Research article
Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses
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* Corresponding author: Mariana Mondragón-Palomino mariana.mondragon@uni-jena.de
1 Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena, Germany
2 Institute for Plant Science, Ruprecht Karls University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
BMC Evolutionary Biology 2009, 9:81 doi:10.1186/1471-2148-9-81
Published: 21 April 2009Additional files
Additional file 1:
Supplemental tables. Table S1. DEF- and GLO-like sequences employed in this study. This manuscript describes the isolation and characterization of those sequences with names in bold type. Table S2. Parameter estimates and LRT of M7 and M8 from monocots. Table S3. Parameter estimates and LRT of MA1 vs. MA in DEF-like genes from Orchidaceae. The branches tested are those labeled with cursive fonts in Figure 3. Table S4. Parameter estimates and LRT of MA1 vs. MA in GLO-like genes from Orchidaceae and Poales. The branches tested are those labeled with fonts in italics in Figure 4.
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Additional file 2:
Condensed alignment of DEF-like proteins from Asparagales included in the phylogenetic analysis illustrated by Figure 1 and Additional files 4 and 5. This alignment only includes variable amino-acid positions shaded according to their chemical property: Red background/green fonts = D, E; Red background/white fonts = H, K, R; Yellow background/green fonts = N, Q; Yellow background/black fonts = S, T; Bright green background/red fonts = L, I, V; Bright green background/white fonts = F, Y, W; Dark green background/red fonts = A, G; Dark green background/white fonts = M, C; White background/black fonts = P.
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Additional file 3:
Condensed alignment of GLO-like proteins from Asparagales included in the phylogenetic analysis illustrated by Figure 2 and Additional files 6and 7. This alignment only includes variable amino-acid positions shaded according to their chemical property as described for Supplementary Figure 1.
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Additional file 4:
Phylogeny of monocot DEF-like genes based on the C-terminal domain.
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Additional file 5:
Phylogeny of monocot DEF-like genes based on the regions encoding the MIKC-domains.
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Additional file 6:
Phylogeny of monocot GLO-like genes based on the positions encoding the MIK-domains.
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Additional file 7:
Phylogeny of monocot GLO-like genes based on the positions encoding the C- terminal domain.
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Additional file 8:
Relative rates of A) nonsynonymous and B) synonymous substitution in DEF-like sequences from the Orchidaceae. Each bar represents the median of the corresponding relative rate of substitution between the pairs of two groups of sequences that yielded statistically significant results after correction for multiple comparisons. All data represented here are the result of two or more comparisons and exclusively involves orchid genes.
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