DOCSLIB.ORG

A Comparative Genomics Study of 23 Aspergillus Species from Section Flavi

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Comparative Genomics Study of 23 Aspergillus Species from Section Flavi ARTICLE https://doi.org/10.1038/s41467-019-14051-y OPEN A comparative genomics study of 23 Aspergillus species from section Flavi Inge Kjærbølling1, Tammi Vesth1, Jens C. Frisvad 1, Jane L. Nybo1, Sebastian Theobald1, Sara Kildgaard1, Thomas Isbrandt Petersen1, Alan Kuo2, Atsushi Sato3, Ellen K. Lyhne1, Martin E. Kogle1, Ad Wiebenga4, Roland S. Kun4, Ronnie J.M. Lubbers4, Miia R. Mäkelä 5, Kerrie Barry2, Mansi Chovatia2, Alicia Clum2, Chris Daum2, Sajeet Haridas 2, Guifen He2, Kurt LaButti 2, Anna Lipzen2, Stephen Mondo2, Jasmyn Pangilinan2, Robert Riley2, Asaf Salamov2, Blake A. Simmons 6, Jon K. Magnuson 6, Bernard Henrissat7, Uffe H. Mortensen 1, Thomas O. Larsen 1, Ronald P. de Vries 4, Igor V. Grigoriev 2,8, 9 6,10 1 1234567890():,; Masayuki Machida , Scott E. Baker & Mikael R. Andersen * Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clus- ters (73 per species) in section Flavi. However, the observed phenotypes (growth char- acteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi. 1 Department of Biotechnology and Bioengineering, Technical University of Denmark, Søltoft Plads 223, 2800 Kongens Lyngby, Denmark. 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA. 3 Kikkoman Corporation, 250 Noda, 278-0037 Noda, Japan. 4 Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands. 5 Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Helsinki, Finland. 6 US Department of Energy Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA 94608, USA. 7 Architecture et Fonction des Macromolécules Biologiques, (CNRS UMR 7257, Aix- Marseille University, 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France. 8 Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA. 9 Kanazawa Institute of Technology, 3 Chome-1, 924-0838 Yatsukaho, Hakusan-shi, Ishikawa-ken, Japan. 10 Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, USA. *email: [email protected] NATURE COMMUNICATIONS | (2020) 11:1106 | https://doi.org/10.1038/s41467-019-14051-y | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-14051-y spergillus section Flavi encompasses a large number of alternative species for industrial use, combat pathogenicity, find A species, many of which have a significant impact on novel bioactives, and to identify useful enzymes. Prior to this human life: some species (e.g., A. oryzae and A. sojae) are project, whole-genome sequences were only available for five routinely used in production of sake, miso, soy sauce, and other species from section Flavi (A. oryzae, A. flavus, A. sojae, A. fermented foods. Moreover, A. oryzae is used industrially for luteovirescens (formerly A. bombycis), and A. parasiticus3,12–15). production of enzymes and secondary metabolite production1–4. They all belong to a closely related clade within the section and In contrast, other Flavi species (e.g., A. flavus and A. parasiticus) thus cover only a small part of the diversity. are notorious for producing highly toxic fungal compounds (e.g., In this study, as part of the Aspergillus genus-sequencing aflatoxins), in addition to infecting and damaging crops5–7. project16,17, we have generated genome sequences for 18 addi- Furthermore, A. flavus has been shown to infect immunocom- tional species plus an additional A. parasiticus isolate, permitting promised humans, and is currently the second most common genomic comparisons across 23 members of section Flavi con- cause of human aspergillosis8,9. taining at least 29 species10. We apply these sequences in tandem In addition, the section includes less known species that, with experimental and phenotypic data on secondary metabolite similar to their (in)famous relatives, display both beneficial and production, growth characteristics, and plant polysaccharide harmful properties. The benefits are found in producers of degradation to link phenotypes to genotypes and quantify the bioactive compounds (such as the anti-insectant N-alkoxypyr- genetic potential of the section. Our analysis is useful for (1) idone metabolite, leporin A, from A. leporis; an antibiotic with exploring novel enzymes and secondary metabolites, (2) opti- antifungal activity, avenaciolide, from A. avenaceus) and enzyme mizing food fermentation and industrial use, and (3) improving producers (including amylases, proteases, and xylanolytic food and feed protection and control. enzymes in A. tamarii and pectin-degrading enzymes in A. alliaceus). On the harmful side, plant pathogens (A. alliaceus on onion bulb, A. nomius on nuts, seeds, and grains) and toxin Results and discussion producers (ochratoxin from A. alliaceus,aflatoxin from A. Assessment of 19 newly sequenced section Flavi genomes.In nomius) are also found among these less studied Flavi spe- this study, we present the whole-genome sequences of 19 species cies10,11, for which no genome sequences have previously been from Aspergillus section Flavi (Fig. 1b). Two of these (A. nomius available. and A. arachidicola18,19) were also published by other groups in Given the importance of section Flavi, it is highly valuable to parallel to this work. We compare these 19 to previously examine the full genetic potential of the section in order to assess sequenced section Flavi species (A. oryzae, A. flavus, A. sojae, and abc Legend for A A. parasiticus 38.4 13,752 75 48.1 270 354,721 34 Unresolved 100 * 100 A. transmontanensis 39.3 14,216 74 48 293 342,792 36 Legend for B 99 A. arachidicola 39.8 13,895 74 48.1 451 349,923 34 A. flavus clade 100 A. tamarii clade A. novoparasiticus 40.9 14,182 73 48 870 276,844 48 A. nomius clade A. sergii 38.3 13,713 75 48.2 262 382,883 33 A. alliaceus clade A. flavus 36.8 12,604 69 48.3 138 2,388,123 6 A. togoensis clade 100 72 A. sojae – 12,738 – – – – – A. leporis clade 81 * A. avenaceus clade A. aflatoxiformans 37.6 13,595 73 48.2 385 240,665 47 This project 94 A. oryzae 37.9 12,030 70 47.2 11 4,887,096 4 100 95 A. minisclerotigenes 37.1 13,415 75 48.3 296 298,536 37 72 A. caelatus 40 13,916 75 47.6 729 115,961 102 * 100 81 A. aflatoxi... A. pseudocaelatus 39.7 13,895 75 47.6 466 210,129 58 100 97 94 A. pseudotamarii 38.2 13,428 74 47.9 249 410,003 29 95 A. oryzae 100 A. minisclerotigenes A. tamarii 38.5 13,331 75 47.5 448 214,496 51 100 A. pseudonomius 37.8 13,384 74 48.4 374 271,263 40 100 100 A. nomius 36.7 12,897 76 48.6 290 332,018 32 A. luteovirescens 37.5 12,265 81 48.8 450 240,792 46 100 A. bertholletius 37 12,948 74 48.2 443 173,958 72 A. alliaceus 40.2 13,099 72 47.1 331 499,171 24 100 100 100 A. albertensis 40.1 12,816 74 47.1 473 296,126 44 100 A. coremiiformis 30.1 9078 75 43 2728 58,658 135 A. leporis 39.4 12,745 74 47.5 615 157,399 82 100 A. avenaceus 33.8 11,293 76 45.6 1528 79,000 112 A. steynii 37.8 13,211 66 49.1 37 3,921,250 4 66 28.3 9764 68 51.2 62 1,703,432 6 90 56 A. campestris A. terreus 29.3 10,406 72 52.7 26 1,912,493 7 100 A. nidulans 30.5 10,680 72 49.3 8 3,759,208 4 80 A. niger ATCC 1015 34.9 11,910 70 50.3 24 1,937,564 6 A. fumigatus Af293 29.4 9781 72 48.8 8 3,948,441 4 P. digitatum 26 9118 67 48.2 100 878,909 8 100 N. crassa 41 10,785 64 48.2 20 6,000,761 3 0.2 Genome Predicted InterPro GC Scaffolds Scaffold L50 Scaffold N50 size (MB) proteins (#) (%) (%) (#) (bp) (#) Fig. 1 Phylogeny and genome statistics of section Flavi plus eight other Aspergillus, Penicillium, and Neurospora species. a Phylogenetic tree constructed using RAxML, MUSCLE, and Gblocks based on 200 monocore genes (a single homolog in each of the species). The red star indicates an uncertain leaf most likely caused by a different gene calling method98–100, and the arrow shows where A. sojae should be placed in the phylogenetic tree. The zoom shows the branching in a clade around A. oryzae. b The colors illustrate the clades found within section Flavi and X indicates species sequenced in this study. Earlier sequenced genomes such as A. oryzae and A. fumigatus were assembled using optical mapping and genetic maps. c Seven bubble plots illustrating key genome numbers and sequencing quality parameter. The bubble sizes have been scaled to each panel and are not comparable across panels. 2 NATURE COMMUNICATIONS | (2020) 11:1106 | https://doi.org/10.1038/s41467-019-14051-y | www.nature.com/naturecommunications NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-14051-y ARTICLE A.
Load more

Recommended publications
  • Characterization of Aspergillus Flavus Soil and Corn Kernel Populations from Eight Mississippi River States Jorge A
    Louisiana State University LSU Digital Commons LSU Master's Theses Graduate School 11-13-2017 Characterization of Aspergillus Flavus Soil and Corn Kernel Populations From Eight Mississippi River States Jorge A. Reyes Pineda Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_theses Part of the Agricultural Science Commons, Agriculture Commons, and the Plant Pathology Commons Recommended Citation Reyes Pineda, Jorge A., "Characterization of Aspergillus Flavus Soil and Corn Kernel Populations From Eight Mississippi River States" (2017). LSU Master's Theses. 4350. https://digitalcommons.lsu.edu/gradschool_theses/4350 This Thesis is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Master's Theses by an authorized graduate school editor of LSU Digital Commons. For more information, please contact [email protected]. CHARACTERIZATION OF ASPERGILLUS FLAVUS SOIL AND CORN KERNEL POPULATIONS FROM EIGHT MISSISSIPPI RIVER STATES A Thesis Submitted to the Graduate Faculty of the Louisiana State University Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Master of Science in The Department of Plant Pathology and Crop Physiology by Jorge A. Reyes Pineda B.S., Universidad Nacional de Agricultura-Honduras 2011 December 2017 ACKNOWLEDGEMENTS I first thank God who gave me the strength and perseverance to complete the requirements for this degree, and second, I thank my family. Without their unconditional support and encouragement, I would have never been able to achieve this endeavor. I would like to thank my advisory committee, Drs.
    [Show full text]
  • Distribution of Methionine Sulfoxide Reductases in Fungi and Conservation of the Free- 2 Methionine-R-Sulfoxide Reductase in Multicellular Eukaryotes
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433065; this version posted February 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Distribution of methionine sulfoxide reductases in fungi and conservation of the free- 2 methionine-R-sulfoxide reductase in multicellular eukaryotes 3 4 Hayat Hage1, Marie-Noëlle Rosso1, Lionel Tarrago1,* 5 6 From: 1Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, 7 Marseille, France. 8 *Correspondence: Lionel Tarrago ([email protected]) 9 10 Running title: Methionine sulfoxide reductases in fungi 11 12 Keywords: fungi, genome, horizontal gene transfer, methionine sulfoxide, methionine sulfoxide 13 reductase, protein oxidation, thiol oxidoreductase. 14 15 Highlights: 16 • Free and protein-bound methionine can be oxidized into methionine sulfoxide (MetO). 17 • Methionine sulfoxide reductases (Msr) reduce MetO in most organisms. 18 • Sequence characterization and phylogenomics revealed strong conservation of Msr in fungi. 19 • fRMsr is widely conserved in unicellular and multicellular fungi. 20 • Some msr genes were acquired from bacteria via horizontal gene transfers. 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.26.433065; this version posted February 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.
    [Show full text]
  • ABSTRACT LEWIS, MARY HUNT. Genetic Structure of Soil
    ABSTRACT LEWIS, MARY HUNT. Genetic Structure of Soil Populations of Aspergillus Section Flavi and Efficacy of Biocontrol of Aflatoxin Contamination in Corn. (Under the direction of Dr. Ignazio Carbone and Dr. Peter S. Ojiambo). Corn is contaminated with aflatoxin, a carcinogenic mycotoxin, when aflatoxigenic strains within Aspergillus section Flavi infect corn kernels. Biocontrol using non- aflatoxigenic strains of A. flavus have been shown to have the greatest potential to control aflatoxin contamination in corn. However, factors that influence the efficacy of biocontrol agents in different locations are not fully understood. One factor affecting the effectiveness biocontrol could be the genetic structure of the native soil populations of Aspergillus section Flavi. In this study, we investigated how the genetic structure of native soil populations of Aspergillus section Flavi could impact the effectiveness of two commercially available biological control products in different locations in the southeastern US. Field trials were conducted in Alabama, Georgia and North Carolina in the 2012 and 2013 growing seasons. Biocontrol products AF36 and Afla-Guard® were applied to the corn at the VT stage. Soil samples were collected prior to and 1-week after biocontrol application and at harvest to determine the genetic structure of soil populations. In all states, A. flavus (61-100%) was the most dominant species within section Flavi, with A. parasiticus (<35%) being the second- most frequently isolated species. A. nomius, A. caelatus and A. tamarii were detected only in Alabama, but at very low frequencies (<5%). Multi-locus sequence typing revealed that prior to biocontrol application in North Carolina in 2012, 48% of the isolates were the same haplotype as the biocontrol strain Afla-Guard, which belongs to lineage IB, while only 6% were of the same haplotype as AF36, which belongs to lineage IC.
    [Show full text]
  • Aspergillus Species and Mycotoxins: Occurrence and Importance in Major Food Commodities
    Aspergillus species and mycotoxins: occurrence and importance in major food commodities Marta Hiromi Taniwaki1*, John I. Pitt2, Naresh Magan3 1Food Technology Institute, ITAL, C.P. 139, Campinas SP, CEP 13078-170, Brazil. Email: [email protected] 2CSIRO Agriculture and Food, P.O. Box 52, North Ryde, NSW 1670, Australia. Email: [email protected] 3Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, Beds. MK43 0AL, U.K. email: [email protected] *Corresponding author: [email protected] Abstract Aspergillus species produce important mycotoxins, in particular aflatoxins, produced by A. flavus and related species, and ochratoxin A, produced by A. ochraceus and related species and also A. carbonarius and (less commonly) A. niger. In this review we briefly discuss the distribution of toxigenic Aspergillus species in nuts, coffee and cocoa beans, dried fruits, grapes, maize, rice and small grains. Future perspectives of distribution of Aspergillus species in foods is briefly discussed taking into account the impacts of climate change and the resilience of these mycotoxigenic species. Introduction Aspergillus is one of the three fungal genera most important in the spoilage of foodstuffs and in the production of mycotoxins, the others being Fusarium and Penicillium. Aspergillus species are the best adapted to growth in the tropics, as common species rarely grow below 10°C and most grow strongly at 37°C or above [1]. Most species that occur commonly in foods are xerophilic, with major toxin producers all able to grow down to, or near to, 0.80 water activity [1]. Some are strictly saprophytic, growing only after harvest, while some are commensals, able to grow in some plant crops and developing nuts or kernels before harvest without causing damage to the crop.
    [Show full text]
  • Paula Cristina Azevedo Rodrigues S L T I F U N O N R T O I S P T
    Universidade do Minho Escola de Engenharia m o f r o f e Paula Cristina Azevedo Rodrigues s l t i f u n o n r t o i s p t e a c i h s i c n l e a d i g n i c r x a e o s t m d a l n f m o a o c m d l Mycobiota and aflatoxigenic profile of n o a t a e n a s t o Portuguese almonds and chestnuts from e i o t u i c g b u u o production to commercialisation t d c r o y o r M P p s e u g i r d o R o d e v e z A a n i t s i r C a l u a P 0 1 0 2 | o h n i M U November 2010 Universidade do Minho Escola de Engenharia Paula Cristina Azevedo Rodrigues Mycobiota and aflatoxigenic profile of Portuguese almonds and chestnuts from production to commercialisation Dissertation for PhD degree in Chemical and Biological Engineering Supervisors Professor Doutor Nelson Lima Doutor Armando Venâncio November 2010 The integral reproduction of this thesis or parts thereof is authorized only for research purposes provided a written declaration for permission of use Universidade do Minho, November 2010 Assinatura: THIS THESIS WAS PARTIALLY SUPPORTED BY FUNDAÇÃO PARA A CIÊNCIA E A TECNOLOGIA AND THE EUROPEAN SOCIAL FUND THROUGH THE GRANT REF . SFRH/BD/28332/2006, AND BY FUNDAÇÃO PARA A CIÊNCIA E A TECNOLOGIA AND POLYTECHNIC INSTITUTE OF BRAGANÇA THROUGH THE GRANT REF .
    [Show full text]
  • The Phylogeny of Plant and Animal Pathogens in the Ascomycota
    Physiological and Molecular Plant Pathology (2001) 59, 165±187 doi:10.1006/pmpp.2001.0355, available online at http://www.idealibrary.com on MINI-REVIEW The phylogeny of plant and animal pathogens in the Ascomycota MARY L. BERBEE* Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada (Accepted for publication August 2001) What makes a fungus pathogenic? In this review, phylogenetic inference is used to speculate on the evolution of plant and animal pathogens in the fungal Phylum Ascomycota. A phylogeny is presented using 297 18S ribosomal DNA sequences from GenBank and it is shown that most known plant pathogens are concentrated in four classes in the Ascomycota. Animal pathogens are also concentrated, but in two ascomycete classes that contain few, if any, plant pathogens. Rather than appearing as a constant character of a class, the ability to cause disease in plants and animals was gained and lost repeatedly. The genes that code for some traits involved in pathogenicity or virulence have been cloned and characterized, and so the evolutionary relationships of a few of the genes for enzymes and toxins known to play roles in diseases were explored. In general, these genes are too narrowly distributed and too recent in origin to explain the broad patterns of origin of pathogens. Co-evolution could potentially be part of an explanation for phylogenetic patterns of pathogenesis. Robust phylogenies not only of the fungi, but also of host plants and animals are becoming available, allowing for critical analysis of the nature of co-evolutionary warfare. Host animals, particularly human hosts have had little obvious eect on fungal evolution and most cases of fungal disease in humans appear to represent an evolutionary dead end for the fungus.
    [Show full text]
  • Taxonomy and Evolution of Aspergillus, Penicillium and Talaromyces in the Omics Era – Past, Present and Future
    Computational and Structural Biotechnology Journal 16 (2018) 197–210 Contents lists available at ScienceDirect journal homepage: www.elsevier.com/locate/csbj Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era – Past, present and future Chi-Ching Tsang a, James Y.M. Tang a, Susanna K.P. Lau a,b,c,d,e,⁎, Patrick C.Y. Woo a,b,c,d,e,⁎ a Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong b Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong c State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong d Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong e Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong article info abstract Article history: Aspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species im- Received 25 October 2017 portant to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxo- Received in revised form 12 March 2018 nomic studies on these fungi are essential since they could provide invaluable information on their Accepted 23 May 2018 evolutionary relationships and define criteria for species recognition. With the advancement of various biological, Available online 31 May 2018 biochemical and computational technologies, different approaches have been adopted for the taxonomy of Asper- gillus, Penicillium and Talaromyces; for example, from traditional morphotyping, phenotyping to chemotyping Keywords: Aspergillus (e.g. lipotyping, proteotypingand metabolotyping) and then mitogenotyping and/or phylotyping. Since different Penicillium taxonomic approaches focus on different sets of characters of the organisms, various classification and identifica- Talaromyces tion schemes would result.
    [Show full text]
  • Challenges in Management of Aflatoxins and Ochratoxin a in Contaminated Raw Materials Esther García Cela
    Nom/Logotip de la Universitat on s’ha llegit la tesi Challenges in management of aflatoxins and ochratoxin A in contaminated raw materials Esther García Cela Dipòsit Legal: L.145-2015 http://hdl.handle.net/10803/285374 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art. 32 del Texto Refundido de la Ley de Propiedad Intelectual (RDL 1/1996).
    [Show full text]
  • Phylogeny of Penicillium and the Segregation of Trichocomaceae Into Three Families
    available online at www.studiesinmycology.org StudieS in Mycology 70: 1–51. 2011. doi:10.3114/sim.2011.70.01 Phylogeny of Penicillium and the segregation of Trichocomaceae into three families J. Houbraken1,2 and R.A. Samson1 1CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; 2Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. *Correspondence: Jos Houbraken, [email protected] Abstract: Species of Trichocomaceae occur commonly and are important to both industry and medicine. They are associated with food spoilage and mycotoxin production and can occur in the indoor environment, causing health hazards by the formation of β-glucans, mycotoxins and surface proteins. Some species are opportunistic pathogens, while others are exploited in biotechnology for the production of enzymes, antibiotics and other products. Penicillium belongs phylogenetically to Trichocomaceae and more than 250 species are currently accepted in this genus. In this study, we investigated the relationship of Penicillium to other genera of Trichocomaceae and studied in detail the phylogeny of the genus itself. In order to study these relationships, partial RPB1, RPB2 (RNA polymerase II genes), Tsr1 (putative ribosome biogenesis protein) and Cct8 (putative chaperonin complex component TCP-1) gene sequences were obtained. The Trichocomaceae are divided in three separate families: Aspergillaceae, Thermoascaceae and Trichocomaceae. The Aspergillaceae are characterised by the formation flask-shaped or cylindrical phialides, asci produced inside cleistothecia or surrounded by Hülle cells and mainly ascospores with a furrow or slit, while the Trichocomaceae are defined by the formation of lanceolate phialides, asci borne within a tuft or layer of loose hyphae and ascospores lacking a slit.
    [Show full text]
  • Discovery of a Sexual Cycle in Aspergillus Lentulus, a Close Relative of A
    Discovery of a Sexual Cycle in Aspergillus lentulus, a Close Relative of A. fumigatus Sameira S. Swilaiman,a Céline M. O’Gorman,a S. Arunmozhi Balajee,b Paul S. Dyera School of Biology, University of Nottingham, University Park, Nottingham, United Kingdoma; Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USAb Aspergillus lentulus was described in 2005 as a new species within the A. fumigatus sensu lato complex. It is an opportunistic human pathogen causing invasive aspergillosis with high mortality rates, and it has been isolated from clinical and environmen- tal sources. The species is morphologically nearly identical to A. fumigatus sensu stricto, and this similarity has resulted in their frequent misidentification. Comparative studies show that A. lentulus has some distinguishing growth features and decreased in vitro susceptibility to several antifungal agents, including amphotericin B and caspofungin. Similar to the once-presumed-asex- ual A. fumigatus, it has only been known to reproduce mitotically. However, we now show that A. lentulus has a heterothallic sexual breeding system. A PCR-based mating-type diagnostic detected isolates of either the MAT1-1 or MAT1-2 genotype, and examination of 26 worldwide clinical and environmental isolates revealed similar ratios of the two mating types (38% versus 62%, respectively). MAT1-1 and MAT1-2 idiomorph regions were analyzed, revealing the presence of characteristic alpha and high-mobility-group (HMG) domain genes, together with other more unusual features such as a MAT1-2-4 gene. We then dem- onstrated that A. lentulus possesses a functional sexual cycle with mature cleistothecia, containing heat-resistant ascospores, being produced after 3 weeks of incubation.
    [Show full text]
  • ABSTRACT MONACELL, JAMES TRENTADUE. Identification Of
    ABSTRACT MONACELL, JAMES TRENTADUE. Identification of Heterokaryon Incompatibility Genes in Aspergillus using Array Comparative Genome Hybridization and Whole Genome Sequencing. (Under the direction of Dr. Ignazio Carbone.) Aspergillus flavus is a filamentous ascomycete most noted as a pathogen of economically important crops such as corn, peanuts, and cotton. A. flavus poses a multifaceted threat causing crop loss, contaminating food with carcinogenic mycotoxins, aflatoxins (AF) and cyclopiazonic acid (CPA), as well as infecting humans and animals. A. flavus contamination has cost millions of dollars in crop loss, several outbreaks of aflatoxins laden foods and dog foods have occurred in recent years resulting in human and animal deaths, in addition to direct infection in immuno-compromised individuals. In addition to sexual reproduction, this fungus has the potential to undergo genetic exchange between compatible strains via heterokaryon formation, or parasexuality. Heterokaryon incompatibility is the inability of two strains to undergo fusion of vegetative fungal cells. This vegetative compatibility system is dictated by a series of heterokaryon incompatibility (het) loci whose alleles must all be identical for stable hyphal fusions to occur. Het loci have been identified in several filamentous fungi. This work provides the first characterization of het loci in Aspergillus flavus and A. parasiticus. Fungal individuals can be grouped into vegetative compatibility groups (VCGs) based on their ability to undergo hyphal fusions and potentially form heterokaryons. A major goal of this work is to seek a better understanding of the mechanisms controlling heterokaryon incompatibility to improve control methods of this important agricultural pathogen. We performed array-Comparative Genome Hybridization (aCGH) for eleven VCGs and a total of 51 strains in Aspergillus section Flavi, including A.
    [Show full text]
  • Sequencing Abstracts Msa Annual Meeting Berkeley, California 7-11 August 2016
    M S A 2 0 1 6 SEQUENCING ABSTRACTS MSA ANNUAL MEETING BERKELEY, CALIFORNIA 7-11 AUGUST 2016 MSA Special Addresses Presidential Address Kerry O’Donnell MSA President 2015–2016 Who do you love? Karling Lecture Arturo Casadevall Johns Hopkins Bloomberg School of Public Health Thoughts on virulence, melanin and the rise of mammals Workshops Nomenclature UNITE Student Workshop on Professional Development Abstracts for Symposia, Contributed formats for downloading and using locally or in a Talks, and Poster Sessions arranged by range of applications (e.g. QIIME, Mothur, SCATA). 4. Analysis tools - UNITE provides variety of analysis last name of primary author. Presenting tools including, for example, massBLASTer for author in *bold. blasting hundreds of sequences in one batch, ITSx for detecting and extracting ITS1 and ITS2 regions of ITS 1. UNITE - Unified system for the DNA based sequences from environmental communities, or fungal species linked to the classification ATOSH for assigning your unknown sequences to *Abarenkov, Kessy (1), Kõljalg, Urmas (1,2), SHs. 5. Custom search functions and unique views to Nilsson, R. Henrik (3), Taylor, Andy F. S. (4), fungal barcode sequences - these include extended Larsson, Karl-Hnerik (5), UNITE Community (6) search filters (e.g. source, locality, habitat, traits) for 1.Natural History Museum, University of Tartu, sequences and SHs, interactive maps and graphs, and Vanemuise 46, Tartu 51014; 2.Institute of Ecology views to the largest unidentified sequence clusters and Earth Sciences, University of Tartu, Lai 40, Tartu formed by sequences from multiple independent 51005, Estonia; 3.Department of Biological and ecological studies, and for which no metadata Environmental Sciences, University of Gothenburg, currently exists.
    [Show full text]