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Abstract Detail


Genetics Section

Duarte, Jill [1], Wall, P. Kerr [1], Edger, Patrick [2], Beckmann, Kevin G. [1], Landherr, Lena [1], Pires, J. Chris [3], Leebens-Mack, Jim [4], dePamphilis, Claude W. [5].

Identification of conserved single copy nuclear genes in Arabidopsis, Populus, and rice and their phylogenetic utility at multiple taxonomic levels.

Although the overwhelming majority of genes found in angiosperms are members of gene families, we have identified a set of genes that are conserved as single copy in the Arabidopsis, Populus, and rice genomes. To characterize these genes, we have performed a number of analyses examining GO annotations, cDNA length, number of exons, expression patterns, and presence in the Selaginella and Physcomitrella genomes. There are 1574 single copy nuclear genes shared jointly by Arabidopsis and rice and 727 of these are single copy in Populus trichocarpa. All three genomes have undergone independent genome-wide duplications, suggesting that a selective process of gene loss has acted on these genes to reduce them to single copy following duplication. The forces leading to selective loss of duplicated genes are still unknown, but the collection of genes is biased toward organellar genes and genes of unknown biological function. The majority of these genes are present in the Selaginella and Physcomitrella draft genomes. Public EST sets for 233 diverse plant species suggest that most of these genes are conserved as single or very low copy genes, though exceptions are seen especially in very recent polyploidy taxa. In order to explore the phylogenetic utility of a number of these genes we have performed a series of phylogenetic analyses using publicly available ESTs, finished cDNA sequences for some lineages, and more detailed analysis in Brassicaceae using a small subset of these genes. We will present: 1) angiosperm-wide phylogenies based on individual gene trees and concatenated alignments of 20 of these genes, and 2) Brassicaceae phylogenies based on individual genomic and cDNA sequences, as well as concatenated cDNA sequences for several conserved single copy genes. Conserved single copy nuclear genes provide a vast source of new evidence for plant phylogeny, genome mapping, and other applications.


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1 - Pennsylvania State University, Department of Biology, 403 Life Sciences Building, University Park, Pennsylvania, 16802, USA
2 - University of Missouri-Columbia, Division of Biological Sciences, 371B Life Sciences Center, 1201 Rollins Road, Columbia, MO, 65211-7310, USA
3 - University of Missouri Columbia, Biological Sciences, 1201 Rollins Road, Life Sciences Center 311, Columbia, Missouri, 65211, USA
4 - University of Georgia, Department of Plant Biology, Athens, Georgia, 30602, USA
5 - Pennsylvania State University, Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, University Park, Pennsylvania, 16802, USA

Keywords:
conserved single copy
angiosperm phylogeny
Brassicaceae
EST
Arabidopsis
Populus
rice.

Presentation Type: Oral Paper:Papers for Sections
Session: CP14
Location: Lake Huron/Hilton
Date: Monday, July 9th, 2007
Time: 2:00 PM
Number: CP14005
Abstract ID:1547


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