Duarte, Jill , Beckmann, Kevin G. , Wall, P. Kerr , Landherr, Lena , Leebens-Mack, Jim , Ma, Hong , dePamphilis, Claude W. .
Evolutionary Dynamics and Phylogenetic Utility of Single Copy Nuclear Genes in Flowering Plants.
ALTHOUGH all major lineages of flowering plants now appear to have undergone repeated rounds of ancient genome duplication (paleopolyploidy) and most genes belong to multigene families, there are numerous nuclear genes that persist as single copies. In order to understand the evolution of single copy nuclear genes, we have undertaken a bioinformatic analysis of ~1500 nuclear genes that are single copy in both Arabidopsis and rice as well as a detailed comparative phylogenetic analysis for twenty single copy nuclear genes. These conserved single copy nuclear genes also have distinct sequence characteristics and functional affiliations. An analysis based on gene ontology GO categories indicates that these genes are overrepresented in the chloroplast and mitochondrion, but underrepresented in a wide variety of GO categories such as transcription factors, kinases, receptors, and response to stimulus. Comparative analysis of 50 plant species that are well represented in EST databases (e.g. TIGR and Floral Genome Project) or ongoing genome projects indicates that paralogs of these genes are relatively rare in plant genomes. Phylogenies indicate that where paralogs do exist, they are typically only recently duplicated genes. Substitution rates for these genes tend to be slower than genes from multi-gene families, but faster than chloroplast genes such as rbcL. In addition, because they tend to remain single copy after duplication, we hypothesize that these genes are likely to maintain low copy number in species that have not yet been surveyed, an exceptional benefit for their use as phylogenetic markers. Preliminary analyses indicate that several of the genes, even with limited sequence data, provide well supported phylogenies for resolving relationships across flowering plants a new source of phylogenetic markers from the nuclear genome for flowering plants.
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1 - Pennsylvania State University, Department of Biology, 403 Life Sciences Building, University Park, Pennsylvania, 16802, USA
2 - Pennsylvania State University, Department of Biology, 202 Mueller Lab, University Park, Pennsylvania, 16802-5301, USA
low-copy nuclear marker
Presentation Type: Oral Paper:Papers for Sections
Date: Tuesday, August 1st, 2006
Time: 9:00 AM