Utility of Amborella trichopoda and Nuphar advena expressed sequence tags for comparative sequence analysis

Authors: Duarte, Jill M.¹; Wall, Kerr P.¹; Zahn, Laura M.²; Soltis, Pamela S.³; Soltis, Douglas E.⁴; Leebens-Mack, Jim⁵; Carlson, John E.⁶; Ma, Hong W.¹; dePamphilis, Claude W.⁷

Source: Taxon, Volume 57, Number 4, November 2008 , pp. 1110-383E(-726)

Publisher: International Association for Plant Taxonomy

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Abstract:

Expressed sequence tags (ESTs) for the basal angiosperms Amborella trichopoda (Amborellaceae) and the water lily Nuphar advena (Nymphaeaceae) have proven valuable in identification of gene pairs to study the timing of duplication events relative to the most recent common ancestor (MRCA) of all extant angiosperms. Here we discuss how ESTs for these taxa are also useful for deducing gene families that were present in the MRCA of all flowering plants. For example, 4,572 gene clusters identified in an analysis of the rice and Arabidopsis proteomes contained putative orthologs of Amborella or Nuphar. Homologs of many developmentally important genes were identified from Amborella or Nuphar in these gene clusters. This number of ancestral genes is expected to increase as the number of Amborella and water lily ESTs increases. Genes found unduplicated in the rice and Arabidopsis genomes may be especially useful for phylogenetic analyses including diverse angiosperm lineages. We identify 595 of these single copy genes with putative orthologs in Amborella or Nuphar. Phylogenetic analysis of one of these nuclear single-copy genes encoding the enzyme carboxymethylenebutenolidase yields a topology that places Amborella and Nuphar as the sisters to all other extant lineages of angiosperms and is generally consistent with current angiosperm phylogenies based mainly on chloroplast, mitochondrial, and nuclear ribosomal sequences.

Keywords: BASAL ANGIOSPERMS; ESTS; MADS BOX; SINGLE COPY GENE; TRANSCRIPTION FACTORS; TRANSCRIPTOME

Document Type: Research article

Affiliations: 1: Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, U.S.A. 2: Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, U.S.A., AAAS, 1200 New York Ave NW, Washington, D.C. 20005, 3: Florida Museum of Natural History, University of Florida, Gainesville, Forida 32611, U.S.A. 4: Department of Botany, University of Florida, Gainesville, Forida 32611, U.S.A. 5: Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, U.S.A., Department of Botany, University of Georgia, Athens 6: The School of Forest Resources and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, U.S.A. 7: Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, U.S.A.;, Email: cwd3@psu.edu

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