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Systematics Section / ASPT

Jansen, Robert K. [1], Raubeson, Linda A. [2], dePamphilis, Claude W. [3], Wyman, Stacia [4], Boore, Jeffrey L. [5], Warnow, Tandy [6], Moret, Bernard [7].

Comparative Chloroplast Genomics - An Overview and Summary of Progress.

This project is sequencing chloroplast genomes of 60 exemplar taxa from the major lineages of seed plants. The genomic sequences are being used to address questions on seed plant phylogeny, with an emphasis on resolving relationships among the major lineages of seed plants and identification of the basal angiosperm group. Another important focus of this work involves examining patterns and mechanisms of genomic rearrangements in several groups that are suspected of having substantial changes in gene order, including conifers, the angiosperm families Campanulaceae and Geraniaceae, and a number of non-photosynthetic taxa. Finally, this project also involves the development of computational tools for the analysis of chloroplast genomes, with an emphasis on annotation, analysis of repeated sequences, and methods for using gene order data for phylogeny reconstruction. We have completed the sequencing of 10 chloroplast genomes, we have draft sequences in the finishing stages for another 27 genomes, and 7 other genomes are ready for sequencing. Some notable accomplishments of our project include: (1) development of new methods for gathering chloroplast genome sequences either by amplifying entire plastid genomes or cloning them into fosmid vectors; (2) development of a chloroplast genome annotation program (DOGMA) and a chloroplast genome database; (3) phylogenetic analyses that greatly expand the sampling of plastid genomes for resolving the relationships among basal angiosperm lineages; and (4) examination of the extent of repeated sequences in chloroplast genomes and their possible role in changes in genome organization.


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1 - University of Texas Austin, Section of Integrative Biology, 1 University Station, A6700, Austin, Texas, 78712-7640, USA
2 - Central Washington State University, Department of Biological Sciences, Ellensburg, Washington, 98926-7537, USA
3 - Pennsylvania State University, Department of Biology and Institute of Molecular Evolutionary Genetics, University Park, Pennsylvania, 16801, USA
4 - Williams College, Computer Science, Williamstown, Massachusetts, 01267, USA
5 - DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA
6 - University of Texas at Austin, Computer Science, Austin, Texas, 78712, USA
7 - University of New Mexico, Computer Science, Albuquerque, New Mexico, 87131, USA

Keywords:
Choroplast Genomes, Angiosperms, Genome Evolution.

Presentation Type: Poster
Session: 33-111
Location: Salon C, D & E - Gov Ballroom/Hilton
Date: Tuesday, August 16th, 2005
Time: 12:30 PM
Abstract ID:344


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