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

蛇口藻属、格罗氏藻属和Ceratcystis属的许多物种都是由树皮甲虫等昆虫传播的，这些真菌通常被称为蓝斑真菌，因为它们会使木材变色，从而降低木材的经济价值。这些真菌也被称为口角类真菌；这一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。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。未来五年的拟议工作将集中于描述Ophiostoma ulmi及其近缘物种如O.novo-ulmi、O.Himal-ulmi和与O.ulmi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，因此可以对许多口蹄类真菌的mtDNA进行测序，而对结果数据的比较分析将为鉴定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，如移动内含子(第一组和第二组内含子)对线粒体DNA基因组进化的影响。有时，这些移动内含子可以插入其他内含子，形成嵌套内含子排列。为了了解这些复杂的内含子实际上是如何在线粒体内处理的，将对RNA进行测序，以恢复剪接中间产物。这些真菌是严格的需氧有机体，因此功能线粒体是必不可少的。可移动的内含子与线粒体缺陷有关，这些元件决定了真菌线粒体基因组的大小和结构。这项工作可能会阐明嵌套内含子的剪接途径，并可能揭示可能作为调控元件的元件。最近有人提出，I组内含子剪接可能成为治疗人类病原真菌或潜在的植物病原体杀菌剂的靶点。获得有关mtDNA内含子剪接和移动内含子对真菌mtDNA的影响的知识，对于制定识别和控制植物病原体的策略，如蓝斑真菌的成员，可能是有价值的信息。此外，这些可移动元件经常编码位点特异的DNA切割酶，即所谓的归巢内切酶。这些酶作为基因组编辑试剂在基因组学和生物技术中有应用。

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.