John E. Carlson - US grants

0207202
de Pamphillis

This research project is designed to accomplish two aims: Aim 1: To construct and array high-quality BAC libraries to provide a genomic resource on a wide range of species. Aim 2: To enable researchers working with green algae, non-seed land plants, and seed plants (including flowering plants) to identify genes critical for understanding plant form and function and how land plants arose and diversified. This project will enable progress toward an understanding of the genetic basis for the transitions that mark the most fundamentally important steps in green plant evolution. The Deep Green community (http://ucjeps.herb.berkeley.edu/bryolab/deepgene/index.html) will help to provide an infrastructure for ongoing scientific exchange. Bioinformatics and a web site will be provided to the community to access these resources (http://www.genome.clemson.edu/).

Selected Species: Desired coverage is given in parentheses. Where two coverage values are listed, two libraries using different restriction enzymes will be made.

Green algae:
Volvox carteri (5x, 5x)
Caulerpa mexicana (8x)
Mesostigma viride (8x)
Coleochaete orbicularus (6.4x, 6.4x)
Chara aspera (6x)

Non-seed plants:
Marchantia polymorpha (8x)
Anthoceros sp. (6.3x, 6.3x)
Lycopodium lucidulum (5.1x, 5.1x)
Angiopteris erecta (6.2x, 6.2x)
Ceratopteris richardii (4.8x, 4.8x)
Marsilea quadrifolia (5.6x, 5.6x)

Seed plants:
Amborella trichopoda (5.5x)
Nuphar adventa (7x)
Acorus gramineus (7x)
Lirodendron tulipifera (7x)
Mimulus guttatus (7x)

Intellectual Merit: Rapid advances in technology are fundamentally altering the biological sciences. Once relegated to extremely expensive and ponderously slow "Big Science" projects, the sequencing, assembly, and annotation of large genomes, such as those found in plants, is increasingly becoming the province of smaller, less expensive consortia. Full inventories of expressed genes can now be obtained for any organism at very modest cost. This "genomics revolution" is touching all aspects of biology, not the least, the study of plant biology. With the increasing ease of obtaining genomic data, the focus must now turn to producing information from the data and synthesizing approaches from sub-disciplines which have historically operated separately. In particular, a detailed understanding of genome evolution, not just individual genes, is becoming an attainable goal. Correlating these molecular data with physiological responses, ecosystem interactions, and crop productivity is a major scientific goal. Towards this end, the 18th Penn State Symposium in Plant Biology: Plant Evolutionary Genetics and Genomics will be held May 18-21, 2011 at Penn State's University Park campus. This meeting will bring together both leading scientists and early-career researchers to exchange results and develop collaborations in this rapidly evolving field. The symposium is the 18th in a very successful series of Plant Physiology / Plant Biology Symposia, which have been held at Penn State since 1986.

Broader Impacts: This meeting will provide critical educational opportunities to undergraduate students, graduate students, post-doctoral researchers, and to early-career faculty members in the following ways: 1) Several speakers will be invited to deliver short talks based upon the quality of submitted poster abstracts. These decisions will emphasize inclusion of early-career faculty members and members of groups under-represented in American science. 2) Travel awards to offset costs of attendance to the meeting will be distributed to select attendees, based upon demonstrated need and upon other factors, with a preference towards undergraduates at small, non-research intensive colleges/universities. 3) Ample time in the symposium schedule will be "unstructured" time at poster sessions and in proximity to refreshments. This arrangement allows maximum interaction between students and the cadre of distinguished scientists serving as plenary speakers. In addition, it is important to note that the topic of our symposium is in a critical area of current science: Increased understanding of plant genetics and genomics may play a key role in the development of a sustainable biofuels industry in the United States and world-wide.

PI: John E. Carlson (Pennsylvania State University)

Co-PIs: Jeanne Romero-Severson (University of Notre Dame), Scott E. Schlarbaum (University of Tennessee - Knoxville), Mark V. Coggeshall (University of Missouri - Columbia), Haiying Liang (Clemson University), Oliver Gailing (Michigan Technological University), and Ketia L. Shumaker (University of West Alabama).

Senior Personnel: Meg Staton (Clemson University) and Nicholas C. Wheeler (Oregon State University).

Most timberlands in the United States are natural forests, of which eastern hardwood forests comprise more than half. The eastern hardwood forests are complex biological systems, covering over 400 million acres of bottomland and riparian sites, major watersheds, mesic sites and upland xeric sites. These forests provide habitat and food for wildlife, stabilization of riparian zones, long-term carbon sequestration and other essential ecosystem services as well as wood and biomass products for human use. The increasing incidence of introduced exotic pests, diseases and invasive plants, combined with climate change and forest fragmentation, threaten the sustainability of these forest ecosystems. Unfortunately, few genomic resources are available for use in studying the consortium of hardwood species that compose the eastern forests. An interdisciplinary team will work together to develop new genomic resources for important species that represent the major taxonomic groups of eastern hardwood trees, from the oldest to more recently evolved, including yellow poplar (Liriodendron tulipifera), sweetgum (Liquidambar styraciflua), honey locust (Gleditsia triacanthos), northern red oak (Quercus rubra), black walnut (Juglans nigra), sugar maple (Acer saccharum), blackgum (Nyssa sylvatica), and green ash (Fraxinus pennsylvannica). The project will produce sequence databases for expressed genes, genetic markers, genetic linkage maps, and reference populations This will provide lasting genomic and biological resources for the discovery and conservation of genes in hardwood trees for growth, adaptation and responses to environmental stresses such as drought, heat, insect pests and disease. These resources will be available to the scientific community and the public through the project website (www.hardwoodgenomics.org). All original sequence data will be deposited in NCBI's Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) and the genetic linkage maps and associated marker data will also be available at the Dendrome database (http://dendrome.ucdavis.edu/).

The broader impacts from this project will include forest health, tree improvement, forest management, molecular evolution, scientific training, and public education. An increasing incidence of exotic pests and diseases, combined with climate change and forest fragmentation, are threats to the sustainability of forest ecosystems and economies. This project will provide powerful new tools to address such forest health issues and the protection and restoration of forest genetic diversity and productivity. The project will also fill gaps in available genomic resources for important groups of flowering plants, including the taxonomic orders Magnoliales (yellow poplar), Proteales (sweetgum), Fabales (honey locust), Fagales (Northern red oak and black walnut), Sapindales (sugar maple), Cornales (blackgum), and Lamiales (green ash). These resources will enrich the scientific community's ability to study the evolution of not only woody plants, but also all angiosperms at a resolution and depth not previously possible. All of the data generated by the project will be deposited in high-visibility public community databases, and all gene clones, libraries, and reference population DNAs will be stored and available to the public at cost. Descriptions of the resources and analyses of the results will also be published as journal articles, at national and international meetings, and through a public web portal hosted by the Clemson University Genomics Institute. This project will also provide for the training of undergraduate, graduate and postdoctoral students in comparative genomics, evolutionary genomics, population genetics, bioinformatics and forest genetics. Educational programs on plant genomics will be developed for Native American public schools in cooperation with the Cherokee Nation, and substantive research experiences will be provided to minority undergraduate students in collaboration with the University of West Alabama.