Genome and Transcriptome Analyzes in the Ectomycorrhizal Fungus Paxillus involutus

Abstract

Mycorrhizal symbioses are formed between plant root systems and compatible fungal hyphae that results in a complex mixed structure. They are found in all ecosystems and with the majority of land plants such as forest trees or crops that are of commercial interest. Mutual exchange of nutrients between the two symbionts is central to the successful functioning of the symbioses. In order to understand the processes involved in the development of this symbiosis and to increase our knowledge in this field of study, I have used new molecular methods emerging from functional genomics, a faster way to link functions to genes. Particularly, I have developed and applied the microarray technology to further characterize this complex type of plant microbe interaction. Using this technique, we can decipher the complex molecular programs that lead to the mycorrhizal symbiosis, survey genome-wide patterns of gene expression within and among species as well as employing the information it contains in quantitative genetics studies. I believe that this new tool will be increasingly used by evolutionary biologists and in molecular ecology studies in the future to address questions such as those presented in this thesis.



This thesis presents information on the genome and the transcriptome characteristics of our model mycorrhizal fungus Paxillus invoulus. Its nuclear haploid genome was estimated to be 21.5 Mbp in length and to contain ca 7,700 genes. An Expressed Sequence Tag (EST) project was initiated to obtain sequence information both on the coding genome of the fungus as well as for one of its plant hosts the European birch (Betula pendula). Based on sequencing information of more than 10,000 ESTs, a unique set of 2,284 cDNAs either of fungal or plant origin were selected and amplified. These were spotted onto glass slides. These DNA chips or cDNA microarrays were used to survey the expression of the genes represented on the arrays at distinct developmental stages during formation of the symbiotic tissue. Notably, it revealed that the plant responds to the fungus and the formation of the symbiotic tissue by undergoing a typical hypersensitive response also observed in plants when attacked by various pathogens. Furthermore, this response was completely repressed in the more mature mycorrhizal tissue which probably allows the formation of a functional mycorrhizal association to occur.



Finally, we use these cDNA microarrays to compare the transcriptome and the genome of isolates presenting phenotypic variations or of different origin. We found that the genome of P. involutus is plastic and contains a high number of divergent genes and / or genes that vary in copy number. Furthermore, transcript profiling in strains presenting different abilities to develop the symbiotic tissue also allowed the characterization of genes related to the symbiosis which show variability due to changes in the promoter elements and levels of transcription factors rather than gene copy number alterations.

• author: Le Quéré, Antoine
• supervisor: [unknown] [unknown]
• opponent: Dr Martin, Francis, UMR INRA-UHP "Interactions Arbres/Micro-Organismes" INRA-Nancy 54280 Champenoux (France)
• organization: Department of Biology; Microbial Ecology (research group)
• publishing date: 2004
• type: Thesis
• publication status: published
• subject: Ecology
• keywords: Mikrobiologi, bakteriologi, virologi, mykologi, virology, mycology, bacteriology, Microbiology, Genome Transcriptome Ectomycorrhiza Paxillus-involutus microarray
• pages: 142 pages
• defense location: Ecology building Blue lecture hall
• defense date: 2004-05-18 10:00:00
• external identifiers: other:ISRN: SE-LUNBDS/NBME-04/1022+ 142 pp
• ISBN: 91-7105-208-9
• language: English
• LU publication?: yes
• additional info: Article: I. Size and complexity of the nuclear genome of the ectomycorrhizal fungus Paxillus involutus (2002) Antoine Le Quéré, Tomas Johansson and Anders Tunlid. Fungal Genetics and Biology 36, 234-241. Article: II. Transcriptional responses of Paxillus involutus and Betula pendula during formation of ectomycorrhizal root tissue (2004) Tomas Johansson, Antoine Le Quéré, Dag Ahrèn, Bengt Söderström, Rikard Erlandsson, Joakim Lundeberg, Mathias Uhlén and Anders Tunlid. Molecular Plant-Microbe Interactions 17, 202-215. Article: III. Genome-wide expression analyzes reveal gene regulation related to distinct developmental stages during the formation of ectomycorrhiza between birch (Betula pendula) and Paxillus involutus (Batsch) Fr. Antoine Le Quéré, Derek Wright, Bengt Söderström, Anders Tunlid and Tomas Johansson. (Manuscript). Article: IV. Genomic variation and plasticity in strains of the ectomycorrhizal fungus Paxillus involutus as analyzed by DNA microarrays. Antoine Le Quéré, Balaji Rajashekar, Andres Schützendübel, Tomas Johansson and Anders Tunlid. (Manuscript). Article: V. Rapid divergence in gene expression related to lack of mutualism in an ectomycorrhizal fungus. Antoine Le Quéré, Andres Schützendübel, Balaji Rajashekar, Björn Canbäck, Jenny Hedh, Susanne Erland, Tomas Johansson and Anders Tunlid. (Manuscript). The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Microbial Ecology (Closed 2011) (011008001)
• id: 5ea894df-a8b2-4beb-b78d-b001371ae555 (old id 466946)
• date added to LUP: 2016-04-04 10:53:48
• date last changed: 2020-09-23 15:15:12