Figures (7)  Tables (1)
    • Figure 1. 

      Phylogenetic relationships of the PUB genes between tomato and Arabidopsis. The seven different subgroups of PUBs are indicated in different colors.

    • Figure 2. 

      (a) Motif structures and (b) gene structures of PUBs in tomato. The different motifs (Motif 1 − Motif 10) are displayed in different colors. The gene structures of PUBs are based on the coding sequences (CDS) and untranslated region (UTR) which are shown in yellow and green.

    • Figure 3. 

      Chromosomal locations of the PUB genes in the tomato genome from Chr1-Chr12. The collinear genes are presented inside the circle in purple. The different types of duplication such as dispersed, segmental, and tandem are marked in red, green, and blue.

    • Figure 4. 

      Expression profiling of the 48 differentially expressed genes in multiple tissues based on RPKM values, including (a) Solanum lycopersicum cv. Heinz and (b) the wild relative Solanum pimpinellifolium. The brown bars represent up-regulated genes and dark blue bars represent down regulation.

    • Figure 5. 

      Expression profiling of the 48 differentially expressed PUB genes from MT data based on RPKM values, including (a) different developmental stages and (b) different organs. Red bars represent up-regulated genes and blue bars represent down-regulation.

    • Figure 6. 

      Relative expressions of SlPUBs (a) and (c) in five different tissues including root, stem, leaf, flower, and flower bud, and two stress conditions i.e., salt (200 mM) and cold stress (4 °C). The principal component analysis for (b) different tissues and (d) stress conditions.

    • Figure 7. 

      Gene function verification of SlPUB10. (a) The proteins’ subcellular locazation in Arabidopsis protoplasts. (b) The activity of SOD and POD in leaves of wild-type (WT) and transgenic tomato lines after salt (200 mM NaCl) and cold treatment (4 °C) for 4 h. The P values indicate the results from pairwise comparisons of one-way ANOVA tests. Different letters represent a significant difference at P < 0.05. (c) The relative expression level of SlPUB10 in transgenic lines. (d) Phenotypes of WT and transgenic lines after 48 h of salt (200 mM NaCl) and cold treatment (4 °C).

    • Gene 1Gene 2KsKaKa/KsSelection pressureGene duplications
      SlPUB3SlPUB40.740.590.80DispersedPurifying
      SlPUB5SlPUB70.680.620.92DispersedPurifying
      SlPUB10SlPUB110.650.590.90DispersedPurifying
      SlPUB13SlPUB140.800.590.73DispersedPurifying
      SlPUB16SlPUB220.580.611.06DispersedPositive
      SlPUB24SlPUB270.700.680.98DispersedPurifying
      SlPUB28SlPUB290.880.630.71DispersedPurifying
      SlPUB30SlPUB320.440.451.03DispersedPositive
      SlPUB33SlPUB350.880.620.70DispersedPurifying
      SlPUB36SlPUB370.460.671.45DispersedPositive
      SlPUB39SlPUB400.780.650.83DispersedPurifying
      SlPUB42SlPUB440.720.530.73DispersedPurifying
      SlPUB47SlPUB480.750.610.82DispersedPurifying
      SlPUB20SlPUB210.220.110.52TandemPurifying
      SlPUB1SlPUB60.630.460.74WGD or SegmentalPurifying
      SlPUB8SlPUB90.650.050.07WGD or SegmentalPurifying
      SlPUB12SlPUB150.740.610.82WGD or SegmentalPurifying
      SlPUB17SlPUB180.760.650.86WGD or SegmentalPurifying
      SlPUB19SlPUB231.080.550.51WGD or SegmentalPurifying
      SlPUB25SlPUB260.760.660.87WGD or SegmentalPurifying
      SlPUB31SlPUB340.770.620.80WGD or SegmentalPurifying
      SlPUB38SlPUB410.790.610.77WGD or SegmentalPurifying
      SlPUB43SlPUB450.800.640.80WGD or SegmentalPurifying

      Table 1. 

      Gene duplications of PUB genes in tomato with outlier Ka/Ks values.