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Comparative Chloroplast Genomics

Raubeson, Linda A. [1], Leigh, Joshua [1], Jansen, Robert K. [2], Boore, Jeffrey L. [3].

Insights into Seed Plant Phylogeny from Comparative Chloroplast Genomics.

Seed plant phylogeny has been the focus of numerous studies over the past two+ decades based primarily on morphology, initially, or sequence data, more recently. Current issues include whether or not extant gymnosperms are monophyletic, the relationship of cycads and Ginkgo to each other and the remaining seed plants, and, especially, the relationship of the Gnetales to the conifers. We are working to bring both new and additional data to bear on these issues. By sequencing complete chloroplast genomes of representative seed plant taxa, we plan to identify instances of rare genomic change (the "new" data) as well as investigate the use of increased numbers of nucleotide characters (the "additional" data) from these exemplar taxa to make inferences of seed plant phylogeny. Earlier studies of cpDNA gene order based on mapping and PCR strategies indicate that Ginkgo and cycads share derived gene order changes, as do Gnetales and conifers. Gene order changes that support the conifer II clade also are present. Based on these data (from mapping and PCR), the placement of Gnetales relative to Conifer I (Pinaceae) and Conifer II (other conifer families) is unclear. Chloroplast genomes from Ginkgo, Cycas, and two conifers in the Conifer II clade are nearing completion. Ephedra is in the early stages of preparation. So far our limited complete genome data confirms earlier work and suggests additional potentially informative rearrangement characters that could be developed as phylogenetic markers. In addition, we are extracting the shared complement of protein-coding genes from these genomes to support sequence-based phylogenetic studies.

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1 - Central Washington State University, Department of Biological Sciences, Ellensburg, Washington, 98926-7537, USA
2 - University of Texas Austin, Section of Integrative Biology, 1 University Station, A6700, Austin, Texas, 78712-7640, USA
3 - DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA

chloroplast genomics
seed plant phylogeny
rare genomic changes.

Presentation Type: Symposium or Colloquium Presentation
Session: 19-3
Location: Salon K - Austin Grand Ballroom/Hilton
Date: Monday, August 15th, 2005
Time: 3:30 PM
Abstract ID:258

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