Tracing the evolution of development among early diverging fungi

真菌可以引起植物疾病，作为菌根伴侣，分解垃圾和木屑，这都是因为它们的身体由管状菌丝（细胞壁包围的细胞细丝）组成。菌丝刺穿底物，同时在复杂的细胞壁上分泌消化酶。这些酶将有机化合物消化成简单的、可扩散的分子，真菌吸收这些分子来促进它们的生长，使真菌成为最重要的陆生真核腐生生物。拟议的研究旨在了解真菌如何进化并适应与陆地植物的相互依赖。新的基因组序列是揭开真菌进化第一步秘密的关键。通过我们上一轮的发现基金以及与美国联合基因组研究所（JGI）成功的群落测序合作，我们对3种真菌的新基因组进行了测序和分析，这些真菌在大约6亿年前，比维管植物起源早1.5亿年左右，彼此分化。我们推断，这些真菌的祖先可以消化陆地植物的藻类亲戚的细胞壁，配备酶来分解果胶，这是植物壁的一个特征。我们对其形态的重建表明，早期真菌的大小是微观的，它们通过一种由不含细胞核的确定生长的根状细丝组成的网络吸收营养。***在我们的研究中，我们将与JGI合作，对另外6-10个基因组进行测序，分析真菌分泌酶的方式和时间，以及控制真菌身体形状的蛋白质如何在微观根状祖先进化成多细胞菌丝现代真菌时发生变化。***具体来说，我们将：***分析真菌分泌的强大细胞壁降解酶的进化，以适应植物性营养。该研究将揭示具有工业应用潜力的新型纤维素分解酶。****追踪蛋白质的进化，如septin和formmins，它们控制细胞内的生长点和交叉壁的位置，并产生典型的真菌形式。真菌和动物在真核生物进化的大背景下是近亲，我们对祖先真菌基因的分析将提示可能在早期动物中指导极性和形态发展的基因/蛋白质。***通过发展现代真菌的进化树，并使用已知年龄的相应化石来确定真菌类群的起源，从而改进真菌地质年龄的估计。真菌分子生物学家社区广泛使用年龄估计，因为他们努力将基因和基因组进化的模式纳入地质时间的视角。***本研究将培养6名博士、3名硕士和6名理学士，将细胞和分子生物学的方法应用于真菌进化生物学的问题

Fungi can cause plant diseases, serve as mycorrhizal partners, and decompose litter and woody debris, all because of the tubular hyphae (filaments of cells, surrounded by a cell wall) that make up their bodies. Hyphae poke and penetrate into substrates while secreting digestive enzymes across their complex cell walls. The enzymes digest organic compounds into simple, diffusible molecules, which fungi absorb to fuel their growth, making fungi the most important terrestrial eukaryotic saprotrophs. The proposed research is directed towards understanding how fungi evolved and adapted to interdependence with land plants. ***New genome sequences are the key to unlocking secrets of the first steps in fungal evolution. Through our last round of Discovery Grant funding and a successful community sequencing collaboration with the US Joint Genome Institute (JGI), we sequenced and analyzed new genomes of 3 fungi that diverged from one another >600 million years ago, ~150 million years before the origin of vascular plants. We inferred that the ancestors of these fungi could digest the cell walls of algal relatives of land plants, being equipped with enzymes to breakdown the pectins that are a feature of plant walls. Our reconstructions of their form suggested that early fungi were microscopic in size and that they absorbed nutrients through a network of rhizoids' thin filaments of determinate growth that contain no nuclei. ***In our proposed research, we will sequence an additional 6-10 genomes, again in collaboration with JGI, analyzing them to find out how and when fungal secreted enzymes diversified, and how the proteins that control the fungal body shape changed as a microscopic rhizoidal ancestor evolved into a multicellular hyphal modern fungus. ***Specifically, we will:*** Analyze evolution of the powerful cell wall degrading enzymes that fungi secrete as an adaptation to plant based nutrition. This research will reveal novel enzymes for cellulose decomposition with potential for industrial applications.**** Trace the evolution of proteins such as septins and formins that control the points of growth and location of crosswalls in a cell, and result in characteristic fungal forms. Fungi and animals are close relatives in the big picture of eukaryote evolution, and our analysis of genes in ancestral fungi will suggest genes/proteins that may have guided polarity and the development of form in early animals.*** Improve estimates of geological ages of fungi by developing evolutionary trees for modern fungi, and using corresponding fossils of known ages to date origins of fungal groups. Age estimates are widely used by the community of fungal molecular biologists as they strive to put patterns of gene and genome evolution into the perspective of geological time.***This research will contribute to training 6 PhD, 3 MSc, and 6 BSc students to apply methods of cell and molecular biology to questions of fungal evolutionary biology.**