Supplementary Information. Drought response transcriptomics are altered in poplar with reduced tonoplast sucrose transporter expression
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1 Supplementary Information Drought response transcriptomics are altered in poplar with reduced tonoplast sucrose transporter expression Liang Jiao Xue, Christopher J. Frost, Chung Jui Tsai, Scott A. Harding Table S1. T DNA insertion site analysis. Figure S1. Plant wide transcript abundance of SUT genes in leaf, xylem, bark and roots of wild type and SUT4 RNAi transgenic plants. Figure S2. Transcript abundance of sucrose cleaving enzymes in different organs of WT and SUT4 RNAi plants under WW conditions. Figure S3. Inter organ correlations of AQP transcript abundance. Figure S4. Heatmap illustration of SUT4 RNAi and DR effects on LEA, HSP20, BSP/VSP transcript abundance in roots. Figure S5. Heatmap illustration of SUT4 RNAi and DR effects on transcript abundance of genes associated with abscisic acid, jasmonic acid and ethylene signaling in roots. Dataset S1. Gene expression analysis by RNA Seq. Dataset S2. Root co expression gene network analysis.
2 Table S1. T DNA insertion site analysis Line Total read pairs (M) Hybrid read pairs 1 Insertion site Nearest genome coordinate (P. trichocarpa v3.0) F 32,5,1 4 Potri.009G Chr09:54300 G 29,853,30 5 intergenic (3 to Potri.004G190400) Chr04: H 12,91, Junction flanking read pairs, with one read of the pair mapping to the T DNA and the other to the genome.
3 250 Transcript abundance (FPKM) WT RNAi Leaf Xylem Bark Root 0 SUT4 SUT3 SUT5 SUT Fig. S1. Plant wide transcript abundance of SUT genes in leaf, xylem, bark and roots of wild type and SUT4 RNAi transgenic plants. Values represent FPKM means ± SD for n=3 biological replicates. Statistical significance of transgenic effect was determined using two sample student s t test (, P 05).
4 Transcript abundance: log 10 (FPKM) CIN sum VIN sum NIN sum SUS sum WT RNAi WT RNAi WT RNAi WT RNAi LEAF XYLEM BARK ROOT Fig. S2. Transcript abundance of sucrose cleaving enzymes in different organs of WT and SUT4 RNAi plants under WW conditions. FPKM values were summed from multiple gene models of each gene family for each biological replicate and log10 transformed. Data are means ± SD of n=3 biological replicates. CIN, cell wall invertase; VIN, vacuolar invertase; NIN, neutral invertase; SUS, sucrose synthase.
5 Potri.01G Potri.01G Potri.008G0500 Potri.00G Potri.00G Potri.004G1300 Potri.010G22200 Potri.010G Potri.008G03900 PIP2. PIP PIP1.2 PIP PIP2.5 PIP2.2 PIP2.3 PIP PIP2.4 PIP2.1 WT L vs. B L vs. X L vs. R R vs. B R vs. X B vs. X RNAi L vs. B L vs. X L vs. R R vs. B R vs. X B vs. X FPKM Potri.009G1300 Potri.00G23900 Potri.001G Potri.003G Potri.009G02200 Potri.001G1800 Potri.008G05000 Potri.004G21500 Potri.00G12100 Potri.01G TIP4.1 TIP TIP2.2 TIP1.2 TIP2.1 TIP TIP TIP TIP TIP2.4 WT L vs. B L vs. X L vs. R R vs. B R vs. X B vs. X RNAi L vs. B L vs. X L vs. R R vs. B R vs. X B vs. X FPKM Potri.001G15000 Fig. S3. Inter organ correlations of AQP transcript abundance. A, PIP genes. B, TIP genes. The upper half of each panel presents correlations between WT organs, and the lower half, RNAi transgenic organs. Values are r2 from linear regressions with n=9 independent comparisons for each gene and organ pair. The FPKM value for each gene is presented as average transcript abundance across all organs. L, leaf; B, bark; X, xylem and R, root.
6 A. LEA Potri.01G04400 Potri.01G0100 Potri.010G Potri.00G14300 Potri.T Potri.002G15000 Potri.009G Potri.00G Potri.004G1900 Potri.009G14500 Potri.015G Potri.011G12900 Potri.001G13000 Potri.014G10100 Potri.005G Potri.001G Potri.01G Potri.001G13200 Potri.002G Potri.004G04000 Potri.009G01900 Potri.T Potri.01G Potri.01G Potri.015G Potri.01G Potri.003G RNAi/WT DR/WW FPKM WW DR WT RNAi B. HSP20 Potri.010G19500 Potri.008G02300 Potri.009G Potri.003G Potri.019G Potri.00G Potri.01G13000 Potri.001G19200 Potri.018G14000 Potri.013G Potri.010G15200 Potri.T C. VSP/BSP Potri.013G Potri.013G10000 Potri.013G Potri.008G Potri.013G Potri.T09300 Potri.013G Potri.019G RNAi/WT DR/WW FPKM WW DR WT RNAi RNAi/WT DR/WW FPKM WW DR WT RNAi Fig. S4. Heatmap illustration of SUT4 RNAi and DR effects on LEA (A), HSP20 (B) and BSP/VSP (C) transcript abundance in roots. Values are log2 transformed fold changes, and genes are arranged by their transcript abundance (FPKM average) in roots. Significant transgenic or DR effects are denoted by bold underlined (Q 5) or bold italics (P 5).
7 A (ABA) RNAi/WT DR/WW PYR/PYL/RCAR WW DR WT RNAi FPKM Potri.003G Potri.001G Potri.00G Potri.01G Potri.003G Potri.010G PP2C Potri.008G Potri.010G Potri.012G Potri.009G Potri.T Potri.001G Potri.015G SnRK2 Potri.002G SnRK3 Potri.00G Potri.01G Potri.010G Potri.010G Potri.018G Potri.01G Potri.00G Potri.018G Potri.019G Potri.014G Potri.018G Potri.011G000 1 Potri.003G Potri.013G Potri.008G ASR1 Potri.005G ABF Potri.014G Potri.004G Potri.009G Potri.002G B (jasmonic acid) JAZ Potri.00G Potri.010G Potri.00G21200 Potri.003G08900 Potri.008G Potri.003G15000 Potri.011G Potri.001G02500 Potri.001G C (ethylene) RNAi/WT DR/WW ERF WW DR WT RNAi FPKM Potri.004G Potri.00G Potri.010G Potri.005G Potri.005G Potri.003G Potri.011G Potri.002G Potri.005G Potri.00G Potri.002G Potri.014G Potri.008G Potri.001G Potri.004G Potri.019G Potri.011G Potri.008G Potri.01G Potri.001G Potri.005G Potri.014G Potri.001G Potri.003G Potri.014G Potri.00G Potri.012G Potri.013G Potri.00G Potri.009G Potri.009G Potri.008G Potri.002G Potri.010G Potri.013G Potri.011G Potri.003G Potri.00G Potri.001G Potri.002G Fig. S5. Heatmap illustration of SUT4 RNAi and DR effects on transcript abundance of genes associated with ABA (A), JA (B) and ethylene (C) signaling in roots. Values are log2 transformed fold changes. Genes are sorted by their transcript abundance (FPKM average) in roots. Significant RNAi or DR effects are denoted by bold underlines (Q 5) or bold italics (P 5). ASR, ABA stress ripening; ABF, ABA responsive element binding factor; ERF, ethylene response factor; JAZ, jasmonate ZIM domain; PP2C, protein phosphatase 2C; PYR/PYL/RCAR, pyrabactin resistance/pyrlike/regulatory components of ABA receptor family; SnRK, sucrose non fermenting 1 (SNF1) related protein kinase.
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