Evolutionary Gain and Loss of Function in Parasitic Plant Genomes

主要研究者：詹姆斯·韦斯特伍德（弗吉尼亚理工学院和州立大学）CoPI：Claude dePamelo（宾夕法尼亚州立大学），迈克尔·蒂姆科（弗吉尼亚大学）和约翰·约德（John Yoder）（加州-戴维斯大学）高级人员：伊娃·科拉科娃和伦伍德·希斯（弗吉尼亚理工学院和州立大学）和亚伦麦基寄生植物从自养到异养的进化转变是适应性植物生物学的一个非凡的例子。它与显著的形态适应（如吸器的发育）和生理变化有关，这些变化使寄生虫能够进入宿主组织并将宿主营养物质重定向到寄生虫。该项目将建立在先前NSF支持的研究的基础上，该研究对跨越植物寄生光谱的三个物种的关键生命阶段的表达基因进行测序：兼性寄生虫（Triphysaria versicolor），光合能力专性寄生虫（Striga hermonthica）和专性全寄生虫[埃及列当（=列当）]。 序列也产生了最近的非寄生亲戚，林登伯格Philippensis，这提供了一个点的对比，寄生物种。这些数据将被用来，沿着从寄生虫和宿主组织的关键阶段的代谢物配置文件，以确定基因和代谢网络，在寄生植物独特的功能。该项目旨在鉴定和表征吸器在连接宿主组织和提取宿主营养物质（如氨基酸和糖转运蛋白和转录因子）方面的功能所必需的基因。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的功能敲除以及寄生虫物种中的直接基因敲除或过表达。对特定基因表达改变的转基因寄生虫的分析将揭示基因和代谢调节的新模式，从而揭示基因是如何进化成能够在植物中寄生的。这项研究的更广泛的影响来自于理解植物基因如何在寄生相互作用的严格限制下进化，以及某些寄生物种（如独脚金和列当属）对植物基因的巨大影响。对非洲发展中国家农业造成的影响。 该项目将强调学生培训，桥梁生物信息学和应用农业的不同领域。 项目人员将与摩洛哥和肯尼亚的同事合作，将项目的基础研究成果转化为寄生性杂草控制方面的进展，寄生性杂草是全世界毁灭性的农业害虫，严重制约发达国家和发展中国家的农业生产力和粮食安全。除了提供关于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过分。随着寄生杂草对全球的威胁不断扩大，对了解其生物学的训练有素的个人的需求将更加突出。认识到这一需要和缺乏训练有素的人员在各级在美国，该项目将培训研究生和博士后学生不仅在实验室在自己的家机构，但通过参与国际实地经验。这些为期9天的国际寄生植物研究的实验室/实地实习将在该项目的第二年和第三年进行，并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，观察实地的藜属，列当属和独脚金属物种，举办研讨会，并获得农学家处理寄生杂草所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研究结果，以协助他们开展研究活动。与科学相结合，学生将从事科学和农业在发展中国家的文化，社会经济和地理方面的研究。 所有序列数据将存放在基因库中，项目中生成的数据和工具将通过项目网站和iPlant Collaborative访问。 代谢组学数据将通过MetabolomeExpress和DROP Met等新兴的公共存储库存储。独脚金和假俭草在联邦登记处登记，现行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联系USDA/APHIS，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.