Evolutionary Gain and Loss of Function in Parasitic Plant Genomes

高级人员：Eva Collakova和Lenwood Heath(弗吉尼亚理工学院和州立大学)和Aaron Mackey(弗吉尼亚大学)寄生植物从自养到异养的进化转变是适应植物生物学的一个非凡的例子。它与显著的形态适应有关，如吸器的发育，以及使寄生虫进入宿主组织并将宿主营养重新定向到寄生虫的生理变化。这个项目将建立在美国国家科学基金会先前支持的一项研究的基础上，该研究对三个物种的关键生活期的表达基因进行了测序，这三个物种跨越了植物寄生的光谱：兼性寄生(杂色三叶草)、具有光合作用的专性寄生(Striga Hermonthica)和专性全寄生[Phelipance(=Orobanche)Aegyptiaca]。序列也是从最接近的非寄生亲缘植物--菲律宾连翘中产生的，这提供了与寄生物种的一个对比点。这些数据将与寄生虫和寄主组织关键阶段的代谢物图谱一起被用来识别在寄生植物中发挥独特作用的基因和代谢网络。该项目旨在确定吸器在连接寄主组织和提取寄主营养物质(如氨基酸和糖转运蛋白和转录因子)方面所必需的基因。候选基因将通过一系列分析来表征，包括详细的时间和空间表达，通过反式特异性基因沉默进行功能敲除，以及在寄生虫物种中直接基因敲除或过度表达。对具有特定基因表达修饰的转基因寄生虫的分析将揭示基因和代谢调节的新模式，这将揭示基因是如何进化的，从而使植物能够寄生。这项研究的更广泛的影响来自于了解植物基因如何在寄生相互作用的严格约束下进化，以及某些寄生物种(如Striga和Orobanche spp.)的巨大影响。对非洲发展中国家的农业造成影响。该项目将强调学生培训，将生物信息学和应用农业的不同领域联系起来。项目人员将与摩洛哥和肯尼亚的同事合作，将项目的基本研究成果转化为控制寄生性杂草的进展。寄生性杂草是世界各地的毁灭性农业害虫，是发达国家和发展中国家农业生产力和粮食安全的重大制约因素。除了提供这组相关植物的基本细胞和代谢规模数据外，该项目还将直接有助于设计控制这些有害害虫的新策略。这种进步对作物生产、粮食安全和人类健康的潜在积极和持久影响怎么强调都不为过。随着来自寄生杂草的全球威胁的扩大，对了解其生物学的训练有素的个人的需求将会加剧。认识到这种需求和美国各级训练有素的人员的匮乏，该项目不仅将在本国机构的实验室培训研究生和博士后，而且将通过国际参与性实地经验来培训。这些为期9天的国际寄生植物研究实验室/田间实习将在该项目的第二年和第三年进行，将把来自美国四个机构的人员带到摩洛哥或肯尼亚与合作者一起工作，观察田间的菲里潘奇、奥罗班奇和斯特里加物种，举办讲习班，并获得处理寄生草的农学家面临的挑战的第一手知识。它还将帮助向非洲研究人员传播项目成果，以协助他们的研究活动。与科学相结合，学生将从事发展中国家科学和农业的文化、社会经济和地理方面的研究。所有序列数据将存放在GenBank中，项目中产生的数据和工具将可通过项目网站和iPLANT Collaborative访问。代谢组数据将通过新陈代谢快递和Drop Met等新兴公共储存库存储。Striga和Phelipance在联邦有害杂草登记处，目前的法规限制这些种子的进口和处理，除非实验室持有有效的USDA/APHIS PPQ 526检疫植物种子许可证。鼓励有兴趣获得本项目中使用或产生的种质的各方首先与美国农业部/APHIS联系，了解如何获得使用这些物种的许可。

PI: James Westwood (Virginia Polytechnic Institute and State University)CoPIs: Claude dePamphilis (Pennsylvania State University), Michael Timko (University of Virginia), and John Yoder (University of California - Davis) Senior Personnel: Eva Collakova and Lenwood Heath (Virginia Polytechnic Institute and State University) and Aaron Mackey (University of Virginia)The evolutionary transition from autotrophism to heterotrophism by parasitic plants is an extraordinary example of adaptive plant biology. It is associated with striking morphological adaptations, such as the development of a haustorium, and physiological changes that enable the parasite to enter host tissue and redirect host nutrients to the parasite. This project will build on a prior NSF-supported study that sequenced expressed genes from key life stages of three species that span the spectrum of plant parasitism: a facultative parasite (Triphysaria versicolor), a photosynthetically-competent obligate parasite (Striga hermonthica), and an obligate holoparasite [Phelipanche (=Orobanche) aegyptiaca]. Sequences were also generated from the closest non-parasitic relative, Lindenbergia philippensis, which provides a point of contrast to the parasitic species. These data will be used, along with metabolite profiles from key stages of parasite and host tissues, to identify gene and metabolic networks that function uniquely in parasitic plants. The project aims to identify and characterize genes that are essential for haustoria function in connecting to host tissues and extracting host nutrients such as amino acid and sugar transporters and transcription factors. Candidate genes will be characterized through a series of analyses including detailed temporal and spatial expression, functional knockout by trans-specific gene silencing, and direct gene knockout or overexpression in the parasite species. Analysis of transgenic parasites with modified expression of specific genes will reveal new patterns of gene and metabolic regulation that will reveal how genes have evolved to enable parasitism in plants. The broader impacts of this research derive from understanding how plant genes evolve under the tight constraints of parasitic interactions and from the large impact that certain parasitic species (e.g. Striga and Orobanche spp.) inflict on agriculture in developing nations of Africa. The project will emphasize student training that bridges diverse fields of bioinformatics and applied agriculture. Project personnel will collaborate with colleagues in Morocco and Kenya to translate basic research findings from the project into progress in control of parasitic weeds.Parasitic weeds are devastating agronomic pests worldwide and a significant constraint to agricultural productivity and food security in developed and developing countries alike. In addition to providing basic cellular and metabolic scale data on this group of related plants that encompass an enormous breadth of morphological and physiological diversity, the project will contribute directly to the design of novel strategies for the control of these noxious pests. The potential positive and lasting impact of such advancement on crop production, food security and human health cannot be overemphasized. As the global threat from parasitic weeds expands, the need for trained individuals who understand their biology will be accentuated. Recognizing this need and the paucity of trained personnel at all levels in the US, this project will train graduate and post-doctoral students not only in the laboratory at their home institutions, but through participatory field experiences internationally. These 9-day laboratory/field practicals in International Parasitic Plant Research will be conducted in the 2nd and 3rd years of this project and will take personnel from the four US institutions to Morocco or Kenya to work with collaborators, observe Phelipanche, Orobanche and Striga species in the field, conduct workshops, and gain first-hand knowledge of the challenges faced by agriculturalists dealing with parasitic weeds. It will also help disseminate project findings to African researchers to assist in their research activities. Integrated with the science, students will engage in study of cultural, socioeconomic, and geographical aspects of science and agriculture in developing countries. All sequence data will be deposited at GenBank and data and tools generated in the project will be accessible through the project website and through the iPlant Collaborative. Metabolomic data will be deposited through emerging public repositories such as MetabolomeExpress and DROP Met. Striga and Phelipanche are on the Federal Registry of Noxious Weeds and current regulations restrict the importation and handling of these seeds except by laboratories holding valid USDA/APHIS PPQ 526 permits for quarantined plant seeds. Parties interested in obtaining germplasm used or generated in this project are encouraged to first contact USDA/APHIS regarding how to obtain permission to work with these species.