores Houbraken & Frisvad
- ser. Virgata Houbraken & Frisvad
- ser. Viridinutantes Houbraken & Frisvad
- ser. Vitricolarum Houbraken & Frisvad
- ser. Wentiorum Houbraken & Frisvad
- ser. Westlingiorum Houbraken & Frisvad
- ser. Whitfieldiorum Houbraken & Frisvad
- ser. Xerophili Houbraken & Frisvad
- series Tularensia (Pitt) Houbraken & Frisvad
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Affiliation(s)
- J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - S. Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - X.-C. Wang
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3, 1st Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - M. Meijer
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - B. Kraak
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - V. Hubka
- Department of Botany, Charles University in Prague, Prague, Czech Republic
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine Technical University of Denmark, Søltofts Plads, B. 221, Kongens Lyngby, DK 2800, Denmark
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13
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Fungal spores: Highly variable and stress-resistant vehicles for distribution and spoilage. Food Microbiol 2018; 81:2-11. [PMID: 30910084 DOI: 10.1016/j.fm.2018.11.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 11/21/2022]
Abstract
This review highlights the variability of fungal spores with respect to cell type, mode of formation and stress resistance. The function of spores is to disperse fungi to new areas and to get them through difficult periods. This also makes them important vehicles for food contamination. Formation of spores is a complex process that is regulated by the cooperation of different transcription factors. The discussion of the biology of spore formation, with the genus Aspergillus as an example, points to possible novel ways to eradicate fungal spore production in food. Fungi can produce different types of spores, sexual and asexually, within the same colony. The absence or presence of sexual spore formation has led to a dual nomenclature for fungi. Molecular techniques have led to a revision of this nomenclature. A number of fungal species form sexual spores, which are exceptionally stress-resistant and survive pasteurization and other treatments. A meta-analysis is provided of numerous D-values of heat-resistant ascospores generated during the years. The relevance of fungal spores for food microbiology has been discussed.
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14
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Rico-Munoz E, Samson RA, Houbraken J. Mould spoilage of foods and beverages: Using the right methodology. Food Microbiol 2018; 81:51-62. [PMID: 30910088 DOI: 10.1016/j.fm.2018.03.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 11/19/2022]
Abstract
Fungal spoilage of products manufactured by the food and beverage industry imposes significant annual global revenue losses. Mould spoilage can also be a food safety issue due to the production of mycotoxins by these moulds. To prevent mould spoilage, it is essential that the associated mycobiota be adequately isolated and accurately identified. The main fungal groups associated with spoilage are the xerophilic, heat-resistant, preservative-resistant, anaerobic and psychrophilic fungi. To assess mould spoilage, the appropriate methodology and media must be used. While classic mycological detection methods can detect a broad range of fungi using well validated protocols, they are time consuming and results can take days or even weeks. New molecular detection methods are faster but require good DNA isolation techniques, expensive equipment and may detect viable and non-viable fungi that probably will not spoil a specific product. Although there is no complete and easy method for the detection of fungi in food it is important to be aware of the limitation of the methodology. More research is needed on the development of methods of detection and identification that are both faster and highly sensitive.
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Affiliation(s)
- Emilia Rico-Munoz
- BCN Research Laboratories, Inc., 2491 Stock Creek Blvd., Rockford, TN 37853, USA.
| | - Robert A Samson
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
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15
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Abstract
Approximately 20% of species in the fungal kingdom are only known to reproduce by asexual means despite the many supposed advantages of sexual reproduction. However, in recent years, sexual cycles have been induced in a series of emblematic "asexual" species. We describe how these discoveries were made, building on observations of evidence for sexual potential or "cryptic sexuality" from population genetic analyses; the presence, distribution, and functionality of mating-type genes; genome analyses revealing the presence of genes linked to sexuality; the functionality of sex-related genes; and formation of sex-related developmental structures. We then describe specific studies that led to the discovery of mating and sex in certain Candida, Aspergillus, Penicillium, and Trichoderma species and discuss the implications of sex including the beneficial exploitation of the sexual cycle. We next consider whether there might be any truly asexual fungal species. We suggest that, although rare, imperfect fungi may genuinely be present in nature and that certain human activities, combined with the genetic flexibility that is a hallmark of the fungal kingdom, might favor the evolution of asexuality under certain conditions. Finally, we argue that fungal species should not be thought of as simply asexual or sexual, but rather as being composed of isolates on a continuum of sexual fertility.
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16
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Douanla-Meli C, Unger JG, Langer E. Multi-approach analysis of the diversity in Colletotrichum cliviae sensu lato. Antonie van Leeuwenhoek 2017; 111:423-435. [PMID: 29094246 DOI: 10.1007/s10482-017-0965-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 10/19/2017] [Indexed: 01/20/2023]
Abstract
Colletotrichum cliviae is a fungal species reported both as pathogen and endophyte with broad geographical distribution. Some purported isolates of this species have been assigned to different taxa, including Colletotrichum aracearum, Colletotrichum orchidearum and Colletotrichum. sichuanensis, for which a preliminary analysis of extensive multilocus (ACT, GAPDH, ITS, TUB2) data in this study revealed high sequence similarity with C. cliviae. We further reassessed the species delineation by using the coalescent method of the generalized mixed Yule-coalescent (GMYC) and Poisson Tree Processes (PTP). Single and multilocus gene trees strongly supported a C. cliviae s. lat. clade including the four species. This clade unfolded eight subclades grouped into three distinct lineages, but no monophyly of any of the four species. GMYC and PTP analyses confidently supported the evolutionary independence of these lineages. C. sichuanensis and C. cliviae, except one isolate, formed the largest lineage. The second lineage was made up of isolates named C. aracearum and some of C. orchidearum sharing the haplotype and the third lineage accommodated two isolates named C. cliviae and C. orchidearum. This finding suggests the synonymization of C. sichuanensis with C. cliviae whereas the taxonomic status of C. aracearum and C. orchidearum still needs clarification. This study lays great stress upon the use of comprehensive data for sequence-based characterisation of species in the C. cliviae s. lat. It also presents the first report of C. cliviae in tropical Africa and on citrus host.
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Affiliation(s)
- C Douanla-Meli
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for National and International Plant Health, Messeweg 11-12, 38104, Brunswick, Germany.
| | - J-G Unger
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for National and International Plant Health, Messeweg 11-12, 38104, Brunswick, Germany
| | - E Langer
- Universität Kassel, Fachgebiet Ökologie, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
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17
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18
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Hagen F, Lumbsch HT, Arsic Arsenijevic V, Badali H, Bertout S, Billmyre RB, Bragulat MR, Cabañes FJ, Carbia M, Chakrabarti A, Chaturvedi S, Chaturvedi V, Chen M, Chowdhary A, Colom MF, Cornely OA, Crous PW, Cuétara MS, Diaz MR, Espinel-Ingroff A, Fakhim H, Falk R, Fang W, Herkert PF, Ferrer Rodríguez C, Fraser JA, Gené J, Guarro J, Idnurm A, Illnait-Zaragozi MT, Khan Z, Khayhan K, Kolecka A, Kurtzman CP, Lagrou K, Liao W, Linares C, Meis JF, Nielsen K, Nyazika TK, Pan W, Pekmezovic M, Polacheck I, Posteraro B, de Queiroz Telles F, Romeo O, Sánchez M, Sampaio A, Sanguinetti M, Sriburee P, Sugita T, Taj-Aldeen SJ, Takashima M, Taylor JW, Theelen B, Tomazin R, Verweij PE, Wahyuningsih R, Wang P, Boekhout T. Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus. mSphere 2017; 2:e00238-17. [PMID: 28875175 PMCID: PMC5577652 DOI: 10.1128/msphere.00238-17] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoformans were raised to species level, and the same was done for five genotypes within C. gattii. In a recent perspective (K. J. Kwon-Chung et al., mSphere 2:e00357-16, 2017, https://doi.org/10.1128/mSphere.00357-16), it was argued that this taxonomic proposal was premature and without consensus in the community. Although the authors of the perspective recognized the existence of genetic diversity, they preferred the use of the informal nomenclature "C. neoformans species complex" and "C. gattii species complex." Here we highlight the advantage of recognizing these seven species, as ignoring these species will impede deciphering further biologically and clinically relevant differences between them, which may in turn delay future clinical advances.
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Affiliation(s)
- Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | | | | | - Hamid Badali
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - Sebastien Bertout
- Unité Mixte Internationale Recherches Translationnelles sur l’Infection à VIH et les Maladies Infectieuses, Laboratoire de Parasitologie et Mycologie Médicale, UFR Pharmacie, Université Montpellier, Montpellier, France
| | - R. Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - M. Rosa Bragulat
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - F. Javier Cabañes
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Mauricio Carbia
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Min Chen
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | | | - Oliver A. Cornely
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
- Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
- Center for Clinical Trials, University Hospital Cologne, Cologne, Germany
| | - Pedro W. Crous
- Phytopathology Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Maria S. Cuétara
- Department of Microbiology, Hospital Severo Ochoa, Madrid, Spain
| | - Mara R. Diaz
- University of Miami, NSF NIEHS Oceans and Human Health Center, Miami, Florida, USA
- Rosentiel School of Marine and Atmospheric Science, Division of Marine Biology and Fisheries, University of Miami, Miami, Florida, USA
| | | | - Hamed Fakhim
- Department of Medical Parasitology and Mycology/Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Rama Falk
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
- Department of Fisheries and Aquaculture, Ministry of Agriculture and Rural Development, Nir-David, Israel
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Patricia F. Herkert
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Postgraduate Program in Microbiology, Parasitology and Pathology, Biological Sciences, Department of Basic Pathology, Federal University of Parana, Curitiba, Brazil
| | | | - James A. Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Josepa Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Josep Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Alexander Idnurm
- School of BioSciences, BioSciences 2, University of Melbourne, Melbourne, Australia
| | | | - Ziauddin Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, Thailand
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Kolecka
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Cletus P. Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Katrien Lagrou
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Carlos Linares
- Medical School, Universidad Miguel Hernández, Alicante, Spain
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Kirsten Nielsen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tinashe K. Nyazika
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
- Malawi-Liverpool-Wellcome Trust, College of Medicine, University of Malawi, Blantyre, Malawi
- School of Tropical Medicine, Liverpool, United Kingdom
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | | | - Itzhack Polacheck
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Brunella Posteraro
- Institute of Public Health (Section of Hygiene), Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Flavio de Queiroz Telles
- Department of Communitarian Health, Hospital de Clínicas, Federal University of Parana, Curitiba, Brazil
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- IRCCS Centro Neurolesi Bonino-Pulejo, Messina, Italy
| | - Manuel Sánchez
- Medical School, Universidad Miguel Hernández, Alicante, Spain
| | - Ana Sampaio
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro (UTAD), Quinta dos Prados, Vila Real, Portugal
| | - Maurizio Sanguinetti
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Pojana Sriburee
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, Noshio, Kiyose, Tokyo, Japan
| | - Saad J. Taj-Aldeen
- Mycology Unit, Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, Japan
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Bart Theelen
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Rok Tomazin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Paul E. Verweij
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Retno Wahyuningsih
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Parasitology, School of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Ping Wang
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
- Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Teun Boekhout
- Institute of Biodiversity and Ecosystems Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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Terfehr D, Dahlmann TA, Kück U. Transcriptome analysis of the two unrelated fungal β-lactam producers Acremonium chrysogenum and Penicillium chrysogenum: Velvet-regulated genes are major targets during conventional strain improvement programs. BMC Genomics 2017; 18:272. [PMID: 28359302 PMCID: PMC5374653 DOI: 10.1186/s12864-017-3663-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/25/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Cephalosporins and penicillins are the most frequently used β-lactam antibiotics for the treatment of human infections worldwide. The main industrial producers of these antibiotics are Acremonium chrysogenum and Penicillium chrysogenum, two taxonomically unrelated fungi. Both were subjects of long-term strain development programs to reach economically relevant antibiotic titers. It is so far unknown, whether equivalent changes in gene expression lead to elevated antibiotic titers in production strains. RESULTS Using the sequence of PcbC, a key enzyme of β-lactam antibiotic biosynthesis, from eighteen different pro- and eukaryotic microorganisms, we have constructed a phylogenetic tree to demonstrate the distant relationship of both fungal producers. To address the question whether both fungi have undergone similar genetic adaptions, we have performed a comparative gene expression analysis of wild-type and production strains. We found that strain improvement is associated with the remodeling of the transcriptional landscape in both fungi. In P. chrysogenum, 748 genes showed differential expression, while 1572 genes from A. chrysogenum are differentially expressed in the industrial strain. Common in both fungi is the upregulation of genes belonging to primary and secondary metabolism, notably those involved in precursor supply for β-lactam production. Other genes not essential for β-lactam production are downregulated with a preference for those responsible for transport processes or biosynthesis of other secondary metabolites. Transcriptional regulation was shown to be an important parameter during strain improvement in different organisms. We therefore investigated deletion strains of the major transcriptional regulator velvet from both production strains. We identified 567 P. chrysogenum and 412 A. chrysogenum Velvet target genes. In both deletion strains, approximately 50% of all secondary metabolite cluster genes are differentially regulated, including β-lactam biosynthesis genes. Most importantly, 35-57% of Velvet target genes are among those that showed differential expression in both improved industrial strains. CONCLUSIONS The major finding of our comparative transcriptome analysis is that strain improvement programs in two unrelated fungal β-lactam antibiotic producers alter the expression of target genes of Velvet, a global regulator of secondary metabolism. From these results, we conclude that regulatory alterations are crucial contributing factors for improved β-lactam antibiotic titers during strain improvement in both fungi.
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Affiliation(s)
- Dominik Terfehr
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-University Bochum, Universitätsstr. 150, Bochum, 44780, Germany
| | - Tim A Dahlmann
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-University Bochum, Universitätsstr. 150, Bochum, 44780, Germany
| | - Ulrich Kück
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-University Bochum, Universitätsstr. 150, Bochum, 44780, Germany.
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Lazarus KL, Benny GL, Ho HM, Smith ME. Phylogenetic systematics of Syncephalis (Zoopagales, Zoopagomycotina), a genus of ubiquitous mycoparasites. Mycologia 2017; 109:333-349. [PMID: 28489971 DOI: 10.1080/00275514.2017.1307005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We examined phylogenetic relationships among species of the mycoparasite genus Syncephalis using sequences from three nuclear ribsosomal DNA genes (18S, 5.8S, and 28S nuc rDNA) and a gene encoding the largest subunit of RNA polymerase II (RPB1). Our data set included 88 Syncephalis isolates comprising 23 named species and several unnamed taxa. We also revived a culturing technique using beef liver and cellophane to grow several Syncephalis isolates without their host fungi to obtain pure parasite DNA. Most isolates, however, were grown in co-cultures with their host fungi, so we designed Syncephalis-specific primers to obtain sequence data. Individual and combined data sets were analyzed by maximum likelihood (ML) and Bayesian methods. We recovered 20 well-supported lineages and 38 operational taxonomic units (OTUs). Most major clades contained isolates from distant localities on multiple continents. There were taxonomic and nomenclature issues within several clades, probably due to high phenotypic plasticity or species dimorphism. We also conducted an analysis of Syncephalis nuc rDNA internal transcribed spacer (ITS) sequences for 31 phylogenetically diverse isolates, and we determined that most Syncephalis species have long ITS sequences relative to other fungi. Although commonly employed eukaryotic and fungal primers are compatible with diverse Syncephalis species, the ITS sequences of Syncepahlis are nonetheless rarely recovered in environmental molecular diversity surveys.
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Affiliation(s)
- Katherine L Lazarus
- a Department of Plant Pathology , 1453 Fifield Hall, P.O. Box 110680, University of Florida , Gainesville , Florida 32611-0680
| | - Gerald L Benny
- a Department of Plant Pathology , 1453 Fifield Hall, P.O. Box 110680, University of Florida , Gainesville , Florida 32611-0680
| | - Hsiao-Man Ho
- b Department of Science Education , National Taipei University of Education , 134, Sect. 2, Heping E. Road, Taipei 106 , Taiwan
| | - Matthew E Smith
- a Department of Plant Pathology , 1453 Fifield Hall, P.O. Box 110680, University of Florida , Gainesville , Florida 32611-0680
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McTaggart LR, Brown EM, Richardson SE. Phylogeographic Analysis of Blastomyces dermatitidis and Blastomyces gilchristii Reveals an Association with North American Freshwater Drainage Basins. PLoS One 2016; 11:e0159396. [PMID: 27428521 PMCID: PMC4948877 DOI: 10.1371/journal.pone.0159396] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/03/2016] [Indexed: 11/25/2022] Open
Abstract
Blastomyces dermatitidis and Blastomyces gilchristii are dimorphic fungal pathogens that cause serious pulmonary and systemic infections in humans. Although their natural habitat is in the environment, little is known about their specific ecologic niche(s). Here, we analyzed 25 microsatellite loci from 169 strains collected from various regions throughout their known endemic range in North America, representing the largest and most geographically diverse collection of isolates studied to date. Genetic analysis of multilocus microsatellite data divided the strains into four populations of B. dermatitidis and four populations of B. gilchristii. B. dermatitidis isolates were recovered from areas throughout North America, while the B. gilchristii strains were restricted to Canada and some northern US states. Furthermore, the populations of both species were associated with major freshwater drainage basins. The four B. dermatitidis populations were partitioned among (1) the Nelson River drainage basin, (2) the St. Lawrence River and northeast Atlantic Ocean Seaboard drainage basins, (3) the Mississippi River System drainage basin, and (4) the Gulf of Mexico Seaboard and southeast Atlantic Ocean Seaboard drainage basins. A similar partitioning of the B. gilchristii populations was observed among the more northerly drainage basins only. These associations suggest that the ecologic niche where the sexual reproduction, growth, and dispersal of B. dermatitidis and B. gilchristii occur is intimately linked to freshwater systems. For most populations, sexual reproduction was rare enough to produce significant linkage disequilibrium among loci but frequent enough that mating-type idiomorphic ratios were not skewed from 1:1. Furthermore, the evolutionary divergence of B. dermatitidis and B. gilchristii was estimated at 1.9 MYA during the Pleistocene epoch. We suggest that repeated glaciations during the Pleistocene period and resulting biotic refugia may have provided the impetus for speciation as theorized for other species associated with temperate freshwater systems.
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Affiliation(s)
- Lisa R. McTaggart
- Public Health Laboratories Toronto, Public Health Ontario, Toronto, Ontario, Canada
- * E-mail:
| | - Elizabeth M. Brown
- Public Health Laboratories Toronto, Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Susan E. Richardson
- Public Health Laboratories Toronto, Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Microbiology, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
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Sweet MJ, Scriven LA, Singleton I. Microsatellites for microbiologists. ADVANCES IN APPLIED MICROBIOLOGY 2016; 81:169-207. [PMID: 22958530 DOI: 10.1016/b978-0-12-394382-8.00005-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Microsatellites are repeating sequences of 2-6base pairs of DNA. Currently, they are used as molecular markers in many organisms, specifically in genetic studies analyzing kinship and population structure. In addition, they can be used to study gene duplication and/or deletion. Although they are used in studies on microorganisms including fungi, bacteria, protists, and archaea, it appears that these genetic markers are not being utilized to their full microbiological potential. Microsatellites have many advantages over other genetic markers currently in use as they are in general species specific, and therefore, cross-contamination by nontarget organisms is rare. Furthermore, microsatellites are suitable for use with fast and cheap DNA extraction methods, with ancient DNA or DNA from hair and fecal samples used in noninvasive sampling, making them widely available as a genetic marker. Microsatellites have already proven to be a useful tool for evolutionary studies of pathogenic microorganisms such as Candida albicans and Helicobacter pylori, and the onset of new sequencing techniques (such as 454, PACBIO, and mini-ion sequencing) means the ability to detect such markers will become less time consuming and cheaper, thus further expanding their potential to answer important microbial ecology questions.
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Affiliation(s)
- Michael J Sweet
- School of Biology, Institute for Research on Sustainability, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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23
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Villarino M, De Cal A, Melgarejo P, Larena I, Espeso EA. The development of genetic and molecular markers to register and commercialize Penicillium rubens (formerly Penicillium oxalicum) strain 212 as a biocontrol agent. Microb Biotechnol 2016; 9:89-99. [PMID: 26467970 PMCID: PMC4720407 DOI: 10.1111/1751-7915.12325] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 11/29/2022] Open
Abstract
Penicillium oxalicum strain 212 (PO212) is an effective biocontrol agent (BCA) against a large number of economically important fungal plant pathogens. For successful registration as a BCA in Europe, PO212 must be accurately identified. In this report, we describe the use of classical genetic and molecular markers to characterize and identify PO212 in order to understand its ecological role in the environment or host. We successfully generated pyrimidine (pyr-) auxotrophic mutants. In addition we also designed specific oligonucleotides for the pyrF gene at their untranslated regions for rapid and reliable identification and classification of strains of P. oxalicum and P. rubens, formerly P. chrysogenum. Using these DNA-based technologies, we found that PO212 is a strain of P. rubens, and is not a strain of P. oxalicum. This work presents PO212 as the unique P. rubens strain to be described as a BCA and the information contained here serves for its registration and commercialization in Europe.
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Affiliation(s)
- Maria Villarino
- SGIT-INIA, Departamento de Protección Vegetal, Madrid, Spain
- CIB-CSIC, Departamento de Biología Celular y Molecular, Madrid, Spain
| | | | | | | | - Eduardo A Espeso
- CIB-CSIC, Departamento de Biología Celular y Molecular, Madrid, Spain
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24
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Diversity and movement of indoor Alternaria alternata across the mainland USA. Fungal Genet Biol 2015; 81:62-72. [PMID: 26004989 DOI: 10.1016/j.fgb.2015.05.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/21/2015] [Accepted: 05/07/2015] [Indexed: 01/11/2023]
Abstract
Alternaria spp. from sect. Alternaria are frequently associated with hypersensitivity pneumonitis, asthma and allergic fungal rhinitis and sinusitis. Since Alternaria is omnipresent in the outdoor environment, it is thought that the indoor spore concentration is mainly influenced by the outdoor spore concentration. However, few studies have investigated indoor Alternaria isolates, or attempted a phylogeographic or population genetic approach to investigate their movement. Therefore, the aim of the current study was to investigate the molecular diversity of indoor Alternaria isolates in the USA, and to test for recombination, using these approaches. Alternaria isolates collected throughout the USA were identified using ITS, gapdh and endoPG gene sequencing. This was followed by genotyping and population genetic inference of isolates belonging to Alternaria sect. Alternaria together with 37 reference isolates, using five microsatellite markers. Phylogenetic analyses revealed that species of Alternaria sect. Alternaria represented 98% (153 isolates) of the indoor isolates collected throughout the USA, of which 137 isolates could be assigned to A. alternata, 15 to the A. arborescens species complex and a single isolate to A. burnsii. The remaining 2% (3 isolates) represented sect. Infectoriae (single isolate) and sect. Pseudoulocladium (2 isolates). Population assignment analyses of the 137 A. alternata isolates suggested that subpopulations did not exist within the sample. The A. alternata isolates were thus divided into four artificial subpopulations to represent four quadrants of the USA. Forty-four isolates representing the south-western quadrant displayed the highest level of uniqueness based on private alleles, while the highest level of gene flow was detected between the south-eastern (32 isolates) and south-western quadrants. Genotypic diversity was high for all quadrants, and a test for linkage disequilibrium suggested that A. alternata has a cryptic sexual cycle. These statistics could be correlated with environmental factors, suggesting that indoor A. alternata isolates, although extremely diverse, have a continental distribution and high levels of gene flow over the continent.
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25
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Nguyen HDT, Jančič S, Meijer M, Tanney JB, Zalar P, Gunde-Cimerman N, Seifert KA. Application of the phylogenetic species concept to Wallemia sebi from house dust and indoor air revealed by multi-locus genealogical concordance. PLoS One 2015; 10:e0120894. [PMID: 25799362 PMCID: PMC4370657 DOI: 10.1371/journal.pone.0120894] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/27/2015] [Indexed: 01/17/2023] Open
Abstract
A worldwide survey of Wallemia occurring in house dust and indoor air was conducted. The isolated strains were identified as W. sebi and W. muriae. Previous studies suggested that the W. sebi phylogenetic clade contained cryptic species but conclusive evidence was lacking because only the internal transcribed spacer (ITS) marker was analyzed. The ITS and four protein-coding genes (MCM7, RPB1, RPB2, and TSR1) were sequenced for 85 isolates. Based on an initial neighbor joining analysis of the concatenated genes, W. muriae remained monophyletic but four clades were found in W. sebi, which we designated as W. sebi clades 1, 2, 3, and 4. We hypothesized that these clades represent distinct phylogenetic species within the Wallemia sebi species complex (WSSC). We then conducted multiple phylogenetic analyses and demonstrated genealogical concordance, which supports the existence of four phylogenetic species within the WSSC. Geographically, W. muriae was only found in Europe, W. sebi clade 3 was only found in Canada, W. sebi clade 4 was found in subtropical regions, while W. sebi clade 1 and 2 were found worldwide. Haplotype analysis showed that W. sebi clades 1 and 2 had multiple haplotypes while W. sebi clades 3 and 4 had one haplotype and may have been under sampled. We describe W. sebi clades 2, 3, and 4 as new species in a companion study.
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Affiliation(s)
- Hai D. T. Nguyen
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
- * E-mail: (HDTN); (KAS)
| | - Sašo Jančič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Martin Meijer
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Joey B. Tanney
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Keith A. Seifert
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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26
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Gladieux P, Feurtey A, Hood ME, Snirc A, Clavel J, Dutech C, Roy M, Giraud T. The population biology of fungal invasions. Mol Ecol 2015; 24:1969-86. [DOI: 10.1111/mec.13028] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 12/16/2022]
Affiliation(s)
- P. Gladieux
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - A. Feurtey
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - M. E. Hood
- Department of Biology; Amherst College; Amherst Massachusetts 01002 USA
| | - A. Snirc
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - J. Clavel
- Conservation des Espèces; Restauration et Suivi des Populations - CRBPO; Muséum National d'Histoire Naturelle-CNRS-Université Pierre et Marie Curie; 55 rue Buffon 75005 Paris France
| | - C. Dutech
- Biodiversité Gènes et Communautés; INRA-Université Bordeaux 1; Site de Pierroton 33610 Cestas France
| | - M. Roy
- Evolution et Diversité Biologique; Université Toulouse Paul Sabatier-Ecole Nationale de Formation Agronomique-CNRS; 118 route de Narbonne 31062 Toulouse France
| | - T. Giraud
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
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27
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28
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Pažoutová S, Pešicová K, Chudíčková M, Šrůtka P, Kolařík M. Delimitation of cryptic species inside Claviceps purpurea. Fungal Biol 2014; 119:7-26. [PMID: 25601146 DOI: 10.1016/j.funbio.2014.10.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 10/07/2014] [Accepted: 10/13/2014] [Indexed: 10/24/2022]
Abstract
Claviceps purpurea is an ovarian parasite infecting grasses (Poaceae) including cereals and forage plants. This fungus produces toxic alkaloids and consumption of contaminated grains can cause ergotism in humans and other mammals. Recent molecular genetics studies have indicated that it included three cryptic species (G1, G2, G3). In this study, reproductive isolation amongst these groups and among material from Phragmites and Molinia was tested using gene flow statistics for five polymorphic loci, and to support these data, phylogenetic affiliations based on gene trees and a multigene phylogeny were used. The four recognized species are characterized based on morphology and host spectrum and formal taxonomic names are proposed. Claviceps purpurea sensu stricto (G1 group) represents a typical rye ergot, but infects various other grasses. Typical hosts of Claviceps humidiphila (new name for G2 species), like Phalaris arundinacea, belong to grasses preferring humid locations. Claviceps spartinae (G3) is specific to chloridoid grasses from salt barches. The material from Phragmites and Molinia can be authenticated with the species Claviceps microcephala for which the new name Claviceps arundinis is proposed here. The divergence time between species was estimated and the tools for species identification are discussed.
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Affiliation(s)
- Sylvie Pažoutová
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Kamila Pešicová
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic; Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic
| | - Milada Chudíčková
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Petr Šrůtka
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 129, 165 21 Prague 6, Czech Republic
| | - Miroslav Kolařík
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.
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Houbraken J, de Vries RP, Samson RA. Modern taxonomy of biotechnologically important Aspergillus and Penicillium species. ADVANCES IN APPLIED MICROBIOLOGY 2014; 86:199-249. [PMID: 24377856 DOI: 10.1016/b978-0-12-800262-9.00004-4] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Taxonomy is a dynamic discipline and name changes of fungi with biotechnological, industrial, or medical importance are often difficult to understand for researchers in the applied field. Species belonging to the genera Aspergillus and Penicillium are commonly used or isolated, and inadequate taxonomy or uncertain nomenclature of these genera can therefore lead to tremendous confusion. Misidentification of strains used in biotechnology can be traced back to (1) recent changes in nomenclature, (2) new taxonomic insights, including description of new species, and/or (3) incorrect identifications. Changes in the recent published International Code of Nomenclature for Algae, Fungi and Plants will lead to numerous name changes of existing Aspergillus and Penicillium species and an overview of the current names of biotechnological important species is given. Furthermore, in (biotechnological) literature old and invalid names are still used, such as Aspergillus awamori, A. foetidus, A. kawachii, Talaromyces emersonii, Acremonium cellulolyticus, and Penicillium funiculosum. An overview of these and other species with their correct names is presented. Furthermore, the biotechnologically important species Talaromyces thermophilus is here combined in Thermomyces as Th. dupontii. The importance of Aspergillus, Penicillium, and related genera is also illustrated by the high number of undertaken genome sequencing projects. A number of these strains are incorrectly identified or atypical strains are selected for these projects. Recommendations for correct strain selection are given here. Phylogenetic analysis shows a close relationship between the genome-sequenced strains of Aspergillus, Penicillium, and Monascus. Talaromyces stipitatus and T. marneffei (syn. Penicillium marneffei) are closely related to Thermomyces lanuginosus and Th. dupontii (syn. Talaromyces thermophilus), and these species appear to be distantly related to Aspergillus and Penicillium. In the last part of this review, an overview of heterothallic reproduction in Aspergillus and Penicillium is given. The new insights in the taxonomy of Aspergillus, Penicillium, and related genera will help to interpret the results generated with comparative genomics studies or other studies dealing with evolution of, for example, enzymes, mating-type loci, virulence genes, and secondary metabolite biosynthetic gene clusters.
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Affiliation(s)
- Jos Houbraken
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands.
| | | | - Robert A Samson
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
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30
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Wong VL, Ellison CE, Eisen MB, Pachter L, Brem RB. Structural variation among wild and industrial strains of Penicillium chrysogenum. PLoS One 2014; 9:e96784. [PMID: 24824901 PMCID: PMC4019546 DOI: 10.1371/journal.pone.0096784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 04/11/2014] [Indexed: 11/24/2022] Open
Abstract
Strain selection and strain improvement are the first, and arguably most important, steps in the industrial production of biological compounds by microorganisms. While traditional methods of mutagenesis and selection have been effective in improving production of compounds at a commercial scale, the genetic changes underpinning the altered phenotypes have remained largely unclear. We utilized high-throughput Illumina short read sequencing of a wild Penicillium chrysogenum strain in order to make whole genome comparisons to a sequenced improved strain (WIS 54–1255). We developed an assembly-free method of identifying chromosomal rearrangements and validated the in silico predictions with a PCR-based assay and Sanger sequencing. Despite many rounds of mutagen treatment and artificial selection, WIS 54–1255 differs from its wild progenitor at only one of the identified rearrangements. We suggest that natural variants predisposed for high penicillin production were instrumental in the success of WIS 54–1255 as an industrial strain. In addition to finding a previously published inversion in the penicillin biosynthesis cluster, we located several genes related to penicillin production associated with these rearrangements. By comparing the configuration of rearrangement events among several historically important strains known to be high penicillin producers to a collection of recently isolated wild strains, we suggest that wild strains with rearrangements similar to those in known high penicillin producers may be viable candidates for further improvement efforts.
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Affiliation(s)
- Valerie L. Wong
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Christopher E. Ellison
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Lior Pachter
- Departments of Mathematics, Molecular and Cell Biology, and Electrical Engineering and Computer Science, University of California Berkeley, Berkeley, California, United States of America
| | - Rachel B. Brem
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
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Stewart JE, Timmer LW, Lawrence CB, Pryor BM, Peever TL. Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen. BMC Evol Biol 2014; 14:38. [PMID: 24593138 PMCID: PMC4015827 DOI: 10.1186/1471-2148-14-38] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/21/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Traditional morphological and biological species concepts are difficult to apply to closely related, asexual taxa because of the lack of an active sexual phase and paucity of morphological characters. Phylogenetic species concepts such as genealogical concordance phylogenetic species recognition (GCPSR) have been extensively used; however, methods that incorporate gene tree uncertainty into species recognition may more accurately and objectively delineate species. Using a worldwide sample of Alternaria alternata sensu lato, causal agent of citrus brown spot, the evolutionary histories of four nuclear loci including an endo-polygalacturonase gene, two anonymous loci, and one microsatellite flanking region were estimated using the coalescent. Species boundaries were estimated using several approaches including those that incorporate uncertainty in gene genealogies when lineage sorting and non-reciprocal monophyly of gene trees is common. RESULTS Coalescent analyses revealed three phylogenetic lineages strongly influenced by incomplete lineage sorting and recombination. Divergence of the citrus 2 lineage from the citrus 1 and citrus 3 lineages was supported at most loci. A consensus of species tree estimation methods supported two species of Alternaria causing citrus brown spot worldwide. Based on substitution rates at the endo-polygalacturonase locus, divergence of the citrus 2 and the 1 and 3 lineages was estimated to have occurred at least 5, 400 years before present, predating the human-mediated movement of citrus and associated pathogens out of SE Asia. CONCLUSIONS The number of Alternaria species identified as causing brown spot of citrus worldwide using morphological criteria has been overestimated. Little support was found for most of these morphospecies using quantitative species recognition approaches. Correct species delimitation of plant-pathogenic fungi is critical for understanding the evolution of pathogenicity, introductions of pathogens to new areas, and for regulating the movement of pathogens to enforce quarantines. This research shows that multilocus phylogenetic methods that allow for recombination and incomplete lineage sorting can be useful for the quantitative delimitation of asexual species that are morphologically indistinguishable. Two phylogenetic species of Alternaria were identified as causing citrus brown spot worldwide. Further research is needed to determine how these species were introduced worldwide, how they differ phenotypically and how these species are maintained.
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Affiliation(s)
- Jane E Stewart
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
- Current address: Department of Plant Pathology, University of Georgia, Athens, Georgia
| | - Lavern W Timmer
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, USA
| | | | - Barry M Pryor
- Division of Plant Pathology and Microbiology, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Tobin L Peever
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
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Peng Q, Yuan Y, Gao M, Chen X, Liu B, Liu P, Wu Y, Wu D. Genomic characteristics and comparative genomics analysis of Penicillium chrysogenum KF-25. BMC Genomics 2014; 15:144. [PMID: 24555742 PMCID: PMC3938070 DOI: 10.1186/1471-2164-15-144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 02/06/2014] [Indexed: 12/14/2022] Open
Abstract
Background Penicillium chrysogenum has been used in producing penicillin and derived β-lactam antibiotics for many years. Although the genome of the mutant strain P. chrysogenum Wisconsin 54-1255 has already been sequenced, the versatility and genetic diversity of this species still needs to be intensively studied. In this study, the genome of the wild-type P. chrysogenum strain KF-25, which has high activity against Ustilaginoidea virens, was sequenced and characterized. Results The genome of KF-25 was about 29.9 Mb in size and contained 9,804 putative open reading frames (orfs). Thirteen genes were predicted to encode two-component system proteins, of which six were putatively involved in osmolarity adaption. There were 33 putative secondary metabolism pathways and numerous genes that were essential in metabolite biosynthesis. Several P. chrysogenum virus untranslated region sequences were found in the KF-25 genome, suggesting that there might be a relationship between the virus and P. chrysogenum in evolution. Comparative genome analysis showed that the genomes of KF-25 and Wisconsin 54-1255 were highly similar, except that KF-25 was 2.3 Mb smaller. Three hundred and fifty-five KF-25 specific genes were found and the biological functions of the proteins encoded by these genes were mainly unknown (232, representing 65%), except for some orfs encoding proteins with predicted functions in transport, metabolism, and signal transduction. Numerous KF-25-specific genes were found to be associated with the pathogenicity and virulence of the strains, which were identical to those of wild-type P. chrysogenum NRRL 1951. Conclusion Genome sequencing and comparative analysis are helpful in further understanding the biology, evolution, and environment adaption of P. chrysogenum, and provide a new tool for identifying further functional metabolites.
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Affiliation(s)
| | | | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
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Species-specific PCR to describe local-scale distributions of four cryptic species in the Penicillium chrysogenum complex. FUNGAL ECOL 2013; 6:419-429. [PMID: 24179477 PMCID: PMC3809933 DOI: 10.1016/j.funeco.2013.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 03/08/2013] [Accepted: 03/13/2013] [Indexed: 11/23/2022]
Abstract
Penicillium chrysogenum is a ubiquitous airborne fungus detected in every sampled region of the Earth. Owing to its role in Alexander Fleming's serendipitous discovery of Penicillin in 1928, the fungus has generated widespread scientific interest; however its natural history is not well understood. Research has demonstrated speciation within P. chrysogenum, describing the existence of four cryptic species. To discriminate the four species, we developed protocols for species-specific diagnostic PCR directly from fungal conidia. 430 Penicillium isolates were collected to apply our rapid diagnostic tool and explore the distribution of these fungi across the London Underground rail transport system revealing significant differences between Underground lines. Phylogenetic analysis of multiple type isolates confirms that the ‘Fleming species’ should be named Penicillium rubens and that divergence of the four ‘Chrysogenum complex’ fungi occurred about 0.75 million yr ago. Finally, the formal naming of two new species, Penicillium floreyi and Penicillium chainii, is performed. We develop species-specific diagnostic PCR tools for four cryptic species. We apply our diagnostic tools in the London Underground transport system. Varied distributions of Penicillium chrysogenum are demonstrated. Alexander Fleming's fungus is confirmed as Penicillium rubens. Two new species in the ‘Chrysogenum complex’ are named: P. floreyi and Penicillium chainii.
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Stewart JE, Thomas KA, Lawrence CB, Dang H, Pryor BM, Timmer LMP, Peever TL. Signatures of recombination in clonal lineages of the citrus brown spot pathogen, Alternaria alternata sensu lato. PHYTOPATHOLOGY 2013; 103:741-749. [PMID: 23441968 DOI: 10.1094/phyto-08-12-0211-r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Most Alternaria spp. are considered asexual but recent molecular evolution analyses of Alternaria mating-type genes show that the mating locus is under strong purifying selection, indicating a possible role in sexual reproduction. The objective of this study was to determine the mode of reproduction of an Alternaria alternata sensu lato population causing citrus brown spot in central Florida. Mating type of each isolate was determined, and isolates were sequenced at six putatively unlinked loci. Three genetically distinct subpopulations (SH1, SH4A, and SH4B) were identified using network and Bayesian population structure analyses. Results demonstrate that most subpopulations of A. alternata associated with citrus are clonal but some have the ability to extensively recombine through a cryptic sexual cycle or parasexual cycle. Although isolates were sampled in close physical proximity (≈2,500-m² area), we were able to reject a random mating model using multilocus gametic disequilibrium tests for two subpopulations, SH1 and SH4B, suggesting that these subpopulations were predominantly asexual. However, three recombination events were identified in SH1 and SH4B and localized to individuals of opposite mating type, possibly indicating meiotic recombination. In contrast, in the third subpopulation (SH4A), where only one mating type was present, extensive reticulation was evident in network analyses, and multilocus gametic disequilibrium tests were consistent with recombination. Recombination among isolates of the same mating type suggests that a nonmeiotic mechanism of recombination such as the parasexual cycle may be operating in this subpopulation. The level of gene flow detected among subpopulations does not appear to be sufficient to prevent differentiation, and perhaps future speciation, of these A. alternata subpopulations.
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Affiliation(s)
- Jane E Stewart
- Department of Plant Pathology, Washington State University, Pullman, USA.
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Rodrigues AM, de Melo Teixeira M, de Hoog GS, Schubach TMP, Pereira SA, Fernandes GF, Bezerra LML, Felipe MS, de Camargo ZP. Phylogenetic analysis reveals a high prevalence of Sporothrix brasiliensis in feline sporotrichosis outbreaks. PLoS Negl Trop Dis 2013; 7:e2281. [PMID: 23818999 PMCID: PMC3688539 DOI: 10.1371/journal.pntd.0002281] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/09/2013] [Indexed: 01/19/2023] Open
Abstract
Sporothrix schenckii, previously assumed to be the sole agent of human and animal sporotrichosis, is in fact a species complex. Recently recognized taxa include S. brasiliensis, S. globosa, S. mexicana, and S. luriei, in addition to S. schenckii sensu stricto. Over the last decades, large epidemics of sporotrichosis occurred in Brazil due to zoonotic transmission, and cats were pointed out as key susceptible hosts. In order to understand the eco-epidemiology of feline sporotrichosis and its role in human sporotrichosis a survey was conducted among symptomatic cats. Prevalence and phylogenetic relationships among feline Sporothrix species were investigated by reconstructing their phylogenetic origin using the calmodulin (CAL) and the translation elongation factor-1 alpha (EF1α) loci in strains originated from Rio de Janeiro (RJ, n = 15), Rio Grande do Sul (RS, n = 10), Paraná (PR, n = 4), São Paulo (SP, n =3) and Minas Gerais (MG, n = 1). Our results showed that S. brasiliensis is highly prevalent among cats (96.9%) with sporotrichosis, while S. schenckii was identified only once. The genotype of Sporothrix from cats was found identical to S. brasiliensis from human sources confirming that the disease is transmitted by cats. Sporothrix brasiliensis presented low genetic diversity compared to its sister taxon S. schenckii. No evidence of recombination in S. brasiliensis was found by split decomposition or PHI-test analysis, suggesting that S. brasiliensis is a clonal species. Strains recovered in states SP, MG and PR share the genotype of the RJ outbreak, different from the RS clone. The occurrence of separate genotypes among strains indicated that the Brazilian S. brasiliensis epidemic has at least two distinct sources. We suggest that cats represent a major host and the main source of cat and human S. brasiliensis infections in Brazil.
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Affiliation(s)
- Anderson Messias Rodrigues
- Departamento de Microbiologia, Imunologia e Parasitologia, Disciplina de Biologia Celular, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Marcus de Melo Teixeira
- Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | | | | | - Sandro Antonio Pereira
- Instituto de Pesquisa Clínica Evandro Chagas (IPEC), Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Geisa Ferreira Fernandes
- Departamento de Microbiologia, Imunologia e Parasitologia, Disciplina de Biologia Celular, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Leila Maria Lopes Bezerra
- Departamento de Biologia Celular e Genética, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Maria Sueli Felipe
- Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília (UCB), Brasília, Distrito Federal, Brazil
| | - Zoilo Pires de Camargo
- Departamento de Microbiologia, Imunologia e Parasitologia, Disciplina de Biologia Celular, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- * E-mail:
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Brown EM, McTaggart LR, Zhang SX, Low DE, Stevens DA, Richardson SE. Phylogenetic analysis reveals a cryptic species Blastomyces gilchristii, sp. nov. within the human pathogenic fungus Blastomyces dermatitidis. PLoS One 2013; 8:e59237. [PMID: 23533607 PMCID: PMC3606480 DOI: 10.1371/journal.pone.0059237] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 02/14/2013] [Indexed: 11/18/2022] Open
Abstract
Background Analysis of the population genetic structure of microbial species is of fundamental importance to many scientific disciplines because it can identify cryptic species, reveal reproductive mode, and elucidate processes that contribute to pathogen evolution. Here, we examined the population genetic structure and geographic differentiation of the sexual, dimorphic fungus Blastomyces dermatitidis, the causative agent of blastomycosis. Methodology/Principal Findings Criteria for Genealogical Concordance Phylogenetic Species Recognition (GCPSR) applied to seven nuclear loci (arf6, chs2, drk1, fads, pyrF, tub1, and its-2) from 78 clinical and environmental isolates identified two previously unrecognized phylogenetic species. Four of seven single gene phylogenies examined (chs2, drk1, pyrF, and its-2) supported the separation of Phylogenetic Species 1 (PS1) and Phylogenetic Species 2 (PS2) which were also well differentiated in the concatenated chs2-drk1-fads-pyrF-tub1-arf6-its2 genealogy with all isolates falling into one of two evolutionarily independent lineages. Phylogenetic species were genetically distinct with interspecific divergence 4-fold greater than intraspecific divergence and a high Fst value (0.772, P<0.001) indicative of restricted gene flow between PS1 and PS2. Whereas panmixia expected of a single freely recombining population was not observed, recombination was detected when PS1 and PS2 were assessed separately, suggesting reproductive isolation. Random mating among PS1 isolates, which were distributed across North America, was only detected after partitioning isolates into six geographic regions. The PS2 population, found predominantly in the hyper-endemic regions of northwestern Ontario, Wisconsin, and Minnesota, contained a substantial clonal component with random mating detected only among unique genotypes in the population. Conclusions/Significance These analyses provide evidence for a genetically divergent clade within Blastomyces dermatitidis, which we use to describe a novel species, Blastomyces gilchristii sp. nov. In addition, we discuss the value of population genetic and phylogenetic analyses as a foundation for disease surveillance, understanding pathogen evolution, and discerning phenotypic differences between phylogenetic species.
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Affiliation(s)
- Elizabeth M. Brown
- Public Health Laboratories Toronto, Public Health Ontario, Toronto, Ontario, Canada
- Department of Microbiology, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Lisa R. McTaggart
- Public Health Laboratories Toronto, Public Health Ontario, Toronto, Ontario, Canada
- * E-mail:
| | - Sean X. Zhang
- Department of Pathology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Donald E. Low
- Public Health Laboratories Toronto, Public Health Ontario, Toronto, Ontario, Canada
- Department of Microbiology, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - David A. Stevens
- Division of Infectious Diseases, Department of Medicine, Santa Clara Valley Medical Center, San Jose, California, United States of America
| | - Susan E. Richardson
- Public Health Laboratories Toronto, Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Microbiology, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
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Sexual reproduction and mating-type-mediated strain development in the penicillin-producing fungus Penicillium chrysogenum. Proc Natl Acad Sci U S A 2013; 110:1476-81. [PMID: 23307807 DOI: 10.1073/pnas.1217943110] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Penicillium chrysogenum is a filamentous fungus of major medical and historical importance, being the original and present-day industrial source of the antibiotic penicillin. The species has been considered asexual for more than 100 y, and despite concerted efforts, it has not been possible to induce sexual reproduction, which has prevented sexual crosses being used for strain improvement. However, using knowledge of mating-type (MAT) gene organization, we now describe conditions under which a sexual cycle can be induced leading to production of meiotic ascospores. Evidence of recombination was obtained using both molecular and phenotypic markers. The identified heterothallic sexual cycle was used for strain development purposes, generating offspring with novel combinations of traits relevant to penicillin production. Furthermore, the MAT1-1-1 mating-type gene, known primarily for a role in governing sexual identity, was also found to control transcription of a wide range of genes with biotechnological relevance including those regulating penicillin production, hyphal morphology, and conidial formation. These discoveries of a sexual cycle and MAT gene function are likely to be of broad relevance for manipulation of other asexual fungi of economic importance.
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Hibbett DS, Taylor JW. Fungal systematics: is a new age of enlightenment at hand? Nat Rev Microbiol 2013; 11:129-33. [DOI: 10.1038/nrmicro2963] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Rouxel M, Mestre P, Comont G, Lehman BL, Schilder A, Delmotte F. Phylogenetic and experimental evidence for host-specialized cryptic species in a biotrophic oomycete. THE NEW PHYTOLOGIST 2013; 197:251-263. [PMID: 23153246 DOI: 10.1111/nph.12016] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 09/22/2012] [Indexed: 05/09/2023]
Abstract
Assortative mating resulting from host plant specialization has been proposed to facilitate rapid ecological divergence in biotrophic plant pathogens. Downy mildews, a major group of biotrophic oomycetes, are prime candidates for testing speciation by host plant specialization. Here, we combined a phylogenetic and morphological approach with cross-pathogenicity tests to investigate host plant specialization and host range expansion in grapevine downy mildew. This destructive disease is caused by Plasmopara viticola, an oomycete endemic to North America on wild species and cultivated grapevines. Multiple genealogies and sporangia morphology provide evidence that P. viticola is a complex of four cryptic species, each associated with different host plants. Cross-inoculation experiments showed complete host plant specialization on Parthenocissus quinquefolia and on Vitis riparia, whereas cryptic species found on V. aestivalis, V. labrusca and V. vinifera were revealed to be less specific. We reconstructed the recent host range expansion of P. viticola from wild to cultivated grapevines, and showed that it was accompanied by an increase in aggressiveness of the pathogen. This case study on grapevine downy mildew illustrates how biotrophic plant pathogens can diversify by host plant specialization and emerge in agrosystems by shifting to cultivated hosts. These results might have important implications for viticulture, including breeding for resistance and disease management.
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Affiliation(s)
- Mélanie Rouxel
- INRA, ISVV, UMR1065 Santé et Agroécologie du Vignoble, F-33883, Villenave d'Ornon, France
- Université de Bordeaux, ISVV, UMR1065 Santé et Agroécologie du Vignoble, F-33883, Villenave d'Ornon, France
| | - Pere Mestre
- INRA, UMR1131 Santé de la Vigne et Qualité du vin, F-68000, Colmar, France
- Université de Strasbourg, UMR1131 Santé de la Vigne et Qualité du vin, F-68000, Colmar, France
| | - Gwenaelle Comont
- INRA, ISVV, UMR1065 Santé et Agroécologie du Vignoble, F-33883, Villenave d'Ornon, France
- Université de Bordeaux, ISVV, UMR1065 Santé et Agroécologie du Vignoble, F-33883, Villenave d'Ornon, France
| | - Brian L Lehman
- Department of Plant Pathology, Michigan State University, East Lansing, MI, 48824, USA
| | - Annemiek Schilder
- Department of Plant Pathology, Michigan State University, East Lansing, MI, 48824, USA
| | - François Delmotte
- INRA, ISVV, UMR1065 Santé et Agroécologie du Vignoble, F-33883, Villenave d'Ornon, France
- Université de Bordeaux, ISVV, UMR1065 Santé et Agroécologie du Vignoble, F-33883, Villenave d'Ornon, France
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New penicillin-producing Penicillium species and an overview of section Chrysogena. Persoonia - Molecular Phylogeny and Evolution of Fungi 2012; 29:78-100. [PMID: 23606767 PMCID: PMC3589797 DOI: 10.3767/003158512x660571] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 11/06/2012] [Indexed: 11/25/2022]
Abstract
Species classified in Penicillium sect. Chrysogena are primary soil-borne and the most well-known members are P. chrysogenum and P. nalgiovense. Penicillium chrysogenum has received much attention because of its role in the production on penicillin and as a contaminant of indoor environments and various food and feedstuffs. Another biotechnologically important species is P. nalgiovense, which is used as a fungal starter culture for the production of fermented meat products. Previous taxonomic studies often had conflicting species circumscriptions. Here, we present a multigene analysis, combined with phenotypic characters and extrolite data, demonstrating that sect. Chrysogena consists of 18 species. Six of these are newly described here (P. allii-sativi, P. desertorum, P. goetzii, P. halotolerans, P. tardochrysogenum, P. vanluykii) and P. lanoscoeruleum was found to be an older name for P. aethiopicum. Each species produces a unique extrolite profile. The species share phenotypic characters, such as good growth on CYA supplemented with 5 % NaCl, ter- or quarterverticillate branched conidiophores and short, ampulliform phialides (< 9 μm). Conidial colours, production of ascomata and ascospores, shape and ornamentation of conidia and growth rates on other agar media are valuable for species identification. Eight species (P. allii-sativi, P. chrysogenum, P. dipodomyis, P. flavigenum, P. nalgiovense, P. rubens, P. tardochrysogenum and P. vanluykii) produce penicillin in culture.
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Henk DA, Shahar-Golan R, Devi KR, Boyce KJ, Zhan N, Fedorova ND, Nierman WC, Hsueh PR, Yuen KY, Sieu TPM, Kinh NV, Wertheim H, Baker SG, Day JN, Vanittanakom N, Bignell EM, Andrianopoulos A, Fisher MC. Clonality despite sex: the evolution of host-associated sexual neighborhoods in the pathogenic fungus Penicillium marneffei. PLoS Pathog 2012; 8:e1002851. [PMID: 23055919 PMCID: PMC3464222 DOI: 10.1371/journal.ppat.1002851] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 06/25/2012] [Indexed: 12/04/2022] Open
Abstract
Molecular genetic approaches typically detect recombination in microbes regardless of assumed asexuality. However, genetic data have shown the AIDS-associated pathogen Penicillium marneffei to have extensive spatial genetic structure at local and regional scales, and although there has been some genetic evidence that a sexual cycle is possible, this haploid fungus is thought to be genetically, as well as morphologically, asexual in nature because of its highly clonal population structure. Here we use comparative genomics, experimental mixed-genotype infections, and population genetic data to elucidate the role of recombination in natural populations of P. marneffei. Genome wide comparisons reveal that all the genes required for meiosis are present in P. marneffei, mating type genes are arranged in a similar manner to that found in other heterothallic fungi, and there is evidence of a putatively meiosis-specific mutational process. Experiments suggest that recombination between isolates of compatible mating types may occur during mammal infection. Population genetic data from 34 isolates from bamboo rats in India, Thailand and Vietnam, and 273 isolates from humans in China, India, Thailand, and Vietnam show that recombination is most likely to occur across spatially and genetically limited distances in natural populations resulting in highly clonal population structure yet sexually reproducing populations. Predicted distributions of three different spatial genetic clusters within P. marneffei overlap with three different bamboo rat host distributions suggesting that recombination within hosts may act to maintain population barriers within P. marneffei.
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Affiliation(s)
- Daniel A Henk
- Department of Infectious Disease Epidemiology, Imperial College, Norfolk Place, London, United Kingdom.
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Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ. Emerging fungal threats to animal, plant and ecosystem health. Nature 2012; 484:186-94. [PMID: 22498624 PMCID: PMC3821985 DOI: 10.1038/nature10947] [Citation(s) in RCA: 1802] [Impact Index Per Article: 150.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 01/25/2012] [Indexed: 01/15/2023]
Abstract
The past two decades have seen an increasing number of virulent infectious diseases in natural populations and managed landscapes. In both animals and plants, an unprecedented number of fungal and fungal-like diseases have recently caused some of the most severe die-offs and extinctions ever witnessed in wild species, and are jeopardizing food security. Human activity is intensifying fungal disease dispersal by modifying natural environments and thus creating new opportunities for evolution. We argue that nascent fungal infections will cause increasing attrition of biodiversity, with wider implications for human and ecosystem health, unless steps are taken to tighten biosecurity worldwide.
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Affiliation(s)
- Matthew C Fisher
- Department of Infectious Disease Epidemiology, Imperial College, London W2 1PG, UK.
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Presence and functionality of mating type genes in the supposedly asexual filamentous fungus Aspergillus oryzae. Appl Environ Microbiol 2012; 78:2819-29. [PMID: 22327593 DOI: 10.1128/aem.07034-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The potential for sexual reproduction in Aspergillus oryzae was assessed by investigating the presence and functionality of MAT genes. Previous genome studies had identified a MAT1-1 gene in the reference strain RIB40. We now report the existence of a complementary MAT1-2 gene and the sequencing of an idiomorphic region from A. oryzae strain AO6. This allowed the development of a PCR diagnostic assay, which detected isolates of the MAT1-1 and MAT1-2 genotypes among 180 strains assayed, including industrial tane-koji isolates. Strains used for sake and miso production showed a near-1:1 ratio of the MAT1-1 and MAT1-2 mating types, whereas strains used for soy sauce production showed a significant bias toward the MAT1-2 mating type. MAT1-1 and MAT1-2 isogenic strains were then created by genetic manipulation of the resident idiomorph, and gene expression was compared by DNA microarray and quantitative real-time PCR (qRT-PCR) methodologies under conditions in which MAT genes were expressed. Thirty-three genes were found to be upregulated more than 10-fold in either the MAT1-1 host strain or the MAT1-2 gene replacement strain relative to each other, showing that both the MAT1-1 and MAT1-2 genes functionally regulate gene expression in A. oryzae in a mating type-dependent manner, the first such report for a supposedly asexual fungus. MAT1-1 expression specifically upregulated an α-pheromone precursor gene, but the functions of most of the genes affected were unknown. The results are consistent with a heterothallic breeding system in A. oryzae, and prospects for the discovery of a sexual cycle are discussed.
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A fungal sexual revolution: Aspergillus and Penicillium show the way. Curr Opin Microbiol 2011; 14:649-54. [DOI: 10.1016/j.mib.2011.10.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 09/29/2011] [Accepted: 10/03/2011] [Indexed: 01/09/2023]
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