Table S1.RNASeq reads information

Sample ID / Library (ID) / Total reads / Mapped reads / Mapping rate
Shoot tip / Library_1 (S.1)
Library_2 (S.2)
Library_3 (S.3) / 17297831
9216579
10204884 / 15644194
8373607
9396915 / 90.4%
90.9%
92.1%
Leaf / Library_1 (L.1)
Library_2 (L.2)
Library_3 (L.3) / 12856050
14946149
16016585 / 11457197
13434665
14459459 / 89.1%
89.9%
90.3%
Phloem / Library_1 (P.1)
Library_2 (P.2)
Library_3 (P.2) / 12743293
13326594
8734282 / 11374255
11939937
7818700 / 89.3%
89.6%
89.5%
Seedling root / Library_1 (R.1)
Library_2 (R.2)
Library_3 (R.3) / 6359785
6672130
11807507 / 5541450
5859990
10765034 / 87.1%
87.8%
91.2%
Xylem / Library_1 (X.1)
Library_2 (X.2)
Library_3 (X.3) / 20011074
14465079
12730479 / 18029860
12765627
11349196 / 90.1%
88.3%
89.1%
Secondary vessel cell / Library_1 (V.1)
Library_2 (V.2)
Library_3 (V.3) / 15152905
12206883
13525843 / 12706031
9784169
11141669 / 83.9%
80.2%
82.4%
Secondary fiber cell / Library_1 (F.1)
Library_2 (F.2)
Library_3 (F.3) / 9908924
11166765
12021840 / 8141303
9391272
10203222 / 82.2%
84.1%
84.9%
Three cell type / Library_1 (T.1)
Library_2 (T.2)
Library_3 (T.3) / 11867933
19664201
17296735 / 10255678
16916447
14815497 / 86.4%
86.0%
85.7%

Table S2:Transcript abundance (Counts per million, cpm) in fiber and vessel cell RNA-seq libraries for 45 identified cell wall component biosynthetic genes and cell type specific TFs

Gene ID (v3) / Gene name / Gene family / Gene type / Transcript counts per million in RNA-seq libraries
F.1 / F.2 / F.3 / V.1 / V.2 / V.3
Cell wall component biosynthetic genes
Potri.002G257900 / CesA4 / CesA / Cellulose / 2973.2 / 1257.0 / 950.6 / 409.1 / 488.1 / 263.2
Potri.006G181900 / CesA7-A / CesA / Cellulose / 2658.1 / 1432.2 / 2089.9 / 196.8 / 470.1 / 197.4
Potri.018G103900 / CesA7-B / CesA / Cellulose / 1288.6 / 719.6 / 500.2 / 190.7 / 188.8 / 187.9
Potri.011G069600 / CesA8-A / CesA / Cellulose / 161.0 / 229.9 / 119.8 / 61.1 / 95.2 / 79.6
Potri.004G059600 / CesA8-B / CesA / Cellulose / 3457.8 / 3371.1 / 5084.8 / 248.9 / 601.7 / 390.6
Potri.008G026400 / CslA1 / HemiCesA / Hemicellulose / 2503.5 / 1428.5 / 2272.7 / 131.6 / 202.1 / 155.3
Potri.010G234100 / CslA2 / HemiCesA / Hemicellulose / 469.7 / 379.2 / 404.1 / 32.0 / 59.1 / 26.5
Potri.009G006500 / FRA8 / HemiCesA / Hemicellulose / 1868.5 / 705.3 / 592.3 / 148.5 / 235.0 / 223.9
Potri.007G107200 / GUX1a / HemiCesA / Hemicellulose / 43.2 / 21.6 / 10.9 / 10.9 / 99.9 / 12.9
Potri.005G061600 / GUX1b / HemiCesA / Hemicellulose / 308.6 / 165.1 / 156.0 / 53.3 / 17.1 / 12.3
Potri.014G029900 / GUX2 / HemiCesA / Hemicellulose / 351.4 / 244.7 / 175.1 / 81.0 / 113.9 / 16.0
Potri.001G068100 / IRX10-1 / HemiCesA / Hemicellulose / 982.5 / 658.5 / 605.0 / 107.2 / 189.7 / 232.6
Potri.003G162000 / IRX10-2 / HemiCesA / Hemicellulose / 41.2 / 11.1 / 3.6 / 22.3 / 7.8 / 64.7
Potri.012G109200 / IRX10-L-A1 / HemiCesA / Hemicellulose / 127.2 / 231.0 / 224.3 / 25.4 / 10.3 / 17.3
Potri.005G141500 / IRX14-1 / HemiCesA / Hemicellulose / 85.0 / 34.3 / 55.8 / 7.5 / 43.8 / 33.9
Potri.007G047500 / IRX14-2 / HemiCesA / Hemicellulose / 451.5 / 214.4 / 303.0 / 29.7 / 64.8 / 213.8
Potri.011G132600 / IRX8-1 / HemiCesA / Hemicellulose / 16.7 / 39.9 / 0.4 / 0.5 / 32.5 / 26.9
Potri.001G416800 / IRX8-2 / HemiCesA / Hemicellulose / 1021.2 / 591.0 / 246.3 / 93.2 / 176.6 / 174.0
Potri.006G131000 / IRX9-1 / HemiCesA / Hemicellulose / 119.5 / 77.4 / 56.9 / 12.0 / 47.8 / 23.1
Potri.016G086400 / IRX9-2 / HemiCesA / Hemicellulose / 589.6 / 281.6 / 251.8 / 125.5 / 153.0 / 83.9
Potri.002G132900 / PARVUS-1 / HemiCesA / Hemicellulose / 21.7 / 25.0 / 15.4 / 3.8 / 4.7 / 10.0
Potri.014G040300 / PARVUS-2 / HemiCesA / Hemicellulose / 160.6 / 89.1 / 95.0 / 49.6 / 19.6 / 23.1
Potri.007G031700 / PARVUS-L-2 / HemiCesA / Hemicellulose / 21.0 / 5.5 / 22.5 / 17.9 / 0.0 / 26.3
Potri.001G036900 / 4CL3 / 4CL / monolignol / 1195.0 / 1195.5 / 615.4 / 436.4 / 447.4 / 330.7
Potri.003G188500 / 4CL5 / 4CL / monolignol / 941.6 / 1448.5 / 537.0 / 287.3 / 304.7 / 183.7
Potri.006G033300 / C3H3 / C3H / monolignol / 1839.9 / 1282.1 / 1000.1 / 304.7 / 419.1 / 403.9
Potri.013G157900 / C4H1 / C4H / monolignol / 1513.8 / 970.5 / 370.9 / 248.1 / 295.7 / 153.1
Potri.019G130700 / C4H2 / C4H / monolignol / 4577.9 / 3038.4 / 1607.4 / 449.0 / 745.3 / 401.6
Potri.009G095800 / CAD1 / CAD / monolignol / 3669.9 / 2303.3 / 1993.2 / 666.5 / 988.8 / 584.8
Potri.005G117500 / CAld5H1 / CAld5H / monolignol / 733.5 / 308.3 / 172.2 / 103.1 / 131.6 / 45.7
Potri.007G016400 / CAld5H2 / CAld5H / monolignol / 662.0 / 449.8 / 257.2 / 130.7 / 89.2 / 96.0
Potri.009G099800 / CCoAOMT1 / CCoAOMT / monolignol / 2660.2 / 1687.4 / 1498.4 / 1048.0 / 1060.0 / 1316.5
Potri.001G304800 / CCoAOMT2 / CCoAOMT / monolignol / 4117.8 / 3713.6 / 1212.6 / 1259.1 / 2023.0 / 1059.5
Potri.008G136600 / CCoAOMT3 / CCoAOMT / monolignol / 304.3 / 254.4 / 327.1 / 86.6 / 37.7 / 71.4
Potri.003G181400 / CCR2 / CCR / monolignol / 820.3 / 544.3 / 708.2 / 458.2 / 335.6 / 328.2
Potri.012G006400 / COMT2 / COMT / monolignol / 12946.3 / 6370.1 / 4750.7 / 3179.4 / 3926.2 / 2731.6
Potri.003G059200 / CSE1 / CSE / monolignol / 446.0 / 248.9 / 138.7 / 180.3 / 157.9 / 107.2
Potri.001G175000 / CSE2 / CSE / monolignol / 142.4 / 157.7 / 93.7 / 49.3 / 31.5 / 10.2
Potri.003G183900 / HCT1 / HCT / monolignol / 2741.5 / 1569.9 / 772.0 / 468.1 / 643.8 / 315.0
Potri.001G042900 / HCT6 / HCT / monolignol / 188.8 / 71.1 / 76.7 / 12.1 / 102.2 / 22.0
Potri.006G126800 / PAL1 / PAL / monolignol / 9228.1 / 8673.8 / 3120.2 / 1529.5 / 1654.3 / 1119.1
Potri.008G038200 / PAL2 / PAL / monolignol / 1869.3 / 1720.7 / 607.5 / 463.7 / 508.1 / 244.3
Potri.016G091100 / PAL3 / PAL / monolignol / 1154.9 / 834.5 / 478.7 / 138.3 / 169.6 / 149.2
Potri.010G224100 / PAL4 / PAL / monolignol / 1154.9 / 834.5 / 478.7 / 138.3 / 169.6 / 149.2
Potri.010G224200 / PAL5 / PAL / monolignol / 517.5 / 399.0 / 218.7 / 72.5 / 94.4 / 78.2
Fiber cell type specific TFs
Potri.008G018400 / bZIP / TF / 31.1 / 16.1 / 19.4 / 0.7 / 0.1 / 0.0
Potri.015G033100 / C2H2 / TF / 89.7 / 46.7 / 92.3 / 0.6 / 0.9 / 0.0
Potri.004G118100 / C2H2 / TF / 28.5 / 17.8 / 49.6 / 0.0 / 0.2 / 0.0
Potri.009G004800 / C2H2 / TF / 20.7 / 26.1 / 37.8 / 0.0 / 0.0 / 0.0
Potri.007G138300 / C3H / TF / 80.5 / 193.3 / 233.3 / 0.0 / 0.1 / 4.6
Potri.001G258400 / C3H / TF / 35.9 / 19.6 / 27.0 / 0.0 / 0.1 / 0.0
Potri.018G083000 / CPP / TF / 8.9 / 19.2 / 6.6 / 0.0 / 0.0 / 0.0
Potri.014G167000 / FAR1 / TF / 11.1 / 29.9 / 5.7 / 0.1 / 0.2 / 0.0
Potri.005G023700 / FAR1 / TF / 1.0 / 17.9 / 29.3 / 0.0 / 0.1 / 0.0
Potri.009G035000 / G2-like / TF / 16.7 / 1.4 / 8.8 / 0.0 / 0.0 / 0.0
Potri.001G243600 / G2-like / TF / 0.1 / 26.8 / 6.2 / 0.0 / 0.0 / 0.0
Potri.004G070500 / GRAS / TF / 6.0 / 12.4 / 11.5 / 0.1 / 0.0 / 0.0
Potri.001G122800 / GRAS / TF / 18.4 / 4.9 / 8.7 / 0.0 / 0.0 / 0.0
Potri.016G056500 / HSF / TF / 142.9 / 181.2 / 81.9 / 12.8 / 21.2 / 0.1
Potri.013G156200 / LBD / TF / 225.5 / 155.1 / 62.1 / 1.9 / 7.4 / 0.1
Potri.003G090300 / LSD / TF / 129.8 / 99.1 / 163.9 / 2.3 / 32.1 / 5.7
Potri.010G154100 / MIKC / TF / 37.0 / 55.5 / 137.9 / 0.2 / 0.0 / 1.5
Potri.001G099800 / MYB010 / MYB / TF / 126.7 / 83.3 / 159.3 / 16.0 / 19.2 / 21.5
Potri.007G106100 / MYB031 / MYB / TF / 126.6 / 82.9 / 116.2 / 0.9 / 0.2 / 19.0
Potri.001G118800 / MYB092 / MYB / TF / 234.7 / 308.2 / 127.7 / 26.9 / 35.3 / 54.8
Potri.003G114100 / MYB125 / MYB / TF / 317.9 / 390.9 / 126.8 / 29.0 / 89.7 / 12.5
Potri.005G186400 / MYB158 / MYB / TF / 64.2 / 27.6 / 32.3 / 0.0 / 0.0 / 0.0
Potri.001G404400 / PNAC101 / NAC / TF / 119.3 / 126.1 / 180.7 / 36.5 / 3.4 / 2.1
Potri.004G049300 / SND2/3-A1 / NAC / TF / 219.9 / 230.2 / 167.1 / 26.6 / 35.3 / 43.9
Potri.018G068700 / SND2/3-L-2 / NAC / TF / 137.2 / 169.0 / 237.6 / 5.2 / 24.6 / 11.5
Potri.T074200 / NAC / TF / 33.4 / 14.1 / 19.7 / 0.1 / 0.0 / 0.9
Potri.001G257600 / NF-YA / TF / 4.4 / 8.3 / 71.6 / 0.2 / 0.0 / 0.0
Potri.001G055000 / NF-YC / TF / 48.7 / 55.8 / 47.5 / 1.6 / 5.8 / 4.5
Potri.005G129500 / TALE / TF / 270.9 / 316.3 / 580.2 / 25.7 / 0.2 / 31.4
Potri.003G056000 / Trihelix / TF / 42.6 / 62.4 / 107.2 / 7.5 / 0.0 / 0.1
Potri.002G243300 / Trihelix / TF / 30.7 / 20.2 / 18.2 / 0.2 / 0.0 / 0.0
Potri.017G088300 / WRKY / TF / 20.2 / 42.0 / 13.4 / 0.1 / 0.1 / 0.0
Vessel cell type specific TFs
Potri.006G167700 / AP2 / TF / 0.0 / 0.0 / 0.0 / 17.0 / 1.2 / 9.0
Potri.005G039800 / bHLH / TF / 2.1 / 19.7 / 0.1 / 114.4 / 69.0 / 115.4
Potri.011G031000 / bHLH / TF / 14.5 / 17.6 / 22.9 / 110.7 / 163.6 / 141.2
Potri.006G037100 / bHLH / TF / 10.2 / 3.9 / 0.6 / 180.7 / 80.1 / 101.5
Potri.003G128000 / bHLH / TF / 6.0 / 0.2 / 10.7 / 27.2 / 114.8 / 96.5
Potri.010G130000 / bHLH / TF / 4.4 / 10.0 / 0.7 / 54.2 / 126.0 / 46.6
Potri.016G035400 / bHLH / TF / 0.0 / 3.2 / 0.1 / 40.3 / 110.8 / 68.9
Potri.011G129500 / bHLH / TF / 1.0 / 2.2 / 0.0 / 52.7 / 70.6 / 91.8
Potri.001G270000 / bHLH / TF / 0.1 / 6.2 / 1.6 / 28.7 / 69.5 / 70.6
Potri.001G410600 / bHLH / TF / 0.0 / 0.4 / 2.3 / 111.3 / 12.6 / 10.5
Potri.002G143300 / bHLH / TF / 0.0 / 0.0 / 0.0 / 18.7 / 11.1 / 10.1
Potri.004G188800 / C2H2 / TF / 9.7 / 25.8 / 32.5 / 51.1 / 89.7 / 254.5
Potri.009G149400 / C2H2 / TF / 7.5 / 11.6 / 2.6 / 31.7 / 67.4 / 99.0
Potri.017G017100 / C2H2 / TF / 0.0 / 0.0 / 0.0 / 0.4 / 1.2 / 40.3
Potri.016G052700 / C2H2 / TF / 0.0 / 0.0 / 0.4 / 10.0 / 40.2 / 34.8
Potri.010G140700 / C2H2 / TF / 0.0 / 0.0 / 0.1 / 4.4 / 33.4 / 34.8
Potri.014G036600 / Dof / TF / 0.1 / 0.0 / 0.0 / 28.1 / 57.1 / 10.4
Potri.007G036400 / Dof / TF / 0.0 / 0.0 / 0.0 / 10.2 / 7.8 / 15.8
Potri.015G070300 / E2F/DP / TF / 0.0 / 0.0 / 0.0 / 41.0 / 1.5 / 44.5
Potri.018G038100 / ERF / TF / 0.0 / 0.0 / 0.1 / 34.8 / 0.0 / 61.8
Potri.014G094500 / ERF / TF / 0.1 / 0.2 / 0.4 / 14.9 / 15.7 / 39.8
Potri.004G161500 / GATA / TF / 8.0 / 7.3 / 0.4 / 145.0 / 89.1 / 71.4
Potri.003G122400 / GRAS / TF / 0.0 / 0.0 / 0.0 / 6.7 / 0.0 / 61.2
Potri.001G372300 / HD-ZIP / TF / 11.0 / 15.5 / 4.2 / 72.2 / 79.9 / 101.6
Potri.008G071500 / LBD / TF / 0.5 / 2.6 / 0.0 / 86.2 / 19.5 / 54.4
Potri.009G027300 / MYB023 / MYB / TF / 86.7 / 140.8 / 86.0 / 1084.3 / 772.8 / 804.9
Potri.012G084100 / MYB148 / MYB / TF / 0.6 / 0.0 / 2.0 / 14.3 / 64.0 / 15.6
Potri.006G221500 / MYB183 / MYB / TF / 0.0 / 0.0 / 0.0 / 16.6 / 0.0 / 36.7
Potri.014G076100 / PNAC020 / NAC / TF / 0.0 / 0.1 / 0.0 / 20.6 / 10.7 / 20.3
Potri.002G154100 / PNAC021 / NAC / TF / 0.3 / 3.6 / 0.2 / 171.7 / 126.7 / 46.3
Potri.012G100700 / SBP / TF / 0.1 / 5.7 / 0.1 / 83.2 / 41.1 / 18.8
Potri.013G008600 / TALE / TF / 0.0 / 0.0 / 0.0 / 25.3 / 25.6 / 12.1
Potri.003G195300 / Trihelix / TF / 55.1 / 70.5 / 19.8 / 261.4 / 250.1 / 132.9
Potri.005G101800 / WOX / TF / 28.7 / 9.2 / 24.1 / 55.1 / 194.3 / 100.2
Potri.014G025300 / WOX / TF / 11.8 / 15.4 / 6.0 / 84.2 / 207.7 / 151.6
Potri.002G124100 / WOX / TF / 9.2 / 1.9 / 0.1 / 57.0 / 84.4 / 47.7
Potri.018G139300 / WRKY / TF / 5.0 / 26.6 / 0.0 / 221.2 / 284.4 / 79.6
Potri.002G164400 / WRKY / TF / 9.4 / 0.1 / 0.0 / 113.5 / 141.1 / 18.4
Potri.006G072400 / WRKY / TF / 7.1 / 10.3 / 0.1 / 112.3 / 73.9 / 102.9
Potri.014G090300 / WRKY / TF / 3.4 / 3.3 / 7.3 / 77.3 / 38.1 / 76.8
Potri.014G024200 / WRKY / TF / 3.6 / 1.6 / 2.8 / 35.0 / 66.4 / 48.8
Potri.018G008500 / WRKY / TF / 0.0 / 0.1 / 0.1 / 55.3 / 0.0 / 19.4
Potri.006G263600 / WRKY / TF / 0.3 / 0.3 / 0.4 / 113.6 / 11.1 / 0.6

Table S3. GO analysis for fiber and vessel cell specific DEGs

GO term ID / GO term domain / GO term name / Number of DEGs / p value
Fiber cell specific DEGs / GO:1902221 / BP / erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process / 4 / 4.27E-02
GO:1902222 / BP / erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process / 4 / 1.20E-03
GO:0009803 / BP / cinnamic acid metabolic process / 3 / 1.02E-02
GO:0009800 / BP / cinnamic acid biosynthetic process / 3 / 1.02E-2
GO:0071554 / BP / cell wall organization or biogenesis / 25 / 8.56E-03
GO:0070589 / BP / cellular component macromolecule biosynthetic process / 10 / 6.47E-06
GO:0044264 / BP / cellular polysaccharide metabolic process / 17 / 1.63E-02
GO:0042546 / BP / cell wall biogenesis / 14 / 2.04E-04
GO:0009832 / BP / plant-type cell wall biogenesis / 10 / 1.06E-03
GO:0005975 / BP / carbohydrate metabolic process / 41 / 1.28E-2
GO:0071944 / CC / cell periphery / 69 / 1.98E-02
GO:0005886 / CC / plasma membrane / 61 / 7.04E-03
GO:0016841 / MF / ammonia-lyase activity / 4 / 1.20E-03
GO:0015020 / MF / glucuronosyltransferase activity / 5 / 4.79E-03
Vessel cell specific DEGs / GO:0009628 / BP / response to abiotic stimulus / 72 / 0.00616
GO:0008150 / BP / biological_process / 545 / 9.21E-05
GO:1901564 / BP / organonitrogen compound metabolic process / 122 / 3.02E-16
GO:0034641 / BP / cellular nitrogen compound metabolic process / 161 / 2.95E-02
GO:0071103 / BP / DNA conformation change / 13 / 3.54E-02
GO:0065009 / BP / regulation of molecular function / 27 / 5.69E-03
GO:0050790 / BP / regulation of catalytic activity / 24 / 2.73E-02
GO:0010383 / BP / cell wall polysaccharide metabolic process / 12 / 1.66E-02
GO:0042546 / BP / cell wall biogenesis / 15 / 3.13E-02
GO:0007389 / BP / pattern specification process / 16 / 7.09E-03
GO:0005575 / CC / cellular_component / 434 / 1.00E-16
GO:0044424 / CC / intracellular part / 268 / 9.88E-03
GO:0005829 / CC / cytosol / 102 / 4.91E-36
GO:0005773 / CC / vacuole / 45 / 5.08E-05
GO:0044391 / CC / ribosomal subunit / 63 / 2.67E-42
GO:0022626 / CC / cytosolic ribosome / 83 / 1.68E-56
GO:0030312 / CC / external encapsulating structure / 89 / 4.27E-32
GO:0005634 / CC / nucleus / 127 / 1.56E-05
GO:0009536 / CC / plastid / 99 / 7.46E-05
GO:0005198 / MF / structural molecule activity / 94 / 2.65E-46
GO:0016798 / MF / hydrolase activity, acting on glycosyl bonds / 33 / 9.67E-03
GO:0005507 / MF / copper ion binding / 24 / 2.97E-03

BP, CC and MF represent biological process, cellular component and molecular function.