DISSERTATION RESEARCH: Systematics, host-specificity, and genome evolution of holoparasitic plants: A case study in Orobanche (Orobanchaceae)

寄生是一种独特的生命史策略，在植物、动物和其他生物中独立进化了几十次。由于其高度的生物多样性和对其寄生模式的良好理解，非光合寄生植物属Orobanche为在系统发育框架中理解寄生的独特宏观和微观进化后果提供了一个绝佳的机会。最近的工作已经确定了进化和遗传后果，包括许多宿主特定的谱系以及宿主到寄生虫的水平基因转移。本研究将利用新大陆小蚁的基因组测序和北美的野外研究来发展以下方面：(1)对寄生植物基因组进化的速度和模式有一个精细的了解；(2)更好地了解寄主宽度；(3)非生物和生物栖息地特征，并进行分类修订。除了推动进化生物学和生态学领域的发展外，对宿主特异性和寄生虫基因组学的进一步了解可能有助于对抗几种对欧洲、亚洲和美洲的番茄、向日葵和其他作物造成严重危害的弓背虫。一名研究生和几名本科生将接受实验室和博物馆研究技术方面的培训，并将有机会在区域和国家会议上介绍研究成果。具体来说，我们将使用基因组浏览方法，结合北美地区的实地研究，研究(1)新世界Orobanche的质体和线粒体进化的精细速度和模式，(2)许多谱系的宿主宽度，(3)非生物和生物栖息地特征，以更好地了解分布，以及(4)谱系的可诊断特征，直接导致分类修订。在几种可用的基因组还原技术中，基因组略读（全基因组鸟枪测序）将提供最具成本效益的方法。捕获基因组DNA的高拷贝部分，包括&amp；核糖体反顺子、质体和有丝分裂基因组，甚至可以从植物标本室薄片上发现的降解物质中提取。

Parasitism is a unique life history strategy that has evolved independently dozens of times in plants, animals, and other organisms. Due to its high biodiversity and a good understanding of its mode of parasitism, the non-photosynthetic parasitic plant genus Orobanche provides a remarkable opportunity for understanding the unique macro- and microevolutionary consequences of parasitism in a phylogenetic framework. Recent work has identified both evolutionary and genetic consequences, including numerous host specific lineages as well as host-to-parasite horizontal gene transfer. This research will use genomic-scale sequencing of new-world Orobanche and field studies across North America to develop the following: (1) a fine-scale understanding of tempo and mode of genome evolution in parasitic plants, (2) a better understanding of host-breadth, and (3) abiotic and biotic habitat characteristics, with a taxonomic revision to follow. In addition to advancing the fields of evolutionary biology and ecology, an improved understanding of host specificity and parasite genomics may be of use in combating several species of Orobanche that cause severe agricultural damage to tomato, sunflower, and other crops in Europe, Asia, and the Americas. One graduate and several undergraduate students will receive training in laboratory and museum research techniques, and will have the opportunity to present the results at regional and national meetings.Specifically, we will use a genome skimming approach, coupled with field studies across North America to study (1) fine-scale tempo and mode of plastid and mitochondrial evolution in new-world Orobanche, (2) host-breadth of numerous lineages, (3) abiotic and biotic habitat characteristics to better understand distributions, and (4) diagnosable features of lineages, leading directly to taxonomic revision. Out of several genome reduction techniques available, genome-skimming (whole-genome shotgun sequencing) will provide the most cost-effective way to
capture the high-copy fraction of genomic DNA, including the
nuclear ribosomal cistron, plastome, and mitogenome, even from degraded material such as that found on herbarium sheets.