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Transcriptome Analysis of Conifer Defense Against Bark Beetle- Associated Blue-Stain Fungi and White Pine Weevil

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Transcriptome Analysis of Conifer Defense Against Bark Beetle- Associated Blue-Stain Fungi and White Pine Weevil TRANSCRIPTOME ANALYSIS OF CONIFER DEFENSE AGAINST BARK BEETLE- ASSOCIATED BLUE-STAIN FUNGI AND WHITE PINE WEEVIL by NATALIA KOLOSOVA B.Sc., Novosibirsk State University, Russia, 1997 M.Sc., Purdue University, USA, 2001 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES (Botany) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) November 2010 © Natalia Kolosova, 2010 Abstract Conifer forests are exposed to a large number of herbivorous insect species and pathogenic fungi, some of which cause extensive epidemics and substantial losses of forest resources. Bark beetles and white pine weevil represent major threats to conifer forest health. Bark beetles vector fungal pathogens, which are involved in killing of the host trees. Conifers employ a variety of defense strategies, including anatomical, chemical and molecular defense mechanisms. Recent development of conifer genomic resources and tools including large EST databases and microarrays have allowed for large-scale analysis of conifer defense. To evaluate transcriptome response of conifer species to fungal pathogens I performed a comparative analysis of the interior spruce (Picea glauca x engelmannii) response to spruce beetle-associated pathogenic blue- stain fungus Leptographium abietinum and the lodgepole pine (Pinus contorta) response to mountain pine beetle-associated pathogenic blue-stain fungus Grosmannia clavigera using a 21,843-clone cDNA spruce microarray platform. In addition, I performed a direct comparison of the interior spruce response to inoculation with the fungus Leptographium abietinum with the response to white pine weevil (Pissodes strobi) herbivory. The microarray analyses revealed substantial changes in the transcriptomes of conifer hosts in response to fungal inoculation or insect feeding with more than a thousand genes significantly differentially expressed in each system and interaction studied. The fungus-induced transcriptomes of spruce and pine shared a large number of similarly responding transcripts with some differences in the dynamics of the induced responses. The transcriptome responses of spruce induced by fungal inoculation and weevil feeding had a large overlap and some treatment-specific trends. Among the most strongly up-regulated transcripts in all interactions were phenylpropanoid pathway transcripts, dirigent protein transcripts, laccases, chitinases and transcripts of the terpenoid pathway. Gene specific expression analysis of selected transcripts confirmed and extended the microarray analysis. Cloning and functional characterization of selected chitinases revealed the presence of chitinolytic activity in two interior spruce and one lodgepole pine class I chitinases. Chitinolytic activity in addition to the strong induction of these chitinases in response to different treatments supported their involvement in conifer defense. ii Table of contents Abstract ........................................................................................................................... ii Table of contents ........................................................................................................... iii List of tables ................................................................................................................... vi List of figures................................................................................................................ viii List of abbreviations ........................................................................................................ x Conifer and fungal species used in the study ............................................................... xiii Acknowledgements ...................................................................................................... xiv Dedication .................................................................................................................... xvi Co-authorship statement ............................................................................................. xvii 1 Introduction: conifer defense against insects and pathogens .................................. 1 1.1 INSECT PESTS AND FUNGAL PAHTOGENS AFFECTING CONIFER SPECIES ............................................................................................................ 1 1.2 CONSTITUTIVE AND INDUCED ANATOMICAL DEFENSES ............................ 2 1.2.1 Conifer anatomical defense strategy ............................................................. 2 1.2.2 Resin ducts ................................................................................................... 3 1.2.3 Polyphenolic parenchyma, sclerenchyma and stone cells............................. 4 1.3 CONSTITUTIVE AND INDUCED CHEMICAL DEFENSES ................................ 4 1.3.1 Terpenoid resin ............................................................................................. 4 1.3.2 Phenolics ...................................................................................................... 6 1.4 MOLECULAR MECHANISMS OF CONIFER DEFENSE RESPONSE ............... 7 1.4.1 Genes involved in the formation of oleoresin ................................................ 7 1.4.2 Genes involved in the production of phenolics .............................................. 8 1.4.3 Antimicrobial proteins in conifers ................................................................ 11 1.5 ELICITORS OF CONIFER DEFENSE .............................................................. 13 1.6 ACQUIRED RESISTANCE IN CONIFERS ....................................................... 15 1.7 MICROARRAY ANALYSIS OF CONIFER DEFENSE ...................................... 17 1.8 THESIS OBJECTIVES ..................................................................................... 19 1.9 REFERENCES ................................................................................................. 21 2 Microarray gene expression profiling of interior spruce (Picea glauca x engelmannii) inoculated with Leptographium abietinum and lodgepole pine (Pinus contorta) inoculated with Grosmannia clavigera ........................................ 32 2.1 INTRODUCTION .............................................................................................. 32 2.2 MATERIAL AND METHODS ............................................................................ 35 2.2.1 Plant material, fungal material and inoculation procedure ........................... 35 2.2.2 Anatomical analysis .................................................................................... 36 2.2.3 Terpenoid extraction and analysis .............................................................. 36 2.2.4 Microarray hybridization and gene expression data analysis ...................... 38 2.2.5 Real-time PCR and gene expression data analysis .................................... 41 2.3 RESULTS ......................................................................................................... 42 2.3.1 Induced formation of traumatic resin ducts in interior spruce and lodgepole pine inoculated with L. abietinum and G. clavigera respectively................................................................................................. 42 2.3.2 Terpenoid accumulation in the bark of interior spruce and lodgepole pine inoculated with blue-stain fungi ........................................................... 44 2.3.3 Inoculation of interior spruce and lodgepole pine with L. abietinum and G. clavigera respectively causes large changes in the transcriptome of both species ............................................................................................... 46 2.3.4 Cluster analysis of differentially expressed transcripts induced by wounding or fungal inoculation in interior spruce and lodgepole pine .......... 49 2.3.5 Strongly induced transcripts in interior spruce and lodgepole pine by wounding and L. abietinum and wounding and G. clavigera respectively .... 51 iii 2.3.6 Functional categorization of interior spruce and lodgepole pine bark transcriptome response to fungal inoculation with L. abietinum and G. clavigera respectively ................................................................................. 57 2.3.7 Induction of phenylpropanoid in interior spruce and lodgepole pine ............ 61 2.3.8 Induction of terpenoid pathways in interior spruce and lodgepole pine........ 68 2.3.9 Induction of chitinases expression in response to G. clavigera and L. abietinum inoculations in interior spruce and lodgepole pine respectively................................................................................................. 72 2.4 DISCUSSION ................................................................................................... 75 2.5 REFERENCES ................................................................................................. 85 3 Comparative analysis of the interior spruce transcriptome response to white pine weevil feeding and fungal inoculation with blue-stain fungus Leptographium abietinum ..................................................................................... 92 3.1 INTRODUCTION .............................................................................................. 92 3.2 MATERIAL AND METHODS ............................................................................ 94 3.2.1 Plant material and weevil treatment ............................................................ 94 3.2.2 Microarray
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