Figure 1.
Phylogeny of species included in this analysis and number of FBA proteins identified.
The tree represents the phylogenetic relationships between the species analyzed. Branch lengths are not in proportion to evolutionary time. The number of FBA proteins identified per species is indicated next to the species name. Species included in the phylogenetic reconstruction of FBA protein evolution are indicated.
Figure 2.
Phylogeny of F-box proteins with C-terminal FBA domains in land plant species.
A, Phylogenetic tree of A. thaliana, V. vinifera, P. trichocarpa, O. sativa, S. bicolor, S. moellendorffii and P. patens FBA proteins. Multiple sequence alignments of the full-length FBA protein sequences were performed using MUSCLE. The phylogenetic tree was generated using ML methods in GARLI. The tree was rooted with the FBA protein sequence of Coccomyxa sp. C-169. The color code corresponds to the different species. B, Ratios of unstable, stable and singleton FBA proteins in the seven analyzed land plant species.
Table 1.
Number of unstable, stable and singleton FBA proteins in A. thaliana, V. vinifera, P. trichocarpa, O. sativa, S. bicolor, S. moellendorffii, P. patens, and C. sp. C-169.
Figure 3.
Evolutionary change in the number of FBA proteins in land plants.
The numbers in rectangles and circles represent the maximum number of genes in ancestral and extant species, respectively. The numbers with plus and minus signs indicate gene gains and losses, respectively, for each branch. Bold lines represent branches with high gene expansion rate. N0: Chloroplastida ancestor, N1: land plant ancestor, N2: angiosperm ancestor, N3: monocot ancestor, N4: eudicot ancestor. Branch lengths are not in proportion to evolutionary time.
Figure 4.
Patterns of selection in FBA genes.
A, Average Ka/Ks [ω by Yang [40] and g by Comeron [41]] ratios calculated over the complete coding sequence of all stable and unstable genes in A. thaliana by comparison to A. lyrata orthologs. Error bars represent SE. The difference is significant according to Kruskal-Wallis test (P<0.01). B, Sliding window plots for the four stable genes. C, Sliding window plots for randomly chosen unstable genes. For sliding window analysis, nucleotide sequences of A. thaliana (indicated by Arabidopsis Genome Initiative identifier) and orthologous nucleotide sequences of A. lyrata (indicated by protein identifier according to the Joint Genome Institute) were used. Window size was 150 bp, and step size was 9 bp. Light gray boxes highlight the position of the F-box domain, and dark gray boxes highlight the FBA-D position.
Figure 5.
Differential expression profiles of phylogenetically closely related FBA genes.
A, Mean expression values for unstable and stable A. thaliana FBA genes extracted from AtGenExpress_Plus-extended_tissue_series [42]. Error bars represent SE. Statistical significance was assessed using Student´s t-test (***P<0.001). B, NJ tree of 211 A. thaliana FBA proteins based on amino acid sequence homology. C, Clustering of 102 A. thaliana FBA proteins based on co-expression data from the AtGenExpress_Plus-extended_tissue_series. Discrepancy in the number of FBA genes/proteins between the trees in A and B results from 109 missing FBA genes on the ATH1 microarray. Two clades were selected for which all genes had representatives in the ATH1-Chip for illustration purposes (highlighted in green and red font). All other genes were collapsed and labeled according to the number of FBA genes within the respective branches.
Table 2.
Number of FBA proteins in non-land plant model species.