Monocots (including such groups as grasses, palms, orchids, and philodendrons) include more than 65,000 species of flowering plants, occur in almost all habitats, and provide the great majority of the human diet. A definitive family tree for this group will be developed and used to understand the broad-scale evolution of monocots over geologic time. A total of 23 genes in 601 species, whole chloroplast genomes in 175 species, and all genes expressed in 50 species will be sequenced and used to reconstruct the evolutionary history of this group. Additionally, phenotypic data from living and fossil species will be collected, and all data will be analyzed integratively to provide a comprehensive understanding of monocot evolution.
The resulting family tree will provide the foundation for many new studies in physiology, ecology, biogeography, and genomics of flowering plants. Web access to all data and results will be provided to researchers and K-12 teachers and students. Several post-doctoral fellows, graduate students, and undergraduates (with a focus on women and minorities) will be trained, and four young faculty will be supported. A museum exhibit on the evolution of flowering plants will be produced for high-profile venues in New York, Chicago, Denver, and Berkeley, and a children's monocot garden exhibit will be developed at the New York Botanical Garden. Posters illustrating monocot diversity and evolution will be distributed to colleges, and staff will give talks at public high schools.
Monocots, with about 60,000 species, represent one of the largest and most diverse major lineages of flowering plants. They include our most important food crops (grains like corn and rice) and many other foods of collectively great value (e.g., bananas, yams, onions, palm oil), plants for energy, animal food and shelter (e.g., switchgrass, pasture grass, bamboo, thatch), plants important in floriculture (e.g., orchids, lilies, bromeliads). and many other plants of economic value. Monocots occupy nearly all terrestrial and shallow aquatic habitats, displaying an immense range of growth habit from small herbaceous plants to large tree-like palms, vines, epiphytes, and submerged water plants. Monocots also display diverse physiologies, including C3 and C4 photosynthesis and non-photosynthetic plants (known as myco-heterotrophs) that feed entirely off of mycorrhizal symbioses. The genomes of monocots vary greatly in size and complexity, and genome doubling (polyploidy) is common. Monocots thus serve as a laboratory for studying plant adaptation to diverse habitats and nutrition modes, and for understanding the origin of plants and processes of economic importance. The NSF MonATOL project is a Tree-of Life project using a wide range of molecular and non-molecular methods to resolve the history of monocots, and use this information to better understand the diversification of this large and important group of plants. This portion of the MonAToL project was focused on developing and implementing methods for building phylogenetic trees from hundreds or thousands of expressed genes obtained from large expressed gene (transcriptome) or genome datasets. Transcriptomes from more than sixty carefully selected species were generated by the project and used for these analyses. We developed and/or refined methods for processing and denovo assembly of transcriptomes, gene classification, and high-speed mining of the datasets to create huge matrices with hundreds or thousands of single- (or low-) copy nuclear genes for phylogenetic analysis. We identified optimal methods for data cleaning, accurate de novo transcriptome assembly and quality evaluation, and methods to improve transcriptome assemblies. An objective classification of plant gene families, based on 22 sequenced plant genomes, provided a scaffold for classifying genes from each assembly. Illumina transcriptome datasets were shown to provide more complete coverage of plant gene space than any prior methods of transcriptome sequencing, at vastly lower cost. Phylogenies built from assembled single copy gene matrices are highly resolved and well supported, and they provide valuable insights into monocot history. Phylogenies are largely congruent with previously published trees based on chloroplast genome sequences, but they also provide greater resolution in some portions of the phylogeny, and suggest that magnoliids may be the closest relatives of monocots. Polyploidy has occurred frequently in monocot history and may be related to major adaptive radiations. These represent the largest datasets assembled to date for monocot phylogenetics, and they provide a case study in new and cost efficient approaches to phylogenetic recovery. In addition to their utility for phylogenetics, transcriptomes are biological "goldmines" for understanding gene families and biochemical pathways, polyploidy and its role in adaptive radiations, horizontal gene transfer, and how novel genes and processes arose in monocots or other organisms. Research training was provided for postdoctoral, graduate, undergraduate, and high school students. A summer Upward Bound course, "The Strangest Plants in the World" was created and introduced about 20 high school students from disadvantaged backgrounds to key concepts of plant biology, physiology, and phylogeny by hands-on study of parasitic, carnivorous, and myco-heterotrophic plants and their unusual structural and physiological adaptations.
