Genomics of Comparative Seed Evolution.

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This project aims to exploit for gene discovery purposes the mechanisms by which nature has tinkered with the genomes of biodiverse plant species to enable the evolution of important economic traits, such as seeds. This approach involves a unique collaboration of scientists with diverse areas of expertise in species evolution, genomics and bioinformatics located at sister institutions in New York: New York University, The New York Botanical Garden, The American Museum of Natural History, and Cold Spring Harbor Laboratories. The approach involves the identification of key plant species in which a trait first evolved and the subsequent sequencing of large portions of the coding regions of these genomes. The next step is to develop and use bioinformatics tools that enable the comparison of large numbers of genes conserved across a set of species which have the trait compared to each other and to their closest related species who do not have the trait. This approach enables the identification of genes and gene characters whose DNA history correlates with the evolution of the species containing the trait. The candidate genes are then tested for their role in determining the trait using comparative studies of gene expression in the biodiverse species, and by mutant analysis in model species such as Arabidopsis. The working example of this approach is to identify the sets of genes that enabled the evolution of seeds, an important evolutionary innovation in plants with important implications for agriculture. This involves the sequencing of portions of the genomes of the most primitive living seed plants, the non-flowering Gymnosperms, on earth since the Mesozoic era. This research transcends and unites genomics and systematics to produce a deeper understanding of seed evolution, while revealing genes involved in important agronomic traits involved in seed development. The findings will have implications for improving seed quality, as much of today's agriculture - from food to textiles- depends on seed products. This project also has systematicists and genomicists working together to train a new class of biologists with interdisciplinary expertise in these two complementary areas. Finally, the approaches and bioinformatics tools developed in this project will be applicable to comparative functional genomic studies in any species, plant or animal.