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Methods and theory of phylogenetic inference

Jansen, Robert K. [2], dePamphilis, Claude W. [1], Raubeson, Linda [4], Leebens-Mack, James [1], McNeal, Joel R. [1], Cui, Liying [1], Zhang, Yan [1], Wyman, Stacia [3], Boore, Jeffrey [5], Kuehl, Jennifer [5].

The utility of whole chloroplast genome sequencing for reconstructing deep nodes in plants with an example from basal angiosperms.

We are sequencing entire chloroplast genomes from seed plants to address two phylogenetic problems, relationships among the major seed plant lineages and identification of basal angiosperm relationships. Our sampling strategy involves sequencing genomes from 55 representatives of all clades of seed plants. To date we have completed sequences for 4 taxa and we have nearly complete drafts for an additional 16 genomes. As part of our effort we have developed new methods for obtaining purified cpDNA and a new program for the annotation of chloroplast genomes. The phylogenetic goals of this project involve performing phylogenetic analyses of the nucleotide, amino acid, and gene order data to assess relationships at these two deep nodes in seed plants. Our current focus has been the basal angiosperm question. Most recent molecular phylogenies using sequences of one to several genes have suggested that Amborella represents the basal, extant flowering plant, or shares this position together with the waterlilies. Last year, the chloroplast genome of Amborella was sequenced and all 61 protein coding genes shared with 12 other sequenced land plant chloroplast genomes were used to assess the position of Amborella (Goremykin et al., 2003, MBE 20: 1499). Those phylogenetic analyses of amino acid and DNA sequence data suggested that Amborella was not basal. We have sequenced five new chloroplast genomes to determine if limited taxon sampling could explain this surprising result. This includes two monocots (Acorus and Yucca), one waterlily (Nuphar), one basal eudicot (Ranunculus), and one more gymnosperm outgroup (Ginkgo). Phylogenetic analyses of amino acids sequences for 61 protein-coding genes for this expanded data set provided strong support for the basal position of Amborella. Overall, these results indicate the power of complete chloroplast genome sequences for phylogeny reconstruction and the importance of increased taxon sampling for resolving deep nodes in angiosperm phylogenies.

1 - Pennsylvania State University, Biology, 313 Wartik, University Park, Pennsylvania, 16802, USA
2 - University of Texas at Austin, Section of Integrative Biology, 1 Universiy Station, #A6700, Austin, Texas, 78712, USA
3 - University of Texas at Austin, Department of Computer Sciences, 1 University Station, #C0500, Austin, Texas, 78712, USA
4 - Central Washington University, Department of Biological Sciences, MS 7537, Ellensburg, Washington, 98926-7537, USA
5 - DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA

basal angiosperms
chloroplast DNA
comparative genomics
seed plants.

Presentation Type: Symposium
Session: 39-3
Location: Alpine A (Snowbird Center)
Date: Tuesday, August 3rd, 2004
Time: 3:45 PM
Abstract ID:308

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