Introns, nested introns and intron encoded proteins in the mitochondrial genomes of fungi.

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Many species of Ophiostoma, Grosmannia and Ceratocystis are vectored by insects such as bark beetles, and these fungi are commonly known as blue-stain fungi as they discolour lumber, thus reducing the economic value of the wood. These fungi are also referred to as the ophiostomatoid fungi; and, this group includes tree pathogens such as the causative agents of Dutch Elm Disease or Oak wilt. This research program focuses in part 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. 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. The proposed work over the next five years 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 O. ulmi complex. The relative low cost and speed of next generation sequencing allows for sequencing of mtDNAs from many ophiostomatoid fungi, and comparative analysis of the resulting data will provide a resource for possible identifying inter-specific markers for identification of economically important fungi. Also comparing the mtDNA of closely related species should reveal the impact of mobile elements such as mobile introns (group I and group II introns) on mtDNA genome evolution. Sometimes these mobile introns can insert into other introns, forming nested intron arrangements. To understand how these complex introns are actually processed within the mitochondria the RNA will be sequenced to recover splicing intermediates. These fungi are strict aerobic organisms, therefore functional mitochondria are essential. Mobile introns have been associated with mitochondrial defects and these elements contribute towards the size and the architecture of fungal mitochondrial genomes. This work may elucidate the splicing pathways for nested introns and possibly reveal elements that could serve as regulatory elements. It has recently been suggested the group I intron splicing could be a target for therapeutic applications with regards to human pathogenic fungi or potential fungicides for plant pathogens. Gaining knowledge about mtDNA intron splicing and the impact of mobile introns on fungal mtDNAs could be valuable information when developing strategies to identify and control plant pathogens, such as members of the blue-stain fungi. In addition these mobile elements frequently encode site-specific DNA cutting enzymes, so called homing endonucleases. These enzymes have application in genomics and biotechnology as genome editing reagents.