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Resolving the green branch of life: Current progress and future challenges

Haberle, Rosemarie C. [1], Jansen, Robert K. [1], Boore, Jeffrey L. [2], Kuehl, Jennifer V. [2].

Comparative chloroplast genomics of Campanulaceae: a model system for understanding mechanisms of genome evolution and the utility of genomic changes for phylogeny reconstruction.

Chloroplast genome structural rearrangements are useful for resolving relationships at deep nodes in green plant phylogenies. How those changes may have occurred, however, is obscured by evolutionary divergence among these distantly related clades. Chloroplast genome structure, gene order and content are highly conserved in flowering plants, although there are notable exceptions in certain families. Within these groups with highly rearranged genomes, comparative analysis allows fine scale examination of potential mechanisms responsible for chloroplast genome rearrangements, such as recombination between repeat sequences. Previous restriction site mapping demonstrated that the chloroplast genomes of Trachelium and other members of the Campanulaceae are the most highly rearranged of all land plants. Some of these rearrangements are shared across the Campanulaceace and substantiate the monophyly of the family, but several divide the family into distinct clades or represent autapomorphies.. We are sequencing the complete chloroplast genomes of 9 taxa representing all major lineages in the family. We have completed sequencing one member of the Campanulaceae (Trachelium), and four other members of the family and the related family Nemacladaceae are now in progress. Detailed analyses of the Trachelium genome have shown that it contains numerous repeat sequences, many associated with endpoints of blocks of rearranged genes. Some of the repeats constitute chloroplast sequence duplications, while others appear to be non-chloroplast in origin. Trachelium has many more repeats than all other sequenced angiosperm chloroplast genomes. With the availability of nearly complete genome sequences of 4 close relatives of Trachelium, we are characterizing and comparing intragenic regions and repeats in these taxa between rearranged blocks of genes to pinpoint causes of rearrangement. Knowledge of mechanisms of gene order changes is needed to better use these types of characters for phylogenetic reconstruction.

1 - University of Texas at Austin, Section of Integrative Biology, 1 Universiy Station, #A6700, Austin, Texas, 78712, USA
2 - DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA


Presentation Type: Symposium
Session: 56-3
Location: Ballroom 3 (Cliff Lodge)
Date: Wednesday, August 4th, 2004
Time: 2:30 PM
Abstract ID:236

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