Systematics Section / ASPT
Raubeson, Linda A. , Campbell, Christopher S. , Connolly, Margaret , Cronn, RC , Dutton, Ashley , Ickert-Bond, Steffi , Kelch, Dean , Li, Jianhua , Liston, Aaron , Little, Damon , Peery, Rhiannon , Schwarzbach, Andrea E. , Stevenson, Dennis Wm. , Willyard, Ann .
Phylogenetic utility of VPCR (variable plastid coding regions) in gymnosperms.
Species level relationships are notoriously difficult to resolve in plants. As part of the Gymnosperm Tree of Life Project, we are examining the utility of a new approach that we call VPCR (variable plastid coding regions). We designed primers to amplify regions of 500-700 base pairs from within rapidly evolving, protein-coding plastid genes. This strategy is designed such that data generation is logistically simple: primers can be universal or nearly so, the amplified region can be completely sequenced as single reads using the PCR primers, alignment is straightforward and models of nucleotide evolution are well developed. Intergenic spacers (IGS), in contrast, may be problematic to amplify (especially given the genomic rearrangements in gymnosperm plastomes), sequence (due to mononucleotide runs), align, and analyze. In addition, predicting which IGS evolves at a higher rate in which lineage can be problematic. Because we are looking for markers that we can apply across all gymnosperms, we decided to investigate this VPCR strategy based on coding regions rather than IGS. Currently we are conducting a feasibility study, focusing on VPCR from five genes: cemA, rpoA, rpoB, rpoC1 and rps4. Tests of subsets of these markers in Ephedra, Pinaceae, and cycads show that they are quite informative at the generic level and provide some help resolving relationships at the species level. The extent to which species are resolved varies depending on their divergence and the rate of sequence evolution in the plastid genomes of different groups.
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1 - Central Washington University, Department of Biological Sciences, 400 E University Way, Ellensburg, WA, 98926-7537, USA
2 - University of Maine, Department of Biological Sciences, 5722 Deering Hall, Orono, Maine, 04469-5722, USA
3 - University of Maine, Department of Biological Sciences, 5772 Deering Hall, Orono, Maine, 04469-5722
4 - USDA Forest Service, Forest Genetics, Pacific Nothwest Research Station, 3200 SW Jefferson Way, Corvallis, Oregon, 97331, USA
5 - Central Washington University, Department of Biological Sciences, 400 E. University Way, Ellensburg, WA, 98926, USA
6 - University of Alaska, Department of Biology and Wildlife, Fairbanks, Alaska, 99775-6960, USA
7 - California Department of Food & Agriculture, 3294 Meadowview Road, Sacramento, California, 95832, USA
8 - Harvard University, Arnold Arboretum, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
9 - Oregon State University, Department of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, Oregon, 97331-2902, USA
10 - The New York Botanical Garden, Lewis B. and Dorothy Cullman Program for Molecular Systematic Studies, 200th St. & Southern Blvd., Bronx, New York, 10458-5126, USA
11 - University of Texas, Biological Sciences, 80 Fort Brown
, Brownsville, Texas, 78520, USA
12 - New York Botanical Garden, Institute of Systematic Botany, 200Th Street & Southern Boulevard, Bronx, New York, 10458-5126, USA
Presentation Type: Oral Paper:Papers for Sections
Location: Continental C/Hilton
Date: Tuesday, July 10th, 2007
Time: 8:15 AM