Table 1.
Classification of ISOPENTENYLTRANSFERASE genes.
Fig 1.
Domain sequences used for HMM profiles.
Original IPPTPfam domain sequences were shorter than the IPTPfam domain by approximately 40 AA at the N-terminus. The expanded profile was retrieved from full sequences and used for the new HMM profile (IPPTPfam_N40.hmm). Arrowhead indicates the starting position of the original IPPTPfam.hmm. Box marked with an asterisk indicate the IPPTPfam region missing in the original IPPTPfam.hmm. Predicted positions of α-helixes are indicated by ‘H’, and those of β-sheet by ‘S’.
Fig 2.
ML tree of the bacterial IPTPfam and IPPTPfam domain genes.
The αLRT (left) and UFBT values (right) are shown along major branches. An asterisk indicates support values < 0.5 and < 50%. Thickened branches indicate support values > 0.9 and > 90%, medium-thick branches indicate > 0.7 and > 70%. A tree with all support values is shown in S7 Fig. The species with both IPTPfam and IPPTPfam domain genes are highlighted blue and yellow. The classification of the species is indicated by two characters at the end of the gene names; Ac: Actinobacteria, Al: α-Proteobacteria, Am: Amoebozoa, Aq: Aquficae, As: Ascomycota, Be: β-Proteobacteria, Ch: Chlamydiae, Cy: Cyanobacteria, Ep: ε-Proteobacteria, Fi: Firmicutes, Fu: Fusobacteria, Ga: γ-Proteobacteria, Sp: Spirochaetes, Th: Thermotogae.
Fig 3.
ML tree of IPPTPfam domain genes across kingdoms.
IPTPfam domain genes were used as outgroup. The αLRT (left) and UFBT support values (right), are shown along the major branches. An asterisk indicates support values < 0.5 and < 50%. Thickened branches indicate support values > 0.9 and > 90%, medium-thick branches indicate > 0.7 and > 70%. Trees with all support values are shown in S8 Fig. A. Bacterial IPPTPfam genes, miaA. B. Plant class I tRNA-IPTs. Two IPPTPfam domain genes from Dictyostelium discoideum are nested in this clade (red arrow). The Mosses IPPTPfam clade included multiple copies of tRNA-IPTs from Sphagnum fallax and Physcomitrella patens. C. Unikont-SAR IPTs. IPPTPfam domain genes of zooplankton, yeast, animals arranged in grades. One copy of the IPPTPfam gene of D. discoideum appeared as sister grade to the animal clade (red arrow). D. Prasinophyte algae tRNA-IPTs. Prasinophyte clade indicated by asterisk and pink box in B and D. E. Plant class II tRNA-IPTs. F. AP-IPTs. Two clades (F1, F2) were observed and the basal angiosperm Amborella trichopoda retained two copies, one belonging to each clade (black arrows). Derived angiosperms retained diverged copies within F2 (F2a,b). The multiple copies of Arabidopsis thaliana (grey arrows) and Oryza sativa (green arrows) are indicated. Arrowheads indicate gene duplication events inferred from NOTUNG analyses (see also Fig 5). Red arrowhead indicates gene duplication event prior to class II tRNA-IPT and AP-IPT splits, and blue and green arrowhead indicates events within plant AP-IPTs.
Fig 4.
Schematic dated tree of life with absence and presence of IPTPfam and IPPTPfam domain genes and IPPTPfam gene clades/grades shown in Fig 3.
Grey-shaded or open squares indicate IPTPfam and IPPTPfam domain presence or absence respectively. Presence (coloured squares) or absence (open squares) of class I tRNA-IPTs, class II tRNA-IPTs, and Adenosine-phosphate IPTs (AP-IPTs) for plants indicated by blue, green, or orange respectively. Class I and class II tRNA-IPTs and AP-IPTs are IPPTPfam domain genes. Shaded-circles indicate the presence of the possible direct ancestral IPPTPfam domain genes of plant class I and class II tRNA-IPTs. LECA: the last eukaryotic common ancestor, CK: point of cytokinin signal establishment [51]. Organism phylogeny is based on the Tree of Life Web Project [52], Qiu et al. [53] and Hug et al. [54], Popper et al. [55], Derelle et al. [56]. Dates are transferred from Magallón et al. [44], Heron et al. [45], Parfrey et al. [46], Battistuzzi et al. [39].
Fig 5.
Duplications and major losses in IPT genes inferred in NOTUNG analyses on the tree of life for plants.
Gene duplication resulting in class II tRNA-IPT and AP-IPT (red arrowhead), was followed by AP-IPT losses in ferns and gymnosperms (`L`in black). AP-IPTs duplications were inferred before or at angiosperm diversification (blue and green arrowheads). D: gene duplications, L: gene losses, `D`in black: duplication leading to class II tRNA-IPT and AP-IPT, `D`in blue: duplications within AP-IPT-1, `D`in grey: duplications within AP-IPT-2, `D`in red: duplication within class II tRNA-IPT, `D`in brown: duplications within class I tRNA-IPT.
Fig 6.
Schematic summary of hypotheses for ISOPENTENYLTRANSFERASE gene evolution inferred in this study.
Lines indicate possible evolutionary pathways from bacterial or eukaryotic ancestral IPPTPfam domain genes to plant IPT genes with IPPTPfam domain. Open boxes: gene loss, shaded boxes: gene gain, LECA: the last eukaryotic common ancestor. A, B. Hypotheses for class I tRNA-IPT evolution. A. class I tRNA-IPTs in plants directly descended from LECA gene and loss in Unikont and SAR independently. B. class I tRNA-IPTs in plants acquired via HGT from bacteria and secondary transfer to brown algae and slime molds. C, D. Hypotheses for class II tRNA-IPT/AP-IPT evolution. C. class II tRNA-IPTs in euphyllophytes were obtained via HGT from eukaryotic organisms, using prasinophytes as stepping stone. D. class II tRNA-IPTs evolved directly from LECA, but loss in brown algae, red algae and in several basal lineages of green plants independently.