Fig 1.
Proposed pathways of IAA homeostasis in carnation stem cuttings.
(A) Auxin biosynthesis. In the middle box, the IPyA pathway is shown, while the IAM pathway is shown in the left-side box. The IAOx pathway, which is restricted to indole-glucosinolate-producing plant species such as Arabidopsis thaliana, Brassica napus or Sinapis alba, is given in the right-side box. (B) Auxin transport. (C) Auxin catabolism. Dashed lines indicate assumed reaction steps for which the corresponding enzymes have yet to be identified. Proteins are abbreviated as follows: ABCB, ATP-binding cassette transporter subfamily B; AMI1, amidase 1; AUX1/LAX, AUX1 and LAX auxin influx carriers; CYP79B2/B3, cytochrome P450 monooxygenase 79B2/B3; DAO, dioxygenase for auxin oxidation; GH3, GRETCHEN HAGEN3 acyl amido synthase; IAMT, indole-3-acetic acid methyltransferase; NIT, nitrilase; PIN, PIN-FORMED auxin efflux facilitators; UGT (group L), UDP glucosyltransferases; TAA1, tryptophan aminotransferase of Arabidopsis 1; TAR, tryptophan aminotransferase-related; YUC, YUCCA. Metabolites are abbreviated as follows: IAA, indole-3-acetic acid; IAA-Asp, indole-3-acetyl-aspartic acid; IAA-Glc, 1-O-(indol-3-ylacetyl)-β-D-glucose; IAM, indol-3-acetamide; IAN, indole-3-acetonitrile; IAOx. indole-3-acetaldoxime; IPyA, indole-3-pyruvic acid; MeIAA, methyl-IAA ester; oxIAA, oxindole-3-IAA; Trp, tryptophan.
Fig 2.
Phylogenetic analyses of the TAA1/TAR gene family in carnation.
Boxes show magnifications of the tree branches containing the (A-C) TAA1/TAR protein family members studied in this work. Full phylogenetic trees are shown in S1 Fig. The evolutionary history was inferred by using the Maximum Likelihood method based on the Le Gascuel model [38]. Trees were drawn to scale, with branch lengths representing the number of substitutions per site. These analyses were conducted in MEGA7 [29], as described in the Materials and methods section. (D) Gene structure and (E) expression profiles of TAA1/TAR genes. UTR regions and exons are represented by white and black boxes, respectively; introns are depicted as gray lines. UTR, intron and exon lengths were determined using previous RNA-seq data [6].
Table 1.
Auxin biosynthesis protein families in carnation.
Fig 3.
Phylogenetic analyses of the YUC gene family in carnation.
Boxes show the magnification of tree branches containing the (A-D) YUC protein family members studied in this work. Full phylogenetic trees are shown in S2 Fig. (E) Gene structure of YUC genes. See legend in Fig 2 for details.
Fig 4.
Phylogenetic analyses of the AMI1 gene family in carnation.
(A) Magnification of the tree branch containing the AMI1 protein family members studied in this work. The full phylogenetic tree is shown in S3 Fig. (B) Gene structure and (C) gene expression profiles of AMI1 genes. See the legend in Fig 2 for details.
Table 2.
Auxin transport protein families in carnation.
Fig 5.
Phylogenetic analyses of (A-C) AUX/LAX, (D-F) PIN and (G-K) ABCB auxin transporter families in carnation.
Full phylogenetic trees are shown in the S4 (AUX/LAX), S5 (PIN) and S6 (ABCB) Figs. See the legend in Fig 2 for details.
Fig 6.
Gene structure of (A) AUX/LAX, (B) PIN and (C) ABCB auxin transporter families in carnation.
See the legend in Fig 2 for details.
Fig 7.
Gene expression profiles of (A) AUX/LAX, (B) PIN and (C) ABCB auxin transporter families in carnation.
Only genes with detectable expression levels in previous experiments [6] were selected.
Fig 8.
Phylogenetic analyses of (A-C) GH3 (group II), (D) UGT74, (E) UGT84, (F) DAO and (G) IAMT1 families in carnation.
Full phylogenetic trees are shown in the S9 (GH3 group II), S11 (group L UGT) and S12 (DAO and IAMT1) Figs. See the legend in Fig 2 for details. (H-I) Gene expression profiles of some (H) GH3 group II, (I) UGT74, UGT84, (J) DAO and (K) IAMT1 genes are shown.
Table 3.
Auxin catabolism protein families in carnation.
Table 4.
Auxin-related metabolites (ng g-1 fresh weight) identified in carnation stem cuttings.