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

Jill M. Duarte, P. Kerr Wall, Laura M. Zahn, Pamela S. Soltis, Douglas E. Soltis, Jim Leebens-Mack, John Edward Carlson, Hong Ma, Claude Walker Depamphilis

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1110-1122
Number of pages13
JournalTaxon
Volume57
Issue number4
StatePublished - Nov 1 2008

Fingerprint

Amborella trichopoda
Nuphar
Amborella
expressed sequence tags
sequence analysis
Angiospermae
angiosperm
gene
water lilies
genes
multigene family
phylogeny
common ancestry
Amborellaceae
ancestry
Arabidopsis
Nymphaeaceae
rice
phylogenetics
proteome

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Plant Science

Cite this

Duarte, J. M., Wall, P. K., Zahn, L. M., Soltis, P. S., Soltis, D. E., Leebens-Mack, J., ... Depamphilis, C. W. (2008). Utility of Amborella trichopoda and Nuphar advena expressed sequence tags for comparative sequence analysis. Taxon, 57(4), 1110-1122.
Duarte, Jill M. ; Wall, P. Kerr ; Zahn, Laura M. ; Soltis, Pamela S. ; Soltis, Douglas E. ; Leebens-Mack, Jim ; Carlson, John Edward ; Ma, Hong ; Depamphilis, Claude Walker. / Utility of Amborella trichopoda and Nuphar advena expressed sequence tags for comparative sequence analysis. In: Taxon. 2008 ; Vol. 57, No. 4. pp. 1110-1122.
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Duarte, JM, Wall, PK, Zahn, LM, Soltis, PS, Soltis, DE, Leebens-Mack, J, Carlson, JE, Ma, H & Depamphilis, CW 2008, 'Utility of Amborella trichopoda and Nuphar advena expressed sequence tags for comparative sequence analysis', Taxon, vol. 57, no. 4, pp. 1110-1122.

Utility of Amborella trichopoda and Nuphar advena expressed sequence tags for comparative sequence analysis. / Duarte, Jill M.; Wall, P. Kerr; Zahn, Laura M.; Soltis, Pamela S.; Soltis, Douglas E.; Leebens-Mack, Jim; Carlson, John Edward; Ma, Hong; Depamphilis, Claude Walker.

In: Taxon, Vol. 57, No. 4, 01.11.2008, p. 1110-1122.

Research output: Contribution to journalArticle

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AU - Duarte, Jill M.

AU - Wall, P. Kerr

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AU - Soltis, Douglas E.

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AU - Ma, Hong

AU - Depamphilis, Claude Walker

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Duarte JM, Wall PK, Zahn LM, Soltis PS, Soltis DE, Leebens-Mack J et al. Utility of Amborella trichopoda and Nuphar advena expressed sequence tags for comparative sequence analysis. Taxon. 2008 Nov 1;57(4):1110-1122.