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Hevea Brasiliensis YEB Recent Publications in this Series between White Rot Pathogen ( of the Interaction A.O OGHENEKARO Molecular Analysis 18/2015 Shaimaa Selim Effects of Dietary Energy on Transcriptional Adaptations and Insulin Resistance in Dairy Cows and Mares 19/2015 Eeva-Liisa Terhonen Environmental Impact of Using Phlebiopsis gigantea in Stump Treatment Against Heterobasidion annosum sensu lato and Screening Root Endophytes to Identify Other Novel DISSERTATIONES SCHOLA DOCTORALIS SCIENTIAE CIRCUMIECTALIS, Control Agents ALIMENTARIAE, BIOLOGICAE. UNIVERSITATIS HELSINKIENSIS 2/2016 20/2015 Antti Karkman Antibiotic Resistance in Human Impacted Environments 21/2015 Taru Lienemann Foodborne Human Isolates of Salmonella and Shiga Toxin -Producing Escherichia coli of Domestic Origin in Finland 22/2015 Suvi Suurnäkki ABBOT O. OGHENEKARO Anatoxin-a and Odorous Metabolites in Cyanobacteria: Molecular Detection of the Producers 23/2015 Nicolas Détry In Silico Genomics of Fungal Oxidoreductase Genes Molecular Analysis of the Interaction between 24/2015 Linda Garlant White Rot Pathogen (Rigidoporus microporus) Ecology and Genomics of Dickeya solani, a New Soft Rot Bacterium Infecting Potatoes 25/2015 Seija Virtanen and Rubber Tree (Hevea brasiliensis) Redox Reactions and Water Quality in Cultivated Boreal Acid Sulphate Soils in Relation to Water Management 26/2015 Ling Zou Crop Rotation as a Tool Towards Sustainable Barley Cropping 27/2015 Pirjo Yli-Hemminki Microbes Regulate Metal and Nutrient Cycling in Fe–Mn Concretions of the Gulf of Finland 28/2015 Venla Jokela Regulation of Flowering and Canopy Structure in Timothy (Phleum pratense L.) 29/2015 Epie Kenedy Etone Sustainable Cropping of Reed Canary Grass for Energy Use Rigidoporus microporus 30/2015 Anna Knuuttila Diagnostics and Epidemiology of Aleutian Mink Disease Virus 31/2015 Jose Martin Ramos Diaz Use of Amaranth, Quinoa, Kañiwa and Lupine for the Development of Gluten-Free Extruded Snacks 32/2015 Aleksandar Klimeski Characterization of Solid Phosphorus-Retaining Materials – from Laboratory to Large-Scale Treatment of Agricultural Runoff 33/2015 Niina Idänheimo Rubber Tree ( ) and The Role of Cysteine-rich Receptor-like Protein Kinases in ROS signaling in Arabidopsis thaliana 34/2015 Susanna Keriö Terpene Analysis and Transcript Profiling of the Conifer Response to Heterobasidion annosum s.l. Infection and Hylobius abietis Feeding 35/2015 Ann-Katrin Llarena Population Genetics and Molecular Epidemiology of Campylobacter jejuni DEPARTMENT OF FOREST SCIENCES Hevea brasiliensis 1/2016 Hanna Help-Rinta-Rahko FACULTY OF AGRICULTURE AND FORESTRY The Interaction of Auxin and Cytokinin Signaling Regulates Primary Root DOCTORAL PROGRAM IN MICROBIOLOGY AND BIOTECHNOLOGY Procambial Patterning, Xylem Cell Fate and Differentiation in Arabidopsis thaliana UNIVERSITY OF HELSINKI ) 2/2016 Helsinki 2016 ISSN 2342-5423 ISBN 978-951-51-1881-3 Department of Forest Sciences Faculty of Agriculture and Forestry and Doctoral program in Microbiology and Biotechnology University of Helsinki Molecular analysis of the interaction between white rot pathogen (Rigidoporus microporus) and rubber tree (Hevea brasiliensis) Abbot O. Oghenekaro ACADEMIC DISSERTATION To be presented for public examination, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, in the lecture room LS7 (Latokartanonkaari 9, B-building) on January 15th 2016 at 12 o’clock. Helsinki 2016 Supervisor Professor Fred O. Asiegbu Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Finland Pre-examiners Professor Yu-Cheng Dai Institute of Microbiology, P.O. Box 61, Beijing Forestry University, Beijing 100083, China Dr. Hakeem O. Shittu Department of Plant Biology & Biotechnology, Faculty of Life Sciences, University of Benin, P.M.B 1154, Benin City, Nigeria Opponent Assoc. Prof. Caroline Mohammed Tasmanian Institute of Agriculture, University of Tasmania, Hobart 7001, Tasmania, Australia Custos Professor Fred O. Asiegbu Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Finland Cover: Healthy rubber trees with flowing latex (left); Basidiocarps of R. microporus on the base (top centre) and collar (lower centre) of white rot infected rubber tree; Characteristic mycelial strand of R. microporus in culture (upper right); Micrograph of R. microporus hypha penetrating the vessel of rubber wood during saprotrophic growth (middle right); Rubber tree clone used for inoculation studies (lower right). ISSN 2342-5423 (Print) ISSN 2342-5431 (Online) ISBN 978-951-51-1881-3 (Paperback) ISBN 978-951-51-1882-0 (PDF) https://ethesis.helsinki.fi/ Hansaprint 2015 To the memory of my father, Awhabro Okotie Oghenekaro CONTENTS ABBREVIATIONS ..................................................................................................................................... 6 LIST OF ORIGINAL PUBLICATIONS AND SUBMITTED MANUSCRIPTS ....................................... 8 ABSTRACT ............................................................................................................................................... 10 1. INTRODUCTION ....................................................................................................................... 12 1.1 Global forestry and tree pests and diseases ........................................................................... 12 1.2 The Para rubber tree, Hevea brasiliensis .............................................................................. 12 1.3 The white rot pathogen, Rigidoporus microporus ................................................................ 13 1.4 Taxonomy and molecular phylogeny of Rigidoporus microporus ....................................... 15 1.5 Wood lignocellulose degradation by white rot basidiomycetes ............................................ 16 1.5.1 Lignin degrading enzymes of wood decay fungi ....................................................... 17 1.5.2 Polysaccharide degrading enzymes of wood decay fungi .......................................... 18 1.5.3 Current advances of next generation sequencing technology in furthering our understanding of fungi transcriptome ......................................................................... 19 1.6 Defence gene expression of forest trees to pests and pathogens ........................................... 20 2. AIMS OF THE STUDY ............................................................................................................. 22 3. MATERIALS AND METHODS ................................................................................................ 23 4. RESULTS AND DISCUSSION ................................................................................................. 24 4.1 Molecular phylogeny of Rigidoporus microporus isolates associated with rubber tree plantations ............................................................................................................................. 24 4.1.1 Analysis of ITS sequences of Rigidoporus microporus isolates ................................ 24 4.1.2 Analysis of β-tubulin sequences of Rigidoporus microporus isolates ....................... 25 4.1.3 Analysis of tef1 sequences of Rigidoporus microporus isolates ................................ 25 4.1.4 Analysis of combined ITS, β-tubulin and tef1 sequences of Rigidoporus microporus isolates ....................................................................................................................... 25 4.1.5 Analysis of LSU sequences of Rigidoporus microporus isolates .............................. 26 4.2 Saprotrophic growth of Rigidoporus microporus on rubber wood ...................................... 27 4.2.1 Mass loss of Hevea brasiliensis wood blocks due to degradation by Rigidoporus microporus isolates ................................................................................................... 27 4.2.2 Effects of temperature on in vitro growth rates of Rigidoporus microporus isolates 28 4.2.3 Light microscopy of structural alterations in wood blocks of Hevea brasiliensis induced by Rigidoporus microporus isolates ............................................................ 28 4.3 Gene expression of Rigidoporus microporus during saprotrophic growth on rubber wood ................................................................................................................................... 29 4.3.1 General overview of the Rigidoporus microporus transcriptome .............................. 29 4.3.2 Rigidoporus microporus genes encoding polysaccharide degrading enzymes during saprotrophic growth on rubber wood ........................................................................ 31 4.3.3 Rigidoporus microporus genes encoding glycolignin attacking enzymes during saprotrophic growth on rubber wood ........................................................................ 32 4.3.4 Rigidoporus microporus genes encoding enzymes involved in fatty acid and rubber tree latex degradation during saprotrophic growth on rubber wood ......................... 34 4.3.5 Rigidoporus microporus ABC transporters and hydrophobins expressed during saprotrophic growth on rubber wood ........................................................................ 35 4.3.6 Rigidoporus microporus genes encoding enzymes involved in pathways related to energy metabolism during saprotrophic growth on rubber wood .............................. 35 4.4 Defence gene expression of Hevea brasiliensis in response
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