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

许多种类的蛇孔菌、格氏菌和角鼻虫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。这些真菌也被称为类蛇口真菌；这一组包括树木病原体，如荷兰榆树病或橡树枯萎病的病原体。这个研究项目部分集中在蓝斑真菌的分类和进化上。表征蓝染真菌的线粒体基因组是本提案长期目标的一部分。更直接的目标是了解真菌线粒体基因组（mtDNA）中移动遗传元件的起源和持久性，并检查这些元件对mtDNA稳定性和这些树状病原体潜在毒力的影响。未来5年的研究工作将集中在对乌尔米蛇及其相关物种（如O. novo-ulmi、O. himal-ulmi和O. ulmi复合体相关物种）的线粒体基因组进行表征。下一代测序的相对低成本和速度允许对许多类蛇口真菌的mtdna进行测序，对结果数据的比较分析将为鉴定具有经济意义的真菌的种间标记提供可能的资源。此外，比较近缘物种的mtDNA可以揭示移动内含子（I类内含子和II类内含子）等可移动元件对mtDNA基因组进化的影响。有时这些可移动的内含子可以插入到其他内含子中，形成嵌套的内含子排列。为了了解这些复杂的内含子是如何在线粒体内实际加工的，RNA将被测序以恢复剪接中间产物。这些真菌是严格的需氧生物，因此功能性线粒体是必不可少的。移动内含子与线粒体缺陷有关，这些元素有助于真菌线粒体基因组的大小和结构。这项工作可能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族内含子剪接可能是人类病原真菌或植物病原体潜在杀菌剂的治疗应用靶点。了解mtDNA内含子剪接和移动内含子对真菌mtDNA的影响，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性DNA切割酶，即归巢内切酶。这些酶作为基因组编辑试剂在基因组学和生物技术中有广泛的应用。

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.