Becoming a fungus: comparative phylogenomic studies of evolution of hyphal growth and absorptive nutrition in 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。然而，系统发育证据表明真菌和动物有共同的祖先，最早的真菌是单细胞的而不是菌丝的；无壁的，可能是吞噬的，而不是通过细胞壁摄取营养；水生的，有鞭毛的阶段，而不是陆地的。重建菌丝结构、分泌消化酶和陆地生长的进化是拟议研究的主要主题。我们将利用七个新的早期分叉真菌基因组序列，这是我们向美国联合基因组研究所提出的成功的社区测序建议的结果。我们将根据系统发育树上的模式来测试祖先真菌是单细胞的还是菌丝的。我们将比较从子囊菌门中得到充分研究的菌丝生长基因和那些从未被分析过的早期分叉真菌的基因。结合基因组序列和来自其他真菌组的新数据，我们将使用对用于消化纤维素等植物物质或用于消化动物组织的保守基因的系统发育分析来推断在真菌中分解植物产品的能力是何时何地进化的。这一分析有可能揭示具有工业应用的新的酶组。结合我对子囊菌和分子钟的持续兴趣，我们还将分析分散的真菌孢子化石的记录，以帮助建立重要多样化的最小年龄。这项研究将有助于培养~4名博士生将分子生物学的方法应用于真菌进化生物学中广泛感兴趣的问题。

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. However, phylogenetic evidence shows fungi and animals share a common ancestor and the earliest fungi were unicellular not hyphal; wall-less and probably phagotrophic instead of ingesting nutrients across a cell wall; and aquatic and with a flagellated stage rather than terrestrial. Reconstructing evolution of hyphal construction, secreted digestive enzymes, and terrestrial growth, are main themes of the proposed research. We will take advantage of seven new genome sequences for early-diverging fungi, the result of our successful community sequencing proposal to the US Joint Genome Institute. We will test whether ancestral fungi were unicellular or hyphal based on patterns in phylogenetic trees. We will compare the well-studied genes for hyphal growth from Ascomycota with those of early-diverging fungi where they have never been analyzed. Combining the genomic sequences with the new data from additional fungal groups, we will use phylogenetic analysis of conserved genes for digesting plant materials such as cellulose or for digesting animal tissue to infer when and where the ability to breakdown plant products evolved in the fungi. This analysis has the potential to reveal new groups of enzymes with industrial applications. Combining my continuing interest in the Ascomycota and molecular clocks, we will also analyze the record of dispersed fungal spore fossils to help establish minimum ages of important diversifications. This research will contribute to training ~4 Ph.D. students to apply methods of molecular biology to questions of broad interest in fungal evolutionary biology.