Tracing the evolution of development among early diverging fungi

真菌可以引起植物疾病，作为菌根伙伴，并分解枯枝落叶和木质碎片，所有这些都是因为构成它们身体的管状菌丝(细胞细丝，被细胞壁包围)。菌丝穿过其复杂的细胞壁分泌消化酶，并穿透底物。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地真核腐生生物。拟议的研究旨在了解真菌是如何进化和适应与陆地植物的相互依存关系的。*新的基因组序列是解开真菌进化第一步秘密的关键。通过我们上一轮的发现资助和与美国联合基因组研究所(JGI)成功的社区测序合作，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6亿年前-gt；；6亿年前，大约在维管束植物起源之前1.5亿年。我们推测，这些真菌的祖先可以消化陆地植物的藻类近亲的细胞壁，配备了酶来分解果胶，果胶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小的，它们通过不含细胞核的确定生长的根状细丝网络吸收营养。*在我们提议的研究中，我们将再次与JGI合作，对另外6-10个基因组进行测序，对它们进行分析，以找出真菌分泌酶的方式和时间的多样化，以及控制真菌体形的蛋白质如何随着微小的根状祖先进化成多细胞菌丝现代真菌而变化。*具体地说，我们将：*分析真菌作为对植物营养的适应而分泌的强大的细胞壁降解酶的进化。这项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，如控制细胞内生长点和交叉球位置的隔膜素和福尔马林，并导致特有的真菌形式。在真核生物进化的大图景中，真菌和动物是近亲，我们对祖先真菌中的基因的分析将表明，可能指导早期动物的极性和形式发展的基因/蛋白质。*通过为现代真菌开发进化树，并使用已知年龄的相应化石来确定真菌群体的起源，来改进真菌的地质年龄估计。年龄估计被真菌分子生物学家社区广泛使用，因为他们努力将基因和基因组进化的模式放在地质时间的角度。*这项研究将有助于培训6名博士、3名硕士和6名理科学生将细胞和分子生物学的方法应用于真菌进化生物学问题。

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.**