Systematic, Genomic, and Transcriptomic Analysis of Mycoparasitic Tolypocladium Species and Their Elaphomyces Hosts
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CUED Phd and Mphil Thesis Classes
High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice. -
<I> Elaphomyces</I>
The genus Elaphomyces (Ascomycota, Eurotiales) a ribosomal DNA-based phylogeny and revised systematics of European 'deer truffles' Paz, A.; Bellanger, J. -M.; Lavoise, C.; Molia, A.; awrynowicz, M.; Larsson, E.; Ibarguren, I. O.; Jeppson, M.; Læssøe, Thomas; Sauve, M.; Richard, F.; Moreau, P. -A. Published in: Persoonia DOI: 10.3767/003158517X697309 Publication date: 2017 Document version Publisher's PDF, also known as Version of record Document license: CC BY-NC-ND Citation for published version (APA): Paz, A., Bellanger, J. -M., Lavoise, C., Molia, A., awrynowicz, M., Larsson, E., Ibarguren, I. O., Jeppson, M., Læssøe, T., Sauve, M., Richard, F., & Moreau, P. -A. (2017). The genus Elaphomyces (Ascomycota, Eurotiales): a ribosomal DNA-based phylogeny and revised systematics of European 'deer truffles'. Persoonia, 38, 197-239. https://doi.org/10.3767/003158517X697309 Download date: 02. okt.. 2021 Persoonia 38, 2017: 197–239 ISSN (Online) 1878-9080 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE https://doi.org/10.3767/003158517X697309 The genus Elaphomyces (Ascomycota, Eurotiales): a ribosomal DNA-based phylogeny and revised systematics of European ‘deer truffles’ A. Paz1, J.-M. Bellanger2, C. Lavoise1, A. Molia3, M. Ławrynowicz4, E. Larsson5, I.O. Ibarguren6, M. Jeppson7, T. Læssøe8, M. Sauve2, F. Richard2, P.-A. Moreau9,* Key words Abstract Elaphomyces (‘deer truffles’) is one of the most important ectomycorrhizal fungal genera in temperate and subarctic forest ecosystems, but also one of the least documented in public databases. The current systemat- Astraeus ics are mainly based on macromorphology, and is not significantly different from that proposed by Vittadini (1831). Eurotiaceae Within the 49 species recognised worldwide, 23 were originally described from Europe and 17 of these were Eurotiomycetes described before the 20th century. -
Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms. -
Natasha Final 1202.Pdf (4.528Mb)
University of São Paulo “Luiz de Queiroz” College of Agriculture Advances in Metarhizium blastospores production and formulation and transcriptome studies of the yeast and filamentous growth Natasha Sant´Anna Iwanicki Thesis presented to obtain the degreee of Doctor in Science. Area: Entomology Piracicaba 2020 UNIVERSITY OF COPENHAGEN FACULTY OF SCIENCE Advances in Metarhizium blastospores production and formulation and transcriptome studies of the yeast and filamentous growth PhD THESIS 2020 – Natasha Sant´Anna Iwanicki Natasha Sant´Anna Iwanicki Agronomic Engineer Advances in Metarhizium blastospores production and formulation and transcriptome studies of the yeast and filamentous growth Advisors: Prof. Dr. ITALO DELALIBERA JUNIOR Prof. PhD and Dr. agro JØRGEN EILENBERG Co-advisor for transcriptomic studies: Associate professor PhD HENRIK H. DE FINE LICHT Thesis presented to obtain the double-degreee of Doctor in Science of the University of São Paulo and PhD at University of Copenhagen. Area: Entomology Piracicaba 2020 2 Dados Internacionais de Catalogação na Publicação DIVISÃO DE BIBLIOTECA – DIBD/ESALQ/USP Iwanicki, Natasha Sant´Anna Advances in Metarhizium blastospores production and formulation and transcriptome studies of the yeast and filamentous growth / Natasha Sant´Anna Iwanicki. - - Piracicaba, 2020. 248 p. Tese (Doutorado) - - USP / Escola Superior de Agricultura “Luiz de Queiroz”. 1. Blastosporos 2. Fermentação líquida 3. Dimorfismo fúngico 4. Fungos entomopatogênicos I. Título 3 4 ACKNOWLEDGMENTS First, I would like to thank my supervisors, Prof. Italo Delalibera Júnior and Prof. Jørgen Eilenberg for their confidence in my potential as a student, for the opportunities they gave me and the knowledge they shared, for their guidance and friendship over these years. I also thank my co-advisors, Prof. -
Eight New<I> Elaphomyces</I> Species
VOLUME 7 JUNE 2021 Fungal Systematics and Evolution PAGES 113–131 doi.org/10.3114/fuse.2021.07.06 Eight new Elaphomyces species (Elaphomycetaceae, Eurotiales, Ascomycota) from eastern North America M.A. Castellano1, C.D. Crabtree2, D. Mitchell3, R.A. Healy4 1US Department of Agriculture, Forest Service, Northern Research Station, 3200 Jefferson Way, Corvallis, OR 97331, USA 2Missouri Department of Natural Resources, Division of State Parks, 7850 N. State Highway V, Ash Grove, MO 65604, USA 33198 Midway Road, Belington, WV 26250, USA 4Department of Plant Pathology, University of Florida, Gainesville, FL 32611 USA *Corresponding author: [email protected] Key words: Abstract: The hypogeous, sequestrate ascomycete genus Elaphomyces is one of the oldest known truffle-like genera.Elaphomyces ectomycorrhizae has a long history of consumption by animals in Europe and was formally described by Nees von Esenbeck in 1820 from Europe. hypogeous fungi Until recently most Elaphomyces specimens in North America were assigned names of European taxa due to lack of specialists new taxa working on this group and difficulty of using pre-modern species descriptions. It has recently been discovered that North America sequestrate fungi has a rich diversity of Elaphomyces species far beyond the four Elaphomyces species described from North America prior to 2012. We describe eight new Elaphomyces species (E. dalemurphyi, E. dunlapii, E. holtsii, E. lougehrigii, E. miketroutii, E. roodyi, E. stevemilleri and E. wazhazhensis) of eastern North America that were collected in habitats from Quebec, Canada south to Florida, USA, west to Texas and Iowa. The ranges of these species vary and with continued sampling may prove to be larger than we have established. -
Elaphomycetaceae, Eurotiales, Ascomycota) from Africa and Madagascar Indicate That the Current Concept of Elaphomyces Is Polyphyletic
Cryptogamie, Mycologie, 2016, 37 (1): 3-14 © 2016 Adac. Tous droits réservés Molecular analyses of first collections of Elaphomyces Nees (Elaphomycetaceae, Eurotiales, Ascomycota) from Africa and Madagascar indicate that the current concept of Elaphomyces is polyphyletic Bart BUYCK a*, Kentaro HOSAKA b, Shelly MASI c & Valerie HOFSTETTER d a Muséum national d’Histoire naturelle, département systématique et Évolution, CP 39, ISYEB, UMR 7205 CNRS MNHN UPMC EPHE, 12 rue Buffon, F-75005 Paris, France b Department of Botany, National Museum of Nature and Science (TNS) Tsukuba, Ibaraki 305-0005, Japan, email: [email protected] c Muséum national d’Histoire naturelle, Musée de l’Homme, 17 place Trocadéro F-75116 Paris, France, email: [email protected] d Department of plant protection, Agroscope Changins-Wädenswil research station, ACW, rte de duiller, 1260, Nyon, Switzerland, email: [email protected] Abstract – First collections are reported for Elaphomyces species from Africa and Madagascar. On the basis of an ITS phylogeny, the authors question the monophyletic nature of family Elaphomycetaceae and of the genus Elaphomyces. The objective of this preliminary paper was not to propose a new phylogeny for Elaphomyces, but rather to draw attention to the very high dissimilarity among ITS sequences for Elaphomyces and to the unfortunate choice of species to represent the genus in most previous phylogenetic publications on Elaphomycetaceae and other cleistothecial ascomycetes. Our study highlights the need for examining the monophyly of this family and to verify the systematic status of Pseudotulostoma as a separate genus for stipitate species. Furthermore, there is an urgent need for an in-depth morphological study, combined with molecular sequencing of the studied taxa, to point out the phylogenetically informative characters of the discussed taxa. -
Cordyceps Medicinal Fungus: Harvest and Use in Tibet
HerbalGram 83 • August – October 2009 83 • August HerbalGram Kew’s 250th Anniversary • Reviving Graeco-Arabic Medicine • St. John’s Wort and Birth Control The Journal of the American Botanical Council Number 83 | August – October 2009 Kew’s 250th Anniversary • Reviving Graeco-Arabic Medicine • Lemongrass for Oral Thrush • Hibiscus for Blood Pressure • St. John’s Wort and BirthWort Control • St. John’s Blood Pressure • HibiscusThrush for Oral for 250th Anniversary Medicine • Reviving Graeco-Arabic • Lemongrass Kew’s US/CAN $6.95 Cordyceps Medicinal Fungus: www.herbalgram.org Harvest and Use in Tibet www.herbalgram.org www.herbalgram.org 2009 HerbalGram 83 | 1 STILL HERBAL AFTER ALL THESE YEARS Celebrating 30 Years of Supporting America’s Health The year 2009 marks Herb Pharm’s 30th anniversary as a leading producer and distributor of therapeutic herbal extracts. During this time we have continually emphasized the importance of using the best quality certified organically cultivated and sustainably-wildcrafted herbs to produce our herbal healthcare products. This is why we created the “Pharm Farm” – our certified organic herb farm, and the “Plant Plant” – our modern, FDA-audited production facility. It is here that we integrate the centuries-old, time-proven knowledge and wisdom of traditional herbal medicine with the herbal sciences and technology of the 21st Century. Equally important, Herb Pharm has taken a leadership role in social and environmental responsibility through projects like our use of the Blue Sky renewable energy program, our farm’s streams and Supporting America’s Health creeks conservation program, and the Botanical Sanctuary program Since 1979 whereby we research and develop practical methods for the conser- vation and organic cultivation of endangered wild medicinal herbs. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Septal Pore Caps in Basidiomycetes Composition and Ultrastructure
Septal Pore Caps in Basidiomycetes Composition and Ultrastructure Septal Pore Caps in Basidiomycetes Composition and Ultrastructure Septumporie-kappen in Basidiomyceten Samenstelling en Ultrastructuur (met een samenvatting in het Nederlands) Proefschrift ter verkrijging van de graad van doctor aan de Universiteit Utrecht op gezag van de rector magnificus, prof.dr. J.C. Stoof, ingevolge het besluit van het college voor promoties in het openbaar te verdedigen op maandag 17 december 2007 des middags te 16.15 uur door Kenneth Gregory Anthony van Driel geboren op 31 oktober 1975 te Terneuzen Promotoren: Prof. dr. A.J. Verkleij Prof. dr. H.A.B. Wösten Co-promotoren: Dr. T. Boekhout Dr. W.H. Müller voor mijn ouders Cover design by Danny Nooren. Scanning electron micrographs of septal pore caps of Rhizoctonia solani made by Wally Müller. Printed at Ponsen & Looijen b.v., Wageningen, The Netherlands. ISBN 978-90-6464-191-6 CONTENTS Chapter 1 General Introduction 9 Chapter 2 Septal Pore Complex Morphology in the Agaricomycotina 27 (Basidiomycota) with Emphasis on the Cantharellales and Hymenochaetales Chapter 3 Laser Microdissection of Fungal Septa as Visualized by 63 Scanning Electron Microscopy Chapter 4 Enrichment of Perforate Septal Pore Caps from the 79 Basidiomycetous Fungus Rhizoctonia solani by Combined Use of French Press, Isopycnic Centrifugation, and Triton X-100 Chapter 5 SPC18, a Novel Septal Pore Cap Protein of Rhizoctonia 95 solani Residing in Septal Pore Caps and Pore-plugs Chapter 6 Summary and General Discussion 113 Samenvatting 123 Nawoord 129 List of Publications 131 Curriculum vitae 133 Chapter 1 General Introduction Kenneth G.A. van Driel*, Arend F. -
Infection of the Silkworm, Bombyx Mori, with Cordyceps Militaris
Journal of Insect Biotechnology and Sericology 71, 61-63 (2002) Infection of the Silkworm, Bombyx mori, with Cordyceps militaris Ruiying Chen* and Masatoshi Ichida Faculty of TextileScience, Kyoto Institute of Technology, Saga-ippongi 1, Ukyou-ku,Kyoto 616-8354, Japan (Received April 3, 2001; Accepted December 29, 2001) To develop techniques to produce stromata of Cordyceps militaris (L.) Link on a large scale, the silkworm, Bombyx mori, was infected and the growth of stroma was investigated. The 5th instar larvae and the pupae of the silkworm reared in a sterilized indoor environment on an artificial diet and were inoculated with C. militaris by spraying, dipping, or by hypodermic injection. The rate of infection differed among the three methods; the highest being in the hypodermic injection. The rate of infection was also higher in the pupae than in the larvae. The formation and growth of the stromata were better in the silkworm pupae. A conidial suspension was injected at different sites on the pupal body. Infection rates, however, did not differ significantly among the sites. The formation and growth of the stromata were not affected by the injection site either. Key words: Cordyceps militaris, silkworm, Bombyx mori, infection, artificial inoculation, stromata suspension was adjusted to 10' conidia/ml. This suspension INTRODUCTION was used in the inoculation experiments. Cordyceps militaris (L.) Link. is a parasitic fungus hosted by many species of lepidopteran pupae. It belongs Rearing of host silkworm to the subdivision Ascomycotina whose stroma is The silkworm, Bombyx mori, was reared in a sterilized baculiform (Shimizu, 1997). Recently, many researches indoor environment on an artificial diet (Chen et al., 1992). -
Multigene Phylogeny and Morphology Reveal a New Species, Ophiocordyceps Vespulae, from Jilin Province, China
Phytotaxa 478 (1): 033–048 ISSN 1179-3155 (print edition) https://www.mapress.com/j/pt/ PHYTOTAXA Copyright © 2021 Magnolia Press Article ISSN 1179-3163 (online edition) https://doi.org/10.11646/phytotaxa.478.1.2 Multigene phylogeny and morphology reveal a new species, Ophiocordyceps vespulae, from Jilin Province, China FENG-YAO LONG1, 2, 6, LI-WU QIN3, 7, YUAN-PIN XIAO2, 4, 8, KEVIN D. HYDE4, 9, SHAO-XIAN WANG3, 10* & TING-CHI WEN1, 2, 5, 11* 1 School of Pharmacy, Guizhou University, Guiyang 550025, Guizhou, China. 2 The Engineering Research Center of Southwest Bio-Pharmaceutical Resources, Ministry of Education, Guizhou University, Guiyang 550025, Guizhou, China. 3 Changbai Mountain Academy of Sciences, Jilin Provincial Joint Key Laboratory of Changbai Mountains Biocoenosis & Biodiversity, Erdaobaihe 133613, Jilin, China. 4 Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand. 5Mushroom Research Institute,Guizhou University,Guiyang,550025,China 6 [email protected]; https://orcid.org/0000-0002-5818-694X 7 [email protected]; https://orcid.org/0000-0002-5586-2885 8 [email protected]; https://orcid.org/0000-0003-1730-3545 9 [email protected]; https://orcid.org/0000-0002-2191-0762 10 [email protected]; https://orcid.org/0000-0002-0921-1790 11 [email protected]; https://orcid.org/0000-0003-1744-5869 *Corresponding author Abstract Ophiocordyceps is entomopathogenic and is the best studied genus in Ophiocordycipitaceae. Members of Ophiocordyceps and ants form sophisticated interactions. However, taxonomy and evolutionary relationships of this group of pathogens remain unclear. During a survey in Changbai Mountains, Jiling Province, China, a new entomogenous species, Ophiocordyceps vespulae sp. -
Coupled Biosynthesis of Cordycepin and Pentostatin in Cordyceps Militaris: Implications for Fungal Biology and Medicinal Natural Products
85 Editorial Commentary Page 1 of 3 Coupled biosynthesis of cordycepin and pentostatin in Cordyceps militaris: implications for fungal biology and medicinal natural products Peter A. D. Wellham1, Dong-Hyun Kim1, Matthias Brock2, Cornelia H. de Moor1,3 1School of Pharmacy, 2School of Life Sciences, 3Arthritis Research UK Pain Centre, University of Nottingham, Nottingham, UK Correspondence to: Cornelia H. de Moor. School of Pharmacy, University Park, Nottingham NG7 2RD, UK. Email: [email protected]. Provenance: This is an invited article commissioned by the Section Editor Tao Wei, PhD (Principal Investigator, Assistant Professor, Microecologics Engineering Research Center of Guangdong Province in South China Agricultural University, Guangzhou, China). Comment on: Xia Y, Luo F, Shang Y, et al. Fungal Cordycepin Biosynthesis Is Coupled with the Production of the Safeguard Molecule Pentostatin. Cell Chem Biol 2017;24:1479-89.e4. Submitted Apr 01, 2019. Accepted for publication Apr 04, 2019. doi: 10.21037/atm.2019.04.25 View this article at: http://dx.doi.org/10.21037/atm.2019.04.25 Cordycepin, or 3'-deoxyadenosine, is a metabolite produced be replicated in people, this could become a very important by the insect-pathogenic fungus Cordyceps militaris (C. militaris) new natural product-derived medicine. and is under intense investigation as a potential lead compound Cordycepin is known to be unstable in animals due for cancer and inflammatory conditions. Cordycepin was to deamination by adenosine deaminases. Much of the originally extracted by Cunningham et al. (1) from a culture efforts towards bringing cordycepin to the clinic have been filtrate of a C. militaris culture that was grown from conidia.