Figure 1.
Maximum-likelihood phylogenetic tree of the angiosperm PIN1.
The ML tree was constructed based on the protein sequences of angiosperm PIN1 using MEGA5.2 with 1000 bootstrap replications and Jones-Taylor-Thornton (JTT) + Gamma Distributed model (Discrete Gamma Categories = 5). These PIN1 protein sequences were searched from Poaceae, Brassicaceae, Fabaceae, Rosaceae, Cucurbitaceae, Malvales, Malpighiales, Rutaceae, Solanaceae, Vitaceae, Caricaceae and Amborellaceae. The scale bar indicates the branch length that corresponds to 0.1 substitutions per site. The species and accession numbers are listed in Table S1.The abbreviations used are as follows: Bd, Brachypodium distachyon; Hv, Hordeum vulgare; Os, Oryza sativa; Pav, Panicum virgatum; Sb, Sorghum bicolor; Si, Setaria italica; Ta, Triticum aestivum; Zm, Zea mays; Al, Arabidopsis lyrata; At, Arabidopsis thaliana; Br, Brassica rapa; Cb, Capsella bursa-pastoris; Ch, Cardamine hirsuta; Cr, Capsella rubella; Th, Thellungiella halophila; Ca, Cicer arietinum; Gm, Glycine max; La, Lupinus albus; Mt, Medicago truncatula; Ps, Pisum sativum; Pv, Phaseolus vulgaris; Fv, Fragaria vesca; Md, Malus domestica; Pp, Prunus persica; Cus, Cucumis sativus; Mc, Momordica charantia; Gr, Gossypium raimondii; Tc, Theobroma cacao; Me, Manihot esculenta; Pt, Populus trichocarpa; Cc, Citrus clementina; Cs, Citrus sinensis; Nt, Nicotiana tabacum; Sl, Solanum lycopersicum; So, Solanum tuberosum; Vv, Vitis vinifera; Cp, Carica papaya; Amt, Amborella trichopoda.
Figure 2.
Numbers of non-synonymous (n) and synonymous (s) substitutions in four groups.
A phylogenetic tree was constructed using 24 PIN1 protein-coding sequences. Shown above each branch is the n/s value. The n/s values for the groups formed by Poaceae, Brassicaceae, Fabaceae, and the mixed group including AmtPIN1 (and excluding their ancestral branches) are shown below their names. The three solid, red nodes represent the positions of the ancestors of the four groups. N and S are the calculated number of non-synonymous and synonymous sites, respectively. Blue arrows (A–E) indicate branches that have undergone positive selection.
Figure 3.
Pairwise comparison plots of dN and dS values for all angiosperm PIN1 genes (A) and each family (order) PIN1 genes (B).
Table 1.
Site model (M7 vs. M8) test for each family PIN1 genes.
Figure 4.
Motif distributions of the angiosperm PIN1 sequences.
A schematic representation of motifs obtained using MEME within the sequences is displayed. Different motifs are highlighted by different colored boxes, Details concerning individual motifs are given in Figure S3.
Figure 5.
A model of AtPIN1 secondary structure.
A predicted membrane-spanning PIN1 structure was generated using the topology-prediction program SOSUI (http://bp.nuap.nagoya-u.ac.jp). Motifs 18 and 20 are specific to Brassicaceae. The distribution of non-conserved sites and the conserved and non-conserved regions are marked in the model.
Figure 6.
“*” means the amino acid is diversified in this position. “•”means there is no amino acid in this position.
Table 2.
Branch and site models test for ancestral protein sequences of each families (orders) PIN1 genes.