Evolutionary genomics of early-diverging fungi living in the gut of insects

昆虫肠道中早期分化真菌的进化基因组学

• 批准号: RGPIN-2020-04293
• 负责人: Wang, Yan
• 金额: $ 2.04万
• 依托单位: University of Toronto
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2021
• 资助国家: 加拿大
• 起止时间: 2021-01-01 至 2022-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=739870
• 关键词: Evolutionary; genomics; early; diverging; fungi

Fungi play critical roles in both aquatic and terrestrial ecosystems. They actively influence and interact with various organisms. However, we are still unclear how fungi adapted to their environments and evolved abilities to communicate with other biological entities. Studies on early-diverging fungal groups have helped reveal the importance of fungi in the terrestrialization of ancient eukaryotes. Due to their crucial phylogenetic placement, further investigation of early-diverging fungi will help us understand more of their natural histories and impacts of symbiotic roles. Harpellales (Zoopagomycota) is a clade of traditional early-diverging fungi, living in the digestive tracts of Diptera insect larvae (e.g., black flies, midges, mosquitoes). Both microscopic and preliminary genomic examinations have identified unexpected patterns in Harpellales, including horizontal gene transfers, potential whole-genome duplications, and electron-dense particles in the fungal basal cells at the interacting surface with insect gut cuticles. However, we still lack a comprehensive understanding to connect the distantly related observations, as well as a "big picture" to make sense of the evolutionary stories behind them. The lack of high-quality genome assemblies of Harpellales prevents us from testing detailed hypotheses regarding the potential multifaceted roles of Harpellales in the gut of disease-transmitting insects. The goal of my research program is to understand the evolutionary genomics of Harpellales and to decode how these fungi interact with their Diptera hosts, using a combination of experimental and computational approaches. This long-term goal will be achieved with three straightforward short-term objectives. Specifically, I will: 1) assemble high-quality Harpellales genomes using long-read sequencing data, 2) investigate gene expression differences of Harpellales with the presence and absence of insect hosts, and 3) examine population genomics of two Harpellales species (Smittium culicis and Zancudomyces culisetae). Overall, the proposed research will aid in clarifying how microbial fungi evolve and interact with insect hosts by using Harpellales and Diptera as examples. This unique symbiotic system will also create novel opportunities to discover unexplored rules of life. My research program will allow us to better understand detailed mechanisms in fungal evolution and host-microbe interactions, covering broad topics of host choice/specificity, genomic duplication, comparative transcriptomics, and population genomics. The research output will also contribute to the development of novel and efficient biocontrol approaches using host-specific microbial fungi targeting larval stages, while current methods mostly focus on the insect adults. Through this research, high-quality training will be provided for the next generation of biologists, especially in fields of mycology, entomology, and evolutionary microbiology.

真菌在水生和陆地生态系统中都扮演着重要的角色。它们积极地影响各种生物体，并与之相互作用。然而，我们仍然不清楚真菌是如何适应环境和进化出与其他生物实体交流的能力的。对早期发散真菌群的研究有助于揭示真菌在古代真核生物陆系化中的重要性。由于它们在系统发育中的重要地位，对早期分叉真菌的进一步研究将有助于我们更多地了解它们的自然历史和共生作用的影响。Harpellales(动物门)是一类传统的早期发散真菌，生活在双翅目昆虫幼虫(如黑蝇、蚊子、蚊子)的消化道中。显微镜和初步基因组检查都发现了Harpellales中意想不到的模式，包括水平基因转移，潜在的全基因组复制，以及位于与昆虫肠道角质层相互作用表面的真菌基底细胞中的电子致密颗粒。然而，我们仍然缺乏一个全面的理解来将遥远的相关观察联系起来，以及一个“大图景”来理解它们背后的进化故事。缺乏高质量的Harpellales基因组组装使我们无法测试关于Harpellales在传播疾病的昆虫肠道中潜在的多方面作用的详细假设。我的研究计划的目标是了解Harpellales的进化基因组学，并使用实验和计算相结合的方法来破译这些真菌如何与它们的双翅目宿主相互作用。这一长期目标将通过三个简单的短期目标来实现。具体地说，我将：1)利用长时间的测序数据组装高质量的Harpellales基因组，2)研究有无寄主情况下Harpellales的基因表达差异，3)研究两个Harpellales物种(Smittium culicis和Zancudmyces culisetae)的种群基因组学。总体而言，拟议的研究将有助于阐明微生物真菌如何进化以及如何与昆虫宿主相互作用，并以半翅目目和双翅目为例。这种独特的共生系统还将创造发现未被探索的生命规律的新机会。我的研究计划将使我们更好地了解真菌进化和宿主-微生物相互作用的详细机制，涵盖宿主选择/专一性、基因组复制、比较转录学和种群基因组学等广泛主题。研究成果还将有助于开发针对幼虫阶段的寄主特异性微生物真菌的新型有效生物防治方法，而目前的方法主要集中在成虫身上。通过这项研究，将为下一代生物学家提供高质量的培训，特别是在真菌学、昆虫学和进化微生物学领域。