Open Access Highly Accessed Research article

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

Jill M Duarte1, P Kerr Wall15, Patrick P Edger2, Lena L Landherr1, Hong Ma14, J Chris Pires2, Jim Leebens-Mack3 and Claude W dePamphilis1*

Author Affiliations

1 Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA

2 Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO 65211-7310, USA

3 Department of Plant Biology, University of Georgia, Athens, GA 30602-7271, USA

4 State Key Laboratory of Genetic Engineering, the Institute of Plant Biology, School of Life Sciences, Institutes of Biomedical Sciences, Center for Evolutionary Biology, Fudan University, 220 Handan Road, Shanghai 200433, PR China

5 BASF Plant Science, Research Triangle Park, NC, 27709, USA

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BMC Evolutionary Biology 2010, 10:61  doi:10.1186/1471-2148-10-61

Published: 24 February 2010

Additional files

Additional file 1:

Identification of all shared single copy nuclear genes among the Arabidopsis, Populus, Vitis and Oryza genomes, as well as the Physcomitrella and Selaginella genomes. Counts for each gene in each genome are provided. Locus ID in Arabidopsis, as well as TAIR8 annotation for symbol, description and slim GO annotation in terms of molecular function, cellular location and biological process are also provided. All tribes can be located in the PlantTribes database at fgp.bio.psu.edu/tribe.php by searching with the appropriate Arabidopsis locus ID.

Format: XLS Size: 11.5MB Download file

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Additional file 2:

BLASTx hits to the Arabidopsis, Populus. Vitis and Oryza conserved single copy nuclear genes for all plants in TIGR Plant Transcript Assemblies that have more than 5 hits to the APVO single copy PlantTribes, showing taxonomic grouping as well as gene counts. Plants in the Plant Transcript Assemblies are referred by their 5 letter abbreviation which is based on the first 3 letters of the genus name, followed by the first 2 letters of the species name. A full listing of the contents of the Plant Transcript Assemblies can be seen at http://plantta.jcvi.org/cgi-bin/plantta_release.pl webcite.

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Additional file 3:

ML and MP trees for the 18 single copy genes based on alignments of EST and finished cDNA sequences are provided as well as the ML and MP bootstrap consensus trees. MP bootstrap consensus trees and all ML trees are available as PDF files and the collection of MP trees for each alignment is available as a .tre file.

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Additional file 4:

Coding sequence length, number of exons and number of domains for all Arabidopsis proteins according to the TAIR8 annotation, with genes identified as to whether they are a member of the APVO PlantTribes.

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Additional file 5:

Alignments for the 18 single copy genes using seed plant ESTs and finished cDNAs are provided in NEXUS format, in addition to the concatenated alignment of 13 single copy genes.

Format: NEX Size: 1.3MB Download file

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Additional file 6:

Alignments used for Brassicaceae phylogeny.

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