Open Access Highly Accessed Research article

Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

Emmanuel Buschiazzo12*, Carol Ritland1, Jörg Bohlmann13 and Kermit Ritland1

Author Affiliations

1 Department of Forest Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada

2 School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, CA 95343 USA

3 Michael Smith Laboratories, University of British Columbia, 2185 East Mall, BC V6T 1Z4, Canada

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BMC Evolutionary Biology 2012, 12:8  doi:10.1186/1471-2148-12-8

Published: 20 January 2012

Additional files

Additional file 1:

Evolutionary measures for angiosperm and gymnosperm orthologues. Includes gene/transcript/EST IDs, ORF length, aligned and analyzed length, and dN, dS and dN/dS estimates.

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Additional file 2:

Annotation and dN/dS values for conifer orthologous genes. A more detailed description based on UniProt, PFAM and Interpro searches is provided for the 100 genes that showed dN/dS > 1, as well putative function where relevant.

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Additional file 3:

Gene set analyses of conifer annotated genes (Fatiscan and logistic regression methods). Includes references to Babelomics and statistical methods, and results of over-represented categories of genes with high and low dN/dS (adjuste p < 0.05, flase discovery rate correction) in InterPro, KEGG pathways, and GO functional cetegories.

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Additional file 4:

dS estimates in conifer and angiosperm genes across Arabidopsis' GO Slim functional categories. Mean dS values for conifer (full circle) and angiosperm (open circle) protein-coding genes. Conifer genes were BLASTed against Arabidopsis gene transcripts, whose GO Slim annotations were used for homologous conifer genes. Brackets represent the standard error of the mean. A: Biological processes; B: Molecular functions; C: Cellular component.

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Additional file 5:

Literature survey for plant mutation rates.

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