DOCSLIB.ORG

Gene Expression Profiling of Wood Decay Fungus Fibroporia Radiculosa Grown On

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Gene Expression Profiling of Wood Decay Fungus Fibroporia Radiculosa Grown On Mississippi State University Scholars Junction Theses and Dissertations Theses and Dissertations 1-1-2016 Gene Expression Profiling of oodW Decay Fungus Fibroporia Radiculosa Grown on Different Organic and Copper Based Preservatives Ayfer Akgul Follow this and additional works at: https://scholarsjunction.msstate.edu/td Recommended Citation Akgul, Ayfer, "Gene Expression Profiling of oodW Decay Fungus Fibroporia Radiculosa Grown on Different Organic and Copper Based Preservatives" (2016). Theses and Dissertations. 2381. https://scholarsjunction.msstate.edu/td/2381 This Dissertation - Open Access is brought to you for free and open access by the Theses and Dissertations at Scholars Junction. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Scholars Junction. For more information, please contact [email protected]. Template B v3.0 (beta): Created by J. Nail 06/2015 Gene expression profiling of wood decay fungus Fibroporia radiculosa grown on different organic and copper based preservatives By TITLE PAGE Ayfer Akgul A Dissertation Submitted to the Faculty of Mississippi State University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Forest Resources in the Department of Sustainable Bioproducts Mississippi State, Mississippi December 2016 Copyright by COPYRIGHT PAGE Ayfer Akgul 2016 Gene expression profiling of wood decay fungus Fibroporia radiculosa grown on different organic and copper based preservatives By APPROVAL PAGE Ayfer Akgul Approved: ____________________________________ Susan V. Diehl (Director of Dissertation) ____________________________________ Darrel D. Nicholas (Committee Member) ____________________________________ Dragica Jeremic Nikolic (Committee Member) ____________________________________ Juliet D. Tang (Committee Member) ____________________________________ Abdolhamid Borazjani (Committee Member / Graduate Coordinator) ____________________________________ George M. Hopper Dean College of Forest Resources Name: Ayfer Akgul ABSTRACT Date of Degree: December 9, 2016 Institution: Mississippi State University Major Field: Forest Resources Major Professor: Dr. Susan V. Diehl Title of Study: Gene expression profiling of wood decay fungus Fibroporia radiculosa grown on different organic and copper based preservatives Pages in Study 224 Candidate for Degree of Doctor of Philosophy Copper tolerant brown rot fungi are able to depolymerize the structure of wood treated with copper or organic wood preservatives. This research used quantitative polymerase chain reaction (qRT-PCR) combined with RNA-seq to explore what genes of the brown-rot fungus, Fibroporia radiculosa, are expressed when the fungus is overcoming the wood preservatives and decaying the wood. The preliminary study of ACQ-treated wood indicated that the hydrogen peroxide needed for wood decay to proceed may come from AAOX (aryl alcohol oxidase), with oxalate regulation by ODC2 (oxalate decarboxylase), and copper regulation by COP (copper resistance P-type ATPase pump). The principal study measured the expression of ten genes at early, mid, and late stages of decay in wood treated with azole, copper, quat, ACQ, CA, plus untreated. Both AAOX and LCC (laccase) were often expressed at their highest levels early in the decay stages, thus either one or both could be involved in early Fenton chemistry. Expression levels of ICL (isocitrate lyase) and GLOXDH (glyoxylate dehydrogenase) were also highest in early decay stages. Of great interest was the complete lack of expression of the COP gene on copper-treated wood at any decay stage. The most surprising and significant result is the impact the quat-treatment had on the metabolism of the fungus, and lack of impact of the azole-treatment. This research indicates that it is the quat that provides the greatest inhibition of F. radiculosa, more so than the copper. Based on RNA Seq, the total number of genes that were up- or down-regulated on the copper- treatment was 473, with 293 on the quat-treatment, and 185 on the azole-treatment. There were a number of genes with unknown protein functions highly expressed. These data distinctly show that gene expression profiles of F. radiculosa are altered by different wood preservative compositions and the duration of wood decay. These genes and this data needs further analysis and study in order to meet the long term goal of understanding the mechanism of copper-tolerance in Fibroporia radiculosa. DEDICATION I am dedicating this research to my husband, Ali Akgul, and my sons, Salih Yigit Akgul and Melih Said Akgul. ii ACKNOWLEDGEMENTS I am grateful to my graduate advisor Dr. Susan Diehl for mentorship, understanding, support, and generous guidance during my research. I am also thankful to my committee members Dr. Darrel D. Nicholas, Dr. Dragica Jeremic Nikolic, Dr. Abdolhamid Borazjani, and Dr. Juliet D. Tang for guidance. Also, I would like to thank Dr. Trey Skrobot for his friendly supports. I extend my thanks to researcher Dr. Seval Ozkan for helping in my first research at MSU. Finally, I am grateful to my husband Ali for helping me in my research and classes during my PhD. iii TABLE OF CONTENTS DEDICATION .................................................................................................................... ii ACKNOWLEDGEMENTS ............................................................................................... iii LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES ............................................................................................................ x CHAPTER I. INTRODUCTION ................................................................................................1 Wood Structure ......................................................................................................1 Wood Preservatives ...............................................................................................6 Wood Biodegradation ............................................................................................8 Overview of White-rot Decay ...............................................................................9 Brown-rot decay ..................................................................................................12 Copper Tolerance ................................................................................................19 Objectives of Research ........................................................................................24 References Cited ..................................................................................................26 II. GENE EXPRESSION ANALYSIS OF WOOD DECAY FUNGUS FIBROPORIA RADICULOSA GROWN IN ACQ-TREATED WOOD ....................................................................................................33 Introduction .........................................................................................................33 Materials and Methods ........................................................................................38 Fungus Isolate ................................................................................................38 Preservative Treatments and Wafer Preparation ...........................................38 Fungal Growth on Copper Treated Wood Blocks .........................................38 Wood Compression Testing ..........................................................................39 RNA Isolation ................................................................................................39 cDNA Synthesis ............................................................................................40 Real-Time qPCR ...........................................................................................41 Results .................................................................................................................42 Wood Compression Strength Loss ................................................................42 RNA Quality ..................................................................................................43 Gene expression Analysis (qRT-PCR) ..........................................................45 Discussion ............................................................................................................54 iv References Cited ..................................................................................................61 III. TRANSCRIPTOMIC ANALYSIS OF WOOD DECAY FUNGUS FIBROPORIA RADICULOSA IN COPPER AND ORGANIC BASED WOOD PRESERVATIVES ....................................................64 Introduction .........................................................................................................64 Materials and Methods ........................................................................................70 Fungus Isolate ................................................................................................70 Preservative Treatments and Ground Wood Preparation ..............................70 Fungal Growth on Ground Wood ..................................................................71 Sample Counting ...........................................................................................73 RNA Isolation ................................................................................................74 cDNA Synthesis ............................................................................................75
Load more

Recommended publications
  • Suppl Table I
    SUPPLEMENTARY TABLE I. Species and isolates included in the study, their vouchers, locality and GenBank accession Species Isolate number Locality ITS GenBank LSU GenBank accession no. accession no. Amylocystis lapponica (Romell) HHB-13400-Sp USA, Alaska KC585237 KC585059 Bondartsev & Singer ex Singer OKM-4418-Sp USA, Montana KC585238 KC585060 KHL-11755 − EU118603 Amyloporia carbonica (Overh.) DAOM-F-8281-T Canada, British KC585239 KC585061 Vampola & Pouzar Columbia FP-105585-Sp USA, Oregon KC585240 KC585062 RLG-12496-Sp USA, Nevada KC585241 KC585063 Wilcox-96 USA, California KC585242 KC585064 Zabel-40-GLN USA, New York KC585243 KC585065 Amyloporia nothofaginea Rajchenb. BAFC519794 Argentina JF713078 − & Gorjón (=MMBP-2011) BAFC519796 (=MBP- Argentina JF713079 − 2011a) Amyloporia sinuosa (Fr.) Rajchenb., FP-105386-Sp USA, New KC585244 KC585066 Gorjón & Pildain Hampshire FP-94464-Sp USA, Idaho KC585245 KC585067 HHB-12878-Sp USA, Alaska KC585246 KC585068 L-14130-Sp USA, New York KC585247 KC585069 L-6192-Sp USA, Colorado KC585248 KC585070 L-9792-Sp USA, Arizona KC585249 KC585071 Pa-3C JapanYamagata KC585250 KC585072 Prefecture Pa-3e JapanShizuoka KC585251 KC585073 Prefecture RLG-2538 USA, New York EU232196 EU232288 X725 (=Miettinen- Finland JQ700270 JQ700270 12407) P-115 (=RLG-2538) USA AJ416068 − P-211 (G-214) Germany, Karlsrube AJ345011 − RLG-1182R USA, Arizona AY966450 AY333831 Amyloporia sitchensis (D.V. Baxter) HHB-5320-Sp USA, Montana KC585252 KC585074 Vampola & Pouzar HHB-5298 USA, Montana − AY333829 HHB-12513 USA, Alaska AY966451 AY333830
    [Show full text]
  • Short-Read Sequencing for Genomic Analysis of the Brown Rot Fungus Fibroporia Radiculosa
    Short-Read Sequencing for Genomic Analysis of the Brown Rot Fungus Fibroporia radiculosa Juliet D. Tang,a Andy D. Perkins,b Tad S. Sonstegard,c Steven G. Schroeder,c Shane C. Burgess,d and Susan V. Diehla Forest Products, Mississippi State University, Mississippi State, Mississippi, USAa; Computer Science and Engineering, Mississippi State University, Mississippi State, Mississippi, USAb; USDA ARS Bovine Functional Genomics Laboratory, Beltsville, Maryland, USAc; and Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, Mississippi, USAd The feasibility of short-read sequencing for genomic analysis was demonstrated for Fibroporia radiculosa, a copper-tolerant fungus that causes brown rot decay of wood. The effect of read quality on genomic assembly was assessed by filtering Illumina GAIIx reads from a single run of a paired-end library (75-nucleotide read length and 300-bp fragment size) at three different stringency levels and then assembling each data set with Velvet. A simple approach was devised to determine which filter strin- gency was “best.” Venn diagrams identified the regions containing reads that were used in an assembly but were of a low-enough quality to be removed by a filter. By plotting base quality histograms of reads in this region, we judged whether a filter was too stringent or not stringent enough. Our best assembly had a genome size of 33.6 Mb, an N50 of 65.8 kb for a k-mer of 51, and a maximum contig length of 347 kb. Using GeneMark, 9,262 genes were predicted. TargetP and SignalP analyses showed that among the 1,213 genes with secreted products, 986 had motifs for signal peptides and 227 had motifs for signal anchors.
    [Show full text]
  • A New Species of Antrodia (Basidiomycota, Polypores) from China
    Mycosphere 8(7): 878–885 (2017) www.mycosphere.org ISSN 2077 7019 Article Doi 10.5943/mycosphere/8/7/4 Copyright © Guizhou Academy of Agricultural Sciences A new species of Antrodia (Basidiomycota, Polypores) from China Chen YY, Wu F* Institute of Microbiology, Beijing Forestry University, Beijing 100083, China Chen YY, Wu F 2017 –A new species of Antrodia (Basidiomycota, Polypores) from China. Mycosphere 8(7), 878–885, Doi 10.5943/mycosphere/8/7/4 Abstract A new species, Antrodia monomitica sp. nov., is described and illustrated from China based on morphological characters and molecular evidence. It is characterized by producing annual, fragile and nodulose basidiomata, a monomitic hyphal system with clamp connections on generative hyphae, hyaline, thin-walled and fusiform to mango-shaped basidiospores (6–7.5 × 2.3– 3 µm), and causing a typical brown rot. In phylogenetic analysis inferred from ITS and nLSU rDNA sequences, the new species forms a distinct lineage in the Antrodia s. l., and has a close relationship with A. oleracea. Key words – Fomitopsidaceae – phylogenetic analysis – taxonomy – wood-decaying fungi Introduction Antrodia P. Karst., typified with Polyporus serpens Fr. (=Antrodia albida (Fr.) Donk (Donk 1960, Ryvarden 1991), is characterized by a resupinate to effused-reflexed growth habit, white or pale colour of the context, a dimitic hyphal system with clamp connections on generative hyphae, hyaline, thin-walled, cylindrical to very narrow ellipsoid basidiospores which are negative in Melzer’s reagent and Cotton Blue, and causing a brown rot (Ryvarden & Melo 2014). Antrodia is a highly heterogeneous genus which is closely related to Fomitopsis P.
    [Show full text]
  • Evidence of Subterranean Termite Feeding Deterrent Produced by Brown Rot Fungus Fibroporia Radiculosa (Peck) Parmasto 1968 (Polyporales, Fomitopsidaceae)
    insects Article Evidence of Subterranean Termite Feeding Deterrent Produced by Brown Rot Fungus Fibroporia radiculosa (Peck) Parmasto 1968 (Polyporales, Fomitopsidaceae) Nadia Nuraniya Kamaluddin 1, Akiko Nakagawa-Izumi 1,*, Shota Nishizawa 1, Ayuko Fukunaga 1, Shuichi Doi 1, Tsuyoshi Yoshimura 2 and Sakae Horisawa 3 1 Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-0872, Japan; [email protected](N.N.K.); [email protected], (S.N.); [email protected] (A.F.); [email protected] (S.D.) 2 Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan; [email protected] 3 School of Environmental Science and Engineering, Kochi University of Technology, Kami, Kochi 782-8502, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-29-853-4578 Academic Editor: Brian T. Forschler Received: 11 April 2016; Accepted: 9 August 2016; Published: 18 August 2016 Abstract: We found that decayed wood stakes with no termite damage collected from a termite-infested field exhibited a deterrent effect against the termite Reticulitermes speratus, Kolbe, 1885. The effect was observed to be lost or reduced by drying. After identification, it was found that the decayed stakes were infected by brown rot fungus Fibroporia radiculosa (Peck) Parmasto, 1968. In a no-choice feeding test, wood blocks decayed by this fungus under laboratory condition deterred R. speratus feeding and n-hexane extract from the decayed stake and blocks induced termite mortality. These data provided an insight into the interaction between wood-rot fungi and wood-feeding termites.
    [Show full text]
  • Wood Research Indoor Fungal Destroyers of Wooden Materials – Their Identification in Present Review
    WOOD RESEARCH 63 (2): 2018 203-214 INDOOR FUNGAL DESTROYERS OF WOODEN MATERIALS – THEIR IDENTIFICATION IN PRESENT REVIEW Ján Gáper Technical University in Zvolen, Faculty of Ecology and Environmental Sciences Department of Biology and Ecology Zvolen, Slovak Republic et University of Ostrava Faculty of Sciences, Department of Biology and Ecology Ostrava, Czech Republic Svetlana Gáperová, Terézia Gašparcová, Simona Kvasnová Matej Bel University, Faculty of Natural Sciences, Department of Biology and Ecology Banská Bystrica, Slovak Republic Peter Pristaš Pavol Jozef Šafárik University, Faculty of Natural Sciences Institute of Biology and Ecology Košice, Slovak Republic Kateřina Náplavová University of Ostrava, Faculty of Sciences, Department of Biology and Ecology Ostrava, Czech Republic et University of Minho Ceb-Centre of Biological Engineering, Campus De Gualtar Braga, Portugal (Received January 2018) ABSTRACT The wood-destroying fungi traditionally were separated from one another primarily on a basis of their sporocarp and/or strain morphology. Their diversity and simple macro- and 203 WOOD RESEARCH micromorphology of fungal structures have been major obstacles for more rapid progress in this regard. However, over the past two decades, there has been substantial progress in our understanding of genetic variability within traditionally recognized morphospecies. In this study we have overviewed genetic variation and phylogeography of macrofungi, which are important destroyers of wooden materials indoor of buildings. Several morphologically defined species of these fungal destroyers (Coniophora puteana, C. olivacea, C. arida, Serpula himantioides) have been shown to actually encompass several genetically isolated lineages (cryptic species). The protective efficacy against cryptic species within traditionally recognized morphospecies through laboratory tests (EN 113) and field trials (EN 252) might be sufficient to better prognosis of decay development in wooden materials for hazard assessment and for proper conservation and management plans.
    [Show full text]
  • Phylogenetic Relationships of Antrodia Species and Related Taxa Based on Analyses of Nuclear Large Subunit Ribosomal DNA Sequences
    Botanical Studies (2010) 51: 53-60. MicrobioLOGY Phylogenetic relationships of Antrodia species and related taxa based on analyses of nuclear large subunit ribosomal DNA sequences Zhi-HeYU1,Sheng-HuaWU2,*,Dong-MeiWANG3,andCheng-TauCHEN2 1College of Life Science, Yangtze University, Jingzhou 434025, Hubei, P.R. China 2Department of Botany, National Museum of Natural Science, Taichung 404, Taiwan 3Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, P.R. China (Received March 24, 2008; Accepted July 10, 2009) ABSTRACT. ThisstudyaimedtoevaluaterelationshipsofAntrodia species and related taxa, including the taxonomic status of some Antrodiaspeciesthathavebeentreatedasseparategenera(Amyloporia,Fibroporia, andTaiwanofungus).AcomprehensivephylogeneticstudyofHomobasidiomycetespresentedbyBinderetal. in 2005, was consulted for sampling the taxa used for this analysis. The genera of the “residual” polyporoid cladeandphlebioidcladeoftheHomobasidiomyceteswerechosenasoutgroups,andthegenerabelonging totheAntrodiacladeandcorepolyporoidcladewereselectedasingroup.Phylogeneticanalysesofthisstudy werebasedonsequencedataderivedfromthenuclearlargesubunitribosomalDNA(nuc-LSUrDNA).The analytical methods of maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI) wereused.Resultsfromthesedifferentanalysesweregenerallyconsistent.Twomaincladeslackinghigh support were detected in the ingroup. Clade A consisted of taxa of the Antrodiaclade,includingalltwelve
    [Show full text]
  • Phylogenetic Position and Taxonomy of Kusaghiporia Usambarensis Gen
    Mycology An International Journal on Fungal Biology ISSN: 2150-1203 (Print) 2150-1211 (Online) Journal homepage: http://www.tandfonline.com/loi/tmyc20 Phylogenetic position and taxonomy of Kusaghiporia usambarensis gen. et sp. nov. (Polyporales) Juma Mahmud Hussein, Donatha Damian Tibuhwa & Sanja Tibell To cite this article: Juma Mahmud Hussein, Donatha Damian Tibuhwa & Sanja Tibell (2018): Phylogenetic position and taxonomy of Kusaghiporia usambarensis gen. et sp. nov. (Polyporales), Mycology, DOI: 10.1080/21501203.2018.1461142 To link to this article: https://doi.org/10.1080/21501203.2018.1461142 © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Published online: 15 Apr 2018. Submit your article to this journal View related articles View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=tmyc20 MYCOLOGY, 2018 https://doi.org/10.1080/21501203.2018.1461142 Phylogenetic position and taxonomy of Kusaghiporia usambarensis gen. et sp. nov. (Polyporales) Juma Mahmud Husseina,b, Donatha Damian Tibuhwab and Sanja Tibella aInstitute of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden; bDepartment of Molecular Biology and Biotechnology, College of Natural & Applied Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania ABSTRACT ARTICLE HISTORY A large polyporoid mushroom from the West Usambara Mountains in North-eastern Tanzania Received 17 November 2017 produces dark brown, up to 60-cm large fruiting bodies that at maturity may weigh more than Accepted 2 April 2018 10 kg. It has a high rate of mycelial growth and regeneration and was found growing on both dry KEYWORDS and green leaves of shrubs; attached to the base of living trees, and it was also observed to Kusaghiporia; molecular degrade dead snakes and insects accidentally coming into contact with it.
    [Show full text]
  • A Revised Family-Level Classification of the Polyporales (Basidiomycota)
    fungal biology 121 (2017) 798e824 journal homepage: www.elsevier.com/locate/funbio A revised family-level classification of the Polyporales (Basidiomycota) Alfredo JUSTOa,*, Otto MIETTINENb, Dimitrios FLOUDASc, € Beatriz ORTIZ-SANTANAd, Elisabet SJOKVISTe, Daniel LINDNERd, d €b f Karen NAKASONE , Tuomo NIEMELA , Karl-Henrik LARSSON , Leif RYVARDENg, David S. HIBBETTa aDepartment of Biology, Clark University, 950 Main St, Worcester, 01610, MA, USA bBotanical Museum, University of Helsinki, PO Box 7, 00014, Helsinki, Finland cDepartment of Biology, Microbial Ecology Group, Lund University, Ecology Building, SE-223 62, Lund, Sweden dCenter for Forest Mycology Research, US Forest Service, Northern Research Station, One Gifford Pinchot Drive, Madison, 53726, WI, USA eScotland’s Rural College, Edinburgh Campus, King’s Buildings, West Mains Road, Edinburgh, EH9 3JG, UK fNatural History Museum, University of Oslo, PO Box 1172, Blindern, NO 0318, Oslo, Norway gInstitute of Biological Sciences, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway article info abstract Article history: Polyporales is strongly supported as a clade of Agaricomycetes, but the lack of a consensus Received 21 April 2017 higher-level classification within the group is a barrier to further taxonomic revision. We Accepted 30 May 2017 amplified nrLSU, nrITS, and rpb1 genes across the Polyporales, with a special focus on the Available online 16 June 2017 latter. We combined the new sequences with molecular data generated during the Poly- Corresponding Editor: PEET project and performed Maximum Likelihood and Bayesian phylogenetic analyses. Ursula Peintner Analyses of our final 3-gene dataset (292 Polyporales taxa) provide a phylogenetic overview of the order that we translate here into a formal family-level classification.
    [Show full text]
  • A Phylogenetic Analysis of Antrodia S.L. Based on Nrdna ITS Sequences, with Emphasis on Rhizomorphic European Species
    Mycol Progress (2012) 11:93–100 DOI 10.1007/s11557-010-0732-z ORIGINAL ARTICLE A phylogenetic analysis of Antrodia s.l. based on nrDNA ITS sequences, with emphasis on rhizomorphic European species Annarosa Bernicchia & Sergio Pérez Gorjón & Petr Vampola & Leif Ryvarden & Antonio Prodi Received: 25 August 2010 /Revised: 28 November 2010 /Accepted: 3 December 2010 /Published online: 24 December 2010 # The Author(s) 2010. This article is published with open access at Springerlink.com Abstract The rhizomorphic European species of Antrodia, Introduction belonging to the traditionally called Antrodia radiculosa group, are investigated. On the basis of morphological and The genus Antrodia P. Karst. in a wide sense includes molecular analysis, the genus Fibroporia is supported. species with a dimitic hyphal system, clamped generative Specimens from Central Europe previously ascribed to hyphae and causing a brown rot (Ryvarden 1991; Ryvarden Antrodia radiculosa constitute a species of their own, and and Gilbertson 1993). The genus thus defined is heteroge- are herein described as Fibroporia bohemica. Moreover, a neous, and it has long been regarded as a polyphyletic new combination, Fibroporia citrina, is proposed. group due to variations in macro- and micromorphological characters such as the structure of basidiomata, basidio- Keywords Antrodia . Fibroporia . Wood-inhabiting fungi . spores morphology, an iodine reaction of hyphae and Polypores . ITS . Molecular phylogeny sexuality (Lombard 1990; Ryvarden 1991; Ryvarden and Gilbertson 1993; Kim et al. 2001). About 50 species have been described (Kirk et al. 2001; Dai and Niemelä 2002), of A. Bernicchia : A. Prodi which around 30 are known to be present in Europe. Dipartimento di Scienze e Tecnologie Agroambientali, Among the polyporoid fungi, Antrodiella Ryvarden & I.
    [Show full text]
  • A Genomic and Transcriptomic Analysis of Wood Decay and Copper Tolerance in the Brown Rot Fungus Fibroporia Radiculosa
    Mississippi State University Scholars Junction Theses and Dissertations Theses and Dissertations 1-1-2011 A genomic and transcriptomic analysis of wood decay and copper tolerance in the brown rot fungus Fibroporia radiculosa Juliet D. Tang Follow this and additional works at: https://scholarsjunction.msstate.edu/td Recommended Citation Tang, Juliet D., "A genomic and transcriptomic analysis of wood decay and copper tolerance in the brown rot fungus Fibroporia radiculosa" (2011). Theses and Dissertations. 143. https://scholarsjunction.msstate.edu/td/143 This Dissertation - Open Access is brought to you for free and open access by the Theses and Dissertations at Scholars Junction. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Scholars Junction. For more information, please contact [email protected]. Template Created By: James Nail 2010 A GENOMIC AND TRANSCRIPTOMIC ANALYSIS OF WOOD DECAY AND COPPER TOLERANCE IN THE BROWN ROT FUNGUS FIBROPORIA RADICULOSA By Juliet Dao-May Tang A Dissertation Submitted to the Faculty of Mississippi State University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Forest Resources in the Department of Forest Products Mississippi State, Mississippi December 2011 Template Created By: James Nail 2010 Copyright 2011 By Juliet Dao-May Tang Template Created By: James Nail 2010 A GENOMIC AND TRANSCRIPTOMIC ANALYSIS OF WOOD DECAY AND COPPER TOLERANCE IN THE BROWN ROT FUNGUS FIBROPORIA RADICULOSA By Juliet Dao-May Tang Approved: _________________________________ _________________________________ Susan V. Diehl Shane C. Burgess Professor of Forest Products Dean of the College of Agriculture and (Director of Dissertation) Life Sciences, University of Arizona (Committee Member) _________________________________ _________________________________ Andy D.
    [Show full text]
  • Genetic Diversity and RNA-Seq Transcriptome Analysis of Tricholoma Matsutake from Sichuan Province, China
    Pol. J. Environ. Stud. Vol. 25, No. 6 (2016), 2327-2338 DOI: 10.15244/pjoes/63297 Original Research Genetic Diversity and RNA-seq Transcriptome Analysis of Tricholoma matsutake from Sichuan Province, China Xiang Ding1, 2, Panpan Wang2, Yiling Hou*2, Mei Wang3, Wanru Hou2, Yuming Li3 1Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, 621000, China 2Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Sciences, China West Normal University, Nanchong, 637009, China 3National Center for Sweet Potato Improvement Centre of Nanchong, Nanchong Academy of Agricultural Sciences, Nanchong, 637001, China Received: 16 March 2016 Accepted: 19 May 2016 Abstract The sequences of the internal transcribed spacer (ITS) regions of ectomycorrhizal fungi collected from Sichuan Province were analyzed using a PCR primer pair specific toT. matsutake. The amplified fragments were sequenced and compared with each other to build a phylogenetic tree. The mRNA deep sequencing approach was adopted to identify differentially expressed T. matsutake genes among the transcriptomes developed from a Xiaojin sample. A phylogenetic analysis of the aligned sequences was performed using maximum-likelihood (ML) and neighbor-joining (NJ) analyses. The results clearly showed that the KD (KM657344) and BT (KM657342) strains were more closely related to each other than to other strains. Moreover, T. matsutake from Sichuan differed from those specimens derived from Heilongjiang, Yunnam, and Guizhou provinces of China, Finland, and Japan. Furthermore, there was extremely high homology among these T. matsutake samples, despite some genetic variation. In addition, the genome of T. matsutake was sequenced using Illumina sequencing technology (RNA-seq).
    [Show full text]
  • Anthoporia, a New Genus in the Polyporales (Agaricomycetes)
    Polish Botanical Journal 61(1): 7–14, 2016 DOI: 10.1515/pbj-2016-0017 ANTHOPORIA, A NEW GENUS IN THE POLYPORALES (AGARICOMYCETES) Dariusz Karasiński & Tuomo Niemelä Abstract: A new genus, Anthoporia Karasiński & Niemelä, is proposed for the brown-rot polypore Polyporus albobrunneus Romell [= Antrodia albobrunnea (Romell) Ryvarden]. The new genus is separated from Antrodia P. Karst. s.str. in several morphological features, and it is only distantly related to Antrodia serpens (Fr.) P. Karst. (generic type of Antrodia) in recently published phylogenies. Additionally, Anthoporia albobrunnea (Romell) Karasiński & Niemelä is described and illustrated based on material collected in Białowieża National Park in northeastern Poland. Key words: Antrodia albobrunnea, Białowieża Primeval Forest, polypores, systematics, wood-inabiting fungi Dariusz Karasiński, Department of Mycology, W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland; e-mail: [email protected] Tuomo Niemelä, Botany Unit, Finnish Museum of Natural History, P.O. Box 7, FI-00014 Helsinki, Finland; e-mail: tuomo. [email protected] Introduction Polyporales is one of the largest orders of the 26 traditionally accepted genera. They showed that class Agaricomycetes (Basidiomycota) including many of these genera are poly- or paraphyletic and ca 1800 species, 150 genera and 40 described in need of a generic reclassification. families (Hibbett et al. 2014). It contains species The genus Antrodia P. Karst. (Polyporales) was having pileate, pileate-stipitate, multiple flabel- described by Karsten (1879) and later redefined liform or resupinate basidiomata with a poroid, by Donk (1960, 1966), who selected Daedalea hydnoid, lamellate, merulioid or smooth hyme- serpens Fr. as its type.
    [Show full text]