Figure 3

Cladogram of PIN proteins. The protein sequences of PINs were obtained from a repository of genomic sequences [62] and were aligned by the package MAFFT (program mafft-linsi, default setting) [63]; the non-homologous parts of the hydrophilic loop were edited out. The cladogram was computed by MrBayes [64] with parameters: lset = invgamma; ngammacat = 6; prset aamodelpr = fixed(wag). The computation was run for 5,000,000 generations, sampled every 100 generations and the first 10,000 generations were discarded. The sequences are divided into different groups according to the sequence similarity of the hydrophilic loop. All members of group 5 have a similar sequence in the hydrophilic loop but subgroup 5a has a site for phosphorylation by PINOID kinase whereas subgroup 5b lacks it. Species abbreviations: At, Arabidopsis thaliana; Alyr, Arabidopsis lyrata; Bradi, Brachypodium distachyon; Cpap, Carica papaya; Glyma, Glycine maxima; Mtru, Medicago truncatula; Osat, Oryza sativa; Ppat, Physcomitrella patens; Ptri, Populus trichocarpa; Smoel, Selaginella moellendorffii; Sb, Sorghum bicolor; Vvin, Vitis vinifera; Zm, Zea mays.