Genome Explorers

Leaders: Mark Johnson and Alison DeLong - Molecular Biology, Cell Biology, and Biochemistry

Elucidating the forces that shape genomes and create new genes

How do new gene functions evolve? One idea is that duplication of an existing gene allows for one member of the pair to evolve a novel function. One gene continues performing the essential function, while the other gene is free to adapt to new functions because the constraints of purifying selection are relaxed. If these new functions are advantageous, a new gene is born.

Plant genomes are replete with gene duplications and large gene families and are therefore fertile ground for testing these ideas about gene and genome evolution. This team of HHMI-Brown Scholars will use genomics and molecular genetic tools available in the genetic model system Arabidopsis to elucidate paths that leading to new gene functions.

For the past two summers Genome Explorers have focused on pollen, a single cell with an essential function in plant reproduction. Pollen deliver sperm to female gametes for fertilization and seed production by extending a tube that rapidly navigates floral tissue to find a precise target. We are particularly interested in discovering signaling mechanisms required for this process and in understanding how this process responds to high temperature.

The team will work together using bioinformatic techniques to explore the gene family landscape of Arabidopsis to identify gene families that are amenable to functional studies. The goal will be to identify gene families that appear to be in the process of evolving new gene functions. To probe the expression of genes in single cell types, we will generate and analyze gene expression data from deep sequencing and microarray experiments. These data, combined with phylogenetic analysis of gene families, can lead to powerful hypotheses about emerging gene functions.

Smaller groups will explore functions of individual gene families. These groups will test their functional hypotheses by conducting reverse genetic analysis and carrying out assays designed to reveal mutant phenotypes that could arise from knock-outs or knock-downs of individual gene family members that have taken on specific functions.  A combination of insertion mutagenesis and team-generated artificial microRNAs will be used to eliminate or reduce the function of specific genes and multiple members of one gene family. 

Genome Explorers will be actively involved in the discovery of new gene functions while they work to determine the rules that govern the invention of these functions.

Plant Reproduction in a changing climate. 

The 2012 United States corn harvest will go down as one of the worst in decades, and models for climate change suggest that growing conditions in the Corn Belt will become increasing unpredictable and inhospitable. Corn kernels, as well as other critical seed crops including rice and wheat, are produced when a pollen tube grows through floral tissue to deliver sperm to female gametes. If fertilization fails, so does the harvest. Fertilization in plants is highly temperature sensitive. ScholarsAs the climate changes, it is likely that traditional crop production areas will become incompatible with successful fertilization. In the summer of 2012, many farmers tended cornfields that failed to produce a crop because of extremely high temperatures during the two-week period when the plants reproduce. At the same time, a group of eight Brown University undergraduates sponsored by the Howard Hughes Medical Institute and led by Profs. Alison DeLong and Mark Johnson (MCB), were beginning a project to understand how pollen responds to heat. The group defined critical temperature thresholds for pollen tube growth and used cutting edge genomics techniques to understand the molecules that pollen makes to beat the heat. The long-term goal of this project is to produce crop plants with thermo-tolerant reproductive systems.