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。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，可能是吞噬性的，而不是通过细胞壁摄取营养；而且是水生的，有鞭毛的阶段，而不是陆地的。菌丝结构、消化酶分泌和陆地生长的重建进化是拟研究的主题。我们将利用7个新的早期分化真菌基因组序列，这是我们向美国联合基因组研究所成功提出的群落测序建议的结果。我们将根据系统发育树的模式测试祖先真菌是单细胞的还是菌丝的。我们将比较研究充分的子囊菌的菌丝生长基因与那些早期分化真菌，他们从来没有分析过。将基因组序列与其他真菌类群的新数据相结合，我们将使用消化植物材料（如纤维素）或消化动物组织的保守基因的系统发育分析来推断真菌中分解植物产物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价值的新酶群。结合我对子囊菌门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，以帮助确定重要多样化的最小年龄。本研究将有助于培养约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关注的问题。

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.