Fig 1.
Phylogenetic tree showing relationships between Sdr4L protein sequences.
(A) The unrooted tree was built with MEGA5 by using sequence alignments of 54 Sdr4L members. The branch support bootstrap values were obtained by 1000 replicates using the NJ method. (B) Proteins showing conserved motifs obtained by MEME analysis are indicated in numbered colored boxes.
Fig 2.
Divergence time estimations between Sdr4L genes in plants based on aligned nucleotide sequences using Bayesian MCMC analysis.
A relaxed molecular clock approach with 20 million MCMC steps was used. Tree was drawn using the divergence of O. sativa and B. distachyon and M. domestica and C. sinensis as anchor points for monocot and dicot lineages, respectively. Number at each node represent estimated time in million years (MYA). The light pick and green circle shows the events of divergence between mono and dicot lineages and duplication in grass genomes, respectively. The major clusters of orthologous genes are shown in different colors and defined in different subgroups (I to VIII).
Table 1.
Functional divergence between Sdr4L subfamilies.
Table 2.
Tests for positive selection among Sdr4L codons of using site models.
Fig 3.
Sequence comparison by multiple clustal alignment of typical Sdr4L protein sequences from monocot and eudicot plant species.
Black arrows indicate predicted protein domains (PD319905 and PDB0A0W9). Critical amino acid sites (CAAS) responsible for functional divergence (Qk > 0.9, Type I and Type II) and phosphorylation sites are marked by pink triangles and blue stars, respectively. Adaptive selection sites for the site and branch site model are indicated by red and blue boxes, respectively. Putative nuclear localization signal (NLS) motifs are boxed.
Fig 4.
Three dimensional structures of rice OsSdr4L (a) and tomato SlSdr4L (b) proteins. The corresponding structures were obtained using i-TASSER [22]. The α-helices and β-strands are shown in green and yellow, respectively. Critical amino acid sites responsible for both positive selection and functional divergence are labeled in red. The edges of amino (N) and carboxyl (COOH) terminals, and random view of predicted domains of I and II (PD319905 and PDB0A0W9) are indicated in light blue.