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Results: 5

1.
Figure 4

Figure 4. Bayesian Consensus Phylograms of the Tribe Sileneae.. From: Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene.

A) The clpP1 exon sequences, and B) the clpP1 intron sequences. Branches in bold have Bayesian posterior probabilities (Bpp) of 1.00. Only Bpp values above 0.90 are shown at nodes. Note that A and B are drawn at different scales. ** indicates taxa that lack introns in clpP1.

Per Erixon, et al. PLoS ONE. 2008;3(1):e1386.
2.
Figure 5

Figure 5. The clpP1 Gene and Flanking Regions with Primer Sites.. From: Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene.

Approximate position of general primers for Sileneae [18] with reference to Spinacia. Boxes correspond to protein coding genes with their name and position in Spinacia. Boxes above the line denote genes that are transcribed from left to right, and those below are transcribed from right to left. Dotted lines represent introns.

Per Erixon, et al. PLoS ONE. 2008;3(1):e1386.
3.
Figure 3

Figure 3. dS and dN Values of Four Chloroplast Genes.. From: Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene.

Diagram shows the pairwise dS values (top) and dN values (bottom) between eleven species of Sileneae and the outgroup (Heliosperma alpestre) for four chloroplast genes (clpP1; 591 bp, psbB; 1527 bp, cemA; 639 bp, and petA; 963 bp). To the right of the vertical gray line is the pairwise comparison between Oenothera elata and Eucalyptus globulus, for the same genes.

Per Erixon, et al. PLoS ONE. 2008;3(1):e1386.
4.
Figure 1

Figure 1. Multiple Copies of the clpP1 Gene Region Found in Two Species.. From: Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene.

DNA fragments sequenced from the clpP1 region (thick black bars) for Lychnis chalcedonica (Lc) and Silene fruticosa (Sf). Shown in gray is the corresponding region, with the genes (boxes) and introns (dotted lines), in Spinacia. Thick white bars indicate non-homologous flanking regions (Lc2 is located differently in the chloroplast genome). Fragments with arrows on the left side consist of a continuous sequence from rbcL to petB (c. 18 kb). Thin lines mark lack of introns. Ψ indicates stop codon. ? indicates unknown flaking regions.

Per Erixon, et al. PLoS ONE. 2008;3(1):e1386.
5.
Figure 2

Figure 2. Positive Selection in the Chloroplast clpP Gene.. From: Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene.

A) dN/dS ratios calculated on the Eudicot tree topology. Numbers on nodes indicate classification as follows: 1 Myrtales, 2 Eurosids II, 5 Eurosids I, 6 Rosids, 13 Caryophyllales, 17 Euasterids I, 19 Euasterids II, 20 Asterids [36]; 3 Hologalegina, 4 Fabaceae [37]; 7, 8, 9 subgenus Behen, 10 subgenus Silene, 11, 12 Sileneae [17]; 14 Solaneae, 15 Solanoideae, 16 Solanaceae [38]. Values on branches are the dN/dS ratios, S: dN = 0, N: dS = 0. Ratios significantly above one (Bonferroni-corrected) are indicated by asterisks: ***P<0.001, *P<0.05. B) dN- and dS-branch (in grey and black, respectively) lengths imposed on topology from Bayesian analysis of third codon positions from the clpP1 exons Numbers on nodes are Bayesian posterior probabilities (Bpp). Only Bpp values>0.50 are shown.

Per Erixon, et al. PLoS ONE. 2008;3(1):e1386.

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