Mobile introns and homing endonuclease genes in the mitochondrial genomes of fungi.

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Blue-stain fungi such as species of Ophiostoma, Grosmannia and Ceratocystis are vectored by insects and are of economic concerns as they discolour lumber, thus reducing the economic value of the wood. These fungi are also referred to as ophiostomatoid fungi and this group includes tree pathogens such as the causative agents of Dutch Elm Disease or Oak wilt. This research program in part focuses on the taxonomy and evolution of blue-stain fungi. Characterizing mitochondrial genomes of blue-stain fungi is part of the long term objectives of this proposal. These fungi are obligate aerobes thus functional mitochondrial are of upmost importance to these organisms in order to be competitive in their natural surroundings. The more immediate goals are to understand the origin and persistence of mobile genetic elements within fungal mitochondrial genomes (mtDNA) and to examine the implications these elements have on mtDNA stability and potentially on the virulence of these tree pathogens. This proposal will focus on characterizing the mitochondrial genomes of Ophiostoma ulmi and related species such as O. novo-ulmi, O. himal-ulmi and species related to the Ophiostoma piceae complex. The relative low cost and speed of next generation sequencing allows for sequencing of about 100 mtDNAs from various representatives of the ophiostomatoid fungi, comparative analysis of the resulting data should provide a resource for possible identifying inter-specific markers for identification of these economically important fungi. Also comparing the mtDNA of closely related species should reveal the impact of mobile elements such as group I and group II introns on mtDNA genome evolution. In addition these mobile elements sometimes encode DNA cutting enzymes, so called homing endonucleases. These enzymes have application in genomics and biotechnology. Homing endonucleases are currently employed in genome editing applications that involved gene replacement, mutagenesis and gene therapy. The proposed study will search for and biochemically analyze homing endonucleases and try to resolve their native DNA target sites and their relationships to each other and other mtDNA mobile elements. Finally this program will study in more detail a homing endonuclease gene that contains an intron. The long term goal is to develop a regulatory switch that permits in vivo regulation of homing endonuclease expression by manipulating intron splicing. It has been suggested that the in vivo control of homing endonuclease activity would allow for more precise timing of the inactivation or modification of genes.