Comparative sequencing of social amoebae in the Dictyostelidae

Baylor College Of Medicine, Houston TX

Investigators

Abstract

This project will generate DNA sequences of two Dictyostelid social amoebae genomes in order to elucidate the complete genetic makeup these interesting soil microorganisms. The data will be generated by whole-genome shotgun sequencing where small pieces of DNA are sequenced by automated methods and re-assembled using sophisticated computational tools and aided by cross-species comparisons. Together with the already completed sequence of Dictyostelium discoideum, the first amoeba genome to be sequenced, these additional genomes will provide an essential resource for a variety of comparative and functional studies. First, because these are social species with complex behavior patterns, including cooperation and cheating, the project would provide the first genome-scale comparative dataset for how social genes evolve. For example, the data will enable the first test of the hypothesis that social conflict drives rapid evolution in the same manner as host-parasite interactions. In addition, comparisons among the sequenced species will reveal functional regions of the genomic DNA, such as gene control elements, by virtue of their conservation across species. The sequencing of additional Dictyostelids will fulfill the goals of the Microbial Genome Sequencing Project in several ways. There is a large community of developmental and cellular biologists with over 100 laboratories worldwide that can take immediate advantage of the new sequence data. There is a web-based gene curation project, www.dictybase.org that organizes all of the information on the Dictyostelids, including gene function predictions that are essential for facilitating cross-species comparisons. Related NSF-funded projects are working on describing and quantifying the biodiversity of the Dictyostelids and other closely related groups like the Mycetazoans. Together, these projects will dramatically improve our understanding the diversity, soil ecology and cross species interactions of the Dictyostelid amoeba. The project will include an intense training component, immersing undergraduate, graduate and postdoctoral students in the activities of the Baylor College of Medicine Human Genome Sequencing Center and in Rice Universitys Department of Ecology and Evolutionary Biology. For example, students will take genes through a variety of experiments from the molecular characterization at Baylor to the evolutionary history and phylogeny at Rice, giving them the widest exposure to the full project. Lab students will also take part in educational initiatives including public presentations, K-12, and undergraduate mentoring. Baylors Center for Educational Outreach will help to guide the K-12 and public endeavors. An inquiry-based discovery activity for elementary school students based on field sampling of social amoebae that are then grown up in class and implemented it in the science laboratory at Longfellow Elementary School, where the P.I.s have long-standing science education ties. The proposed activity are aligned with recommendations of the National Science Education Standards (National Research Council, 1996) for Life Science (grades K-4) and the Texas Essential Knowledge and Skills (www.tea.state.tx.us/teks/) related to the basic needs of organisms and life cycles. Other outreach sites will include the Houston Arboretum, and the Nature Discovery Center. An exhibit, with posters, plates with social amoebae and a handout directing people to our website and the places where social amoebae are found in the Houston area. Both of these exhibits will reach 260,000 visitors annually, including over 20,000 children, for these are popular field trip destinations. Students will learn about social amoebae, and also develop an appreciation for the diversity of soil organisms beneath their feet in the forest.