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, 145 (3), 593-600

Genome-wide Annotation of Remorins, a Plant-Specific Protein Family: Evolutionary and Functional Perspectives

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Genome-wide Annotation of Remorins, a Plant-Specific Protein Family: Evolutionary and Functional Perspectives

Sylvain Raffaele et al. Plant Physiol.

Figures

Figure 1.
Figure 1.
The remorin signature. Highly conserved residues within the Remorin_C domain of the 85 remorin proteins that were considered for phylogenetic analysis are shown. Prediction of the position along the heptad repeat of the coiled-coil structure is given in the top panel. pos., Position in Remorin_C domain alignment; ρ, aromatic residues; +, positively charged residues; φ, aliphatic residues; % refers to the number of sequences showing the indicated residue at the indicated position, among the list of 85 remorins given in Supplemental Table S1.
Figure 2.
Figure 2.
Phylogenetic and domain organization of the remorin family based on their protein sequences. The right box shows the color code used to indicate evolutionary positions within the plant kingdom (according to the Angiosperm Phylogeny Group, 2003) and domain elements used for classification. In the diagrams domain lengths are proportional to the average protein sequence length (except for groups 5 and 6, for which the representation of the N-terminal region is intercepted by “//,” indicating a variable length of this module within these two groups). Underlined sequences contain Remorin_N domains identified by InterProScan. Bootstrap values (%) are given along the most important branch points. True branch lengths were inferred by maximum-likelihood analysis; the upper-left scale represents a probability of 0.1 amino acid changes per site. The tree was reconstructed using parsimony analysis. For clarity of the figure, a shortened nomenclature was used (e.g. At1.1 for AtRem1.1). The first number in the proposed name indicates the corresponding group (e.g. At1.3 is the third member of group 1). Abbreviations: Ac, Adiantum capillus-veneris; Ak, Amborella trichopoda; Ap, Allium cepa; At, Arabidopsis; Cr, C. richardii; Mc, Mesembryanthemum crystallinum; Mt, M. truncatula; Na, Nuphar advena; Nt, tobacco; Os, rice; Pa, Persea americana; Pd, Pinus taeda; Pi, Pinus pinaster; Pp, P. patens; Ps, Picea sitchensis; Pt, P. trichocarpa; Sl, tomato; St, Solanum tuberosum; Wm, Welwitschia mirabilis; Zm, Zea mays.
Figure 3.
Figure 3.
Coexpression analysis of remorins throughout the Arabidopsis transcriptome. Expression data from hybridizations using At22k Affymetrix GeneChips were used to retrieve a list containing 100 genes showing highest Pearson correlation coefficients for different remorin genes at http://www.bar.utoronto.ca/. Graphs represent the normalized frequency of each function in the list of well-correlated genes compared to randomly selected genes among the Arabidopsis genome (Toufighi et al., 2005). Error bars indicate variation over 100 different sets of randomly selected genes.

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