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Award Abstract #0227314
YIA-PGR: Tools for Plant Comparative Genomics
| NSF Org: |
DBI
Division of Biological Infrastructure
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| Initial Amendment Date: |
September 10, 2002 |
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| Latest Amendment Date: |
June 16, 2006 |
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| Award Number: |
0227314 |
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| Award Instrument: |
Continuing grant |
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| Program Manager: |
Diane Jofuku Okamuro
DBI Division of Biological Infrastructure
BIO Directorate for Biological Sciences
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| Start Date: |
September 1, 2002 |
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| Expires: |
August 31, 2008 (Estimated) |
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| Awarded Amount to Date: |
$1010845 |
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| Investigator(s): |
Todd Vision tjv@bio.unc.edu (Principal Investigator)
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| Sponsor: |
University of North Carolina at Chapel Hill
104 AIRPORT DR STE 2200
CHAPEL HILL, NC 27599 919/966-3411
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| NSF Program(s): |
PLANT GENOME RESEARCH RESOURCE,
PLANT GENOME RESEARCH PROJECT
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| Field Application(s): |
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| Program Reference Code(s): |
BIOT, 9297, 9184
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| Program Element Code(s): |
7577, 1329
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ABSTRACT
The diversity of model systems presents both challenges and opportunities for applying comparative and phylogenetic approaches to questions in plant functional genomics. New methodologies are needed in order to describe features of biological sequences and maps across multiple organisms that are related by a known phylogeny, as opposed to making either simple pair-wise comparisons or 'flat' comparisons among multiple organisms that ignore the presence of phylogenetic structure. This research focuses on two test applications of phylogenomics: (1) identifying conserved motifs and residues that define particular lineages within a gene family and (2) reconstructing genome rearrangement events along a phylogeny in such a way as to be able to predict gene content and order in sparsely sampled genomes. Because some of the methodology proposed is computationally intensive and requires the integration of data from a variety of public sources, this work is complemented by the development of an online plant phylogenomics database called Phytome. In collaboration with the Partnership for Minority Advancement in the Biosciences, an inquiry-based K-12 educational module is developed and delivered to targeted public schools in North Carolina through a mobile science teaching laboratory.
Information regarding all the deliverables for our Plant Genome Project will
be posted at the following URL:
http://www.phytome.org
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
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Bouck A, Vision TJ. "The molecular ecologist's guide to expressed sequence tags," Molecular Ecology, v.16, 2007, p. 907.
Cheng F, Hartmann S, Gupta M, Ibrahim JG, Vision TJ. "A hierarchical model for incomplete alignments in phylogenetic inference," Bioinformatics, v.25, 2009, p. 592.
Crayton ME, Powell B, Vision TJ, Giddings MC. "Tracking the evolution of alternatively spliced exons in the Dscam gene family," BMC Evolutionary Biology, v.6, 2006, p. 16.
Crayton ME, Powell B, Vision TJ, Giddings MC. "Tracking the evolution of alternatively spliced exons in the Dscam gene family," BMC Evolutionary Biology, v.6, 2006, p. 16.
Faddah DA, Ganko EW, McCoach C, Pickrell JK, Hanlon SE, Mann, FG, Mieczkowska JO, Jones CD, Lieb JD, Vision TJ. "Systematic identification of balanced transposition polymorphisms in yeast," PLoS Genetics, v.5, 2009, p. e1000502.
Ganko E, Meyers BC, Vision TJ. "Divergence in expression between duplicated genes in Arabidopsis," Molecular Biology and Evolution, v.24, 2007, p. 2298.
Gaulton KJ, Mohlke KL, Vision TJ. "A computational system to select candidate genes for complex human traits," Bioinformatics, v.23, 2007, p. 1132.
Hartmann S, Lu D, Phillips J, Vision TJ. "Phytome: a platform for plant comparative genomics," Nucleic Acids Research, v.34, 2006, p. D724.
Hartmann S, Lu D, Phillips J, Vision TJ. "Phytome: a platform for plant comparative genomics," Nucleic Acids Research, v.34, 2006, p. D724.
Hartmann S, Vision TJ. "Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?," BMC Evolutionary Biology, v.8, 2008, p. 95.
Hemminger BM, Saelim B, Sullivan PF, Vision TJ. "Comparison of Full-text Searching to Metadata Searching for Genes in Two Biomedical Literature Cohorts," Journal of the American Society for Information Science and Technology (JASIST), v.58, 2007, p. 2341.
Huan L, Prins J, Wang W, Vision TJ. "Reconstruction of Ancestral Gene Order after Segmental Duplication and Gene Loss," Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003, p. 484.
Huan L, Prins J, Wang W, Vision TJ. "Reconstruction of Ancestral Gene Order after Segmental Duplication and Gene Loss," Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003, p. 484.
Knies JL, Dank KK, Vision TJ, Hoffman N, Swanstrom RI, Burch CL. "Compensatory evolution in RNA secondary structures increases substitution rate variation among sites," Molecular Biology and Evolution, v.25, 2008, p. 1778.
Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S and 21 others. "Taking the first steps towards a standard for reporting in phylogenies: Minimal Information About a Phylogenetic Analysis (MIAPA)," OMICS, v.10, 2006, p. 231.
Remington DL, Vision TJ, Guilfoyle TJ, Reed JW. "Contrasting modes of diversification in the Aux/IAA and ARF gene families," Plant Physiology, v.135, 2004, p. 1738.
Remington DL, Vision TJ, Guilfoyle TJ, Reed JW. "Contrasting modes of diversification in the Aux/IAA and ARF gene families," Plant Physiology, v.135, 2004, p. 1738.
Todd Vision. "Gene order evolution in plants: a slow but sure shuffle," New Phytologist, v.168, 2005, p. 51.
Vision TJ. "An international showcase of bioinformatics research (meeting report)," Genome Biology, v.2003, 4, p. 337.
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