The Genetics of Arbuscular Mycorrhizal Fungi

生物肥料是一种生态友好，可持续的方式来提高植物产量。这引起了生物技术公司的极大关注，特别是丛枝菌根真菌（AMF）;一组多核和看似无性的真菌，与大多数植物的根部形成有益的联系。 在过去的6年里，我的研究采用了前沿单核测序和比较基因组学来了解AMF的遗传学。我们证明了一些AMF菌株，我们称之为AM双核体，携带数千个细胞核，这些细胞核是一个大细胞中两个亲本基因型的拷贝。每个细胞核都有一个交配型位点，与其他真菌中决定性身份的位点相似，表明AMF可以进行有性生殖。 我们现在的目标是利用这些生物信息来提高这些真菌的环境应用。然而，要实现这一目标，与AM双核体及其基因组的起源和功能相关的关键问题仍有待了解。我的研究计划的长期目标是阐明AMF中驱动核多样性和基因组进化的力量。我的实验室将通过三个相关的目标来实现这一目标：（1）研究AM双核作用对真菌和植物伴侣生物学的影响。我们将进行转录组学和表型分析，以确定两个共存的核基因型如何有助于跨生命阶段和植物宿主的AM双核体的共生潜力。(2)明确AM双核体中共存的两种核基因型的起源和进化。我们将获得和比较高质量的基因组数据，从AM双核，AM同核体和单个核分离的dilobacterium菌株使用长读测序。这些数据将使我们能够确定AM双核体的进化起源，将它们的进化模式与同核亲戚的进化模式进行比较，并理解细胞核如何在双核菌丝体中共同进化。(3)确定AMF中触发核交换的遗传决定因素。我们将使用蛋白质组学和显微镜方法来确定是什么触发AMF菌株交叉（交配），并将利用这些信息来产生遗传新菌株。该计划产生的数据将有助于阐明这些生物体中产生遗传和基因组多样性的机制，从而有助于其环境应用和我们对复杂遗传系统的理解。通过拟议的研究，HQP将获得尖端方法（单细胞/细胞核分析），一流测序工具（MinION，10 X Chromium）和编程技能（Python，Perl）以及蛋白质组学和显微镜方法的经验。我的项目还将积极让学员参与外展活动，包括一些解决EDI障碍的活动。 凭借这种高度互补的技能，HQP将继续在工业，政府和学术界担任有影响力的职位。

Bio-fertilizers are an eco-friendly, sustainable way to boost plant yields. This has attracted considerable attention from biotech companies towards particularly the Arbuscular Mycorrhizal Fungi (AMF); a group of multinucleated and seemingly asexual fungi that form beneficial associations with the roots of most plants. In the past 6 years my research used cutting edge-single nucleus sequencing and comparative genomics to understand the genetics of AMF. We demonstrated that some AMF strains, which we refer to as AM dikaryons, carry thousands of nuclei that are copies of two parental genotypes in one large cell. Each nucleus harbors a mating-type locus similar to those that dictate sexual identity in other fungi, indicating that AMF can undergo sexual reproduction. We now aim to use this biological information to enhance the environmental application of these fungi. To achieve this, however, key questions related to origin and function of AM dikaryons and their genomes remain to be understood. The long-term goal of my research program is to elucidate the forces driving nuclear diversity and genome evolution in AMF. My lab will work towards this goal by focusing on three related objectives: (1) To investigate the impact of AM dikaryosis on the biology of the fungal and plant partners. We will perform transcriptomics and phenotype analyses to identify how two co-existing nuclear genotypes contribute to the symbiotic potential of AM dikaryons across life-stages and plant hosts. (2) To identify the origin and evolution of the two nuclear genotypes that co-exist in AM dikaryons. We will obtain and compare high-quality genome data from AM dikaryons, AM homokaryons and individual nuclei isolated from dikaryotic strains using long-read sequencing. This data will allow us to identify the evolutionary origins of AM dikaryons, compare their mode of evolution with those of homokaryotic relatives, and comprehend how nuclei co-evolve within the dikaryotic mycelium. (3) To identify the genetic determinants that trigger nuclear exchange in AMF. We will use proteomics and microscopy approaches to determine what triggers AMF strains to cross (mate) and will aim to use this information to generate genetically new strains. The data generated in this program will help elucidate the mechanisms that generate genetic and genomic diversity in these organisms, thereby contributing to their environmental application and to our understanding of complex genetic systems. Through the proposed research, HQP will gain experience with cutting edge methods (single-cell/nucleus analyses), best in class sequencing tools (MinION, 10X Chromium) and programming skills (Python, Perl), and with proteomics and microscopy approaches. My program will also actively involve trainees in outreach activities, including some that address barriers to EDI. With this highly complementary skillset, HQP will continue to move on to impactful positions in industry, government and academia.