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

蓝斑真菌，如蛇口藻属、罗汉果属和Ceratcystis属，是由昆虫传播的，由于它们使木材变色，从而降低了木材的经济价值，因此引起了经济关注。这些真菌也被称为蛇口类真菌，这类真菌包括树木病原体，如荷兰榆树病或橡树枯萎病的病原体。这项研究计划部分集中在蓝斑真菌的分类和进化上。确定蓝斑真菌线粒体基因组的特征是这项提案的长期目标的一部分。这些真菌是专性需氧菌，因此功能线粒体对这些生物来说是最重要的，以便在自然环境中具有竞争力。更直接的目标是了解真菌线粒体基因组(MtDNA)中可移动遗传元件的起源和持久性，并研究这些元件对mtDNA稳定性的影响，以及对这些树木病原体的潜在毒力的影响。这项建议将集中于描述Ophiostoma ulmi及其近缘物种，如O.novo-ulmi、O.Himal-ulmi和与Ophiostoma Piceae复合体相关的物种的线粒体基因组。下一代测序的成本和速度相对较低，允许对来自不同代表的蛇口菌类真菌的约100个mtDNA进行测序，因此对所得数据的比较分析应该为鉴定这些经济上重要的真菌提供可能的种间标记。此外，比较近缘物种的线粒体DNA应该揭示移动元件，如第一组和第二组内含子对线粒体DNA基因组进化的影响。此外，这些可移动的元件有时编码DNA切割酶，即所谓的归巢内切酶。这些酶在基因组学和生物技术中有应用。归巢内切酶目前被用于基因组编辑应用，涉及基因替换、突变和基因治疗。这项拟议的研究将寻找并生化分析归巢内切酶，并试图解决它们的天然DNA靶点以及它们彼此之间和其他mtDNA移动元件之间的关系。最后，这个项目将更详细地研究含有内含子的归巢内切酶基因。长期目标是开发一种调节开关，允许通过操纵内含子剪接在体内调节归巢内核酸酶的表达。有人提出，在体内控制归巢内切酶的活性将允许更准确地确定基因失活或修饰的时间。

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.