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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (7): 1583-1600.doi: 10.3724/SP.J.1006.2022.14121

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Analysis of drought responsive regulatory network in sugarcane based on transcriptome and WGCNA

LI Pei-Ting1(), ZHAO Zhen-Li1, HUANG Chao-Hua1, HUANG Guo-Qiang1, XU Liang-Nian1, DENG Zu-Hu1, ZHANG Yu2,*(), ZHAO Xin-Wang1,3,4,*()   

  1. 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
    2Fujian Key Laboratory of Plant Functional Biology and Green Agriculture / College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
    3Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, Guangxi, China
    4Fujian Key Laboratory of Sugarcane Biology, Genetics and Breeding, Ministry of Agriculture and Rural Affairs / Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
  • Received:2021-07-13 Accepted:2021-10-19 Online:2022-07-12 Published:2021-11-25
  • Contact: ZHANG Yu,ZHAO Xin-Wang E-mail:lipeiting147258@163.com;yuzhang@fafu.edu.cn;zhxinwang@126.com
  • Supported by:
    Youth Fund Project of the National Natural Science Foundation of China(31801423);Youth Fund Project of the National Natural Science Foundation of China(32001437)

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Abstract:

Drought is one of the important factors restricting the development of sugarcane industry. Previous studies have shown that E. arundinaceus has good resistance genes, which can be inherited through distant hybridization. In this study, we used YCE96-40, a F1 hybrid clone of E. arundinaceus and sugarcane, as material to analyze the transcriptome of leaves and roots after drought treatment for 0 and 24 hours at seedling stage. We compared the differences in response of roots and leaves to drought at transcriptional level, and identified 21,885 differentially expressed genes (DEGs) (DR vs CR: 10176, DL vs CL: 7907). The root response to drought stress was more intense. GO functional enrichment analysis showed that DEGs in roots and leaves were enriched in items related to dehydration response and hormone signal transduction process, such as “response to osmotic stress biological process” and “response to water shortage biological process”. Different from leaves, a large number of DEGs in roots were significantly enriched in the items related to cell membrane. Several lignin related DEGs were identified in roots, which indicated that lignin was involved in root drought response. Through WGCNA analysis of all DEGs, a total of 11 gene co-expression modules were identified, including five modules significantly related to root after drought treatment and two modules significantly related to leaf after drought treatment. Furthermore, 26 transcription factors were selected as candidate transcription factors for drought response in sugarcane, and the regulatory network was constructed. The results provide theoretical guidance for further understanding the molecular mechanism of sugarcane drought resistance and sugarcane drought resistance breeding.

Key words: sugarcane, drought resistance, transcriptome, weighted gene co-expression network, transcription factor

Table 1

Primers for RT-qPCR"

基因ID
Gene ID		 正向引物
Forward sequence (5°-3°)		 反向引物
Reverse sequence (5°-3°)
Cluster-14906.81942 GTGGCGGCCCTTACGAATGA GCCCGTACCATGCATTGCGA
Cluster-14906.153942 TTCTGCACGCCTGAGAGCTG CACGCCATCAGCCCATCTGT
Cluster-14906.115135 GCCCATATTGGACCAGAGCCA GCTCTAGCAGTGGATGTCGCA
Cluster-14906.152933 GATCTGAGGCTGTGCGTGCT AGGCGCTGCTGCTGATTCTT
Cluster-14906.154818 AGCGAGTGGCTCCTCTGACA TGGACGTGCCAATTCCAGTTTGT
Cluster-14906.156090 CTTCAACCCGCTGCACAGGA TCGGCGATGTCGTGTAACCG
Cluster-14906.142139 CTGACGCAGCAGAAGAGGCA GTCGATCGCTCCACTGCCAT
Cluster-14906.147361 GCCGACGAGCAGAAGGTGAA ACAGGCCCGAGAACATGCTG
Cluster-14906.157951 GATGTCGGTGCTGGTAAAAT CAACGACATTATCACACCAT
Cluster-14906.136592 CGAGGAACTACTACCGGTGC CCGAGTATGGAGGCGAGAAG
Cluster-14906.146281 GGCACACGTGACCTGCTTCT CGGCGTCTGCTGGTTGAAGA
Cluster-14906.123506 TGGAGCCCACCACGAGGTAT CTTCCGAACACGCCCTCCAG
GAPDH CACGGCCACTGGAAGCA TCCTCAGGGTTCCTGATGCC

Table S1

Statistics of RNA-seq results"

样本编号Sample ID 总读数(百万)
Total reads (in millions)		 总数据
Total data (Gb)		 GC (%) Q30 (%) 比对率
Number of aligned reads to
splicing transcriptome (%)
CL_1 71146938 10.67 55.66 92.55 68.12
CL_2 64776612 9.72 55.9 90.08 68.12
CL_3 62901160 9.44 56.77 90.59 67.98
DL_1 58972730 8.85 55.35 91.34 65.55
DL_2 61055990 9.16 54.95 91.87 66.39
DL_3 75358428 11.3 54.26 90.49 65.4
CR_1 61805904 9.27 53.74 92.03 65.93
CR_2 68885630 10.33 54.58 91.75 65.02
CR_3 69318686 10.4 53.87 91.84 66.56
DR_1 72940638 10.94 54.98 89.98 64.31
DR_2 62329192 9.35 55.32 92.12 66.25
DR_3 75884494 11.38 56.23 89.81 63.35

Fig. 1

Number of DEGs in different datasets CL: untreated leaves; DL: drought treated leaves; CR: untreated roots; DR: drought treated roots."

Fig. 2

Top 20 items of GO enrichment of DEGs in sugarcane roots and leaves A: DR vs. CR DEGs enriched go entries; B: DL vs. CL DEGs enriched go entries. The vertical axis represents the number of genes and the horizontal axis represents go entries. CL: untreated leaves; DL: drought treated leaves; CR: untreated roots; DR: drought treated roots."

Table S2

Table S4 GO terms significantly enriched in roots"

GO条目GO_trem 描述
Description		 条目类型Term_type p值矫正值
FDR		 DEGs数量
DEGs number
GO:0006804 过氧化物酶反应Obsolete peroxidase reaction BP 4.02E-34 185
GO:0044710 单生物代谢过程Single-organism metabolic process BP 2.95E-32 4319
GO:0006979 对氧化应激的反应Response to oxidative stress BP 4.4E-32 271
GO:0009628 对非生物刺激的反应Response to abiotic stimulus BP 4.4E-32 558
GO:1901700 对含氧化合物的反应Response to oxygen-containing compound BP 4.4E-32 396
GO:0055114 氧化还原过程Oxidation-reduction process BP 1.75E-31 1687
GO:0001101 对酸性化学物质的反应Response to acid chemical BP 1.96E-31 319
GO:0044699 单生物过程Single-organism process BP 3.51E-27 6670
GO:0042221 对化学物质的反应Response to chemical BP 1.57E-22 812
GO:0009415 对水的反应Response to water BP 3.42E-21 138
GO:0009737 脱落酸反应Response to abscisic acid BP 5.87E-19 177
GO:0006970 渗透胁迫反应Response to osmotic stress BP 1.1E-18 217
GO:0009719 对内源性刺激的反应Response to endogenous stimulus BP 1.77E-18 359
GO:0009414 对缺水的反应Response to water deprivation BP 1.98E-18 116
GO:0005975 碳水化合物代谢过程Carbohydrate metabolic process BP 3.04E-17 972
GO:0009651 盐胁迫反应Response to salt stress BP 4.57E-17 201
GO:0009725 对激素的反应Response to hormone BP 1.54E-16 340
GO:0033993 对脂质的反应Response to lipid BP 7.82E-16 202
GO:0010033 对有机物的反应Response to organic substance BP 9.23E-16 406
GO:0008152 代谢过程Metabolic process BP 4.92E-15 8200
GO:0005667 转录因子复合物Transcription factor complex CC 9.68E-16 763
GO:0071944 细胞外围Cell periphery CC 4.83E-15 1239
GO:0016020 膜Membrane CC 1.29E-13 3886
GO:0031224 膜的固有成分Intrinsic component of membrane CC 3.45E-12 1911
GO:0048046 质外体Apoplast CC 3.98E-12 151
GO:0016021 膜的组成部分Integral component of membrane CC 5.1E-12 1869
GO:0005773 液泡Vacuole CC 5.26E-11 287
GO:0005886 质膜Plasma membrane CC 1.71E-10 945
GO:0005680 后期促进复合体Anaphase-promoting complex CC 8.84E-10 180
GO:0000152 核泛素连接酶复合物Nuclear ubiquitin ligase complex CC 1.24E-09 180
GO:0005618 细胞壁Cell wall CC 8.72E-09 236
GO:0044425 膜部件Membrane part CC 1.36E-07 2276
GO:0031461 Cullin-RING泛素连接酶复合物Cullin-RING ubiquitin ligase complex CC 1.55E-07 185
GO:0031012 细胞外基质Extracellular matrix CC 4.46E-07 83
GO:0030312 细胞外矩阵External encapsulating structure CC 6.09E-07 300
GO:0000151 泛素连接酶复合物Ubiquitin ligase complex CC 9.98E-07 204
GO:0005578 蛋白质细胞外基质Proteinaceous extracellular matrix CC 3.23E-05 69
GO:0005811 脂质颗粒Lipid particle CC 0.000125 21
GO:0005576 胞外区Extracellular region CC 0.000181 751
GO:0000325 植物型液泡Plant-type vacuole CC 0.000289 51
GO:0020037 血红素结合Heme binding MF 1.55E-34 443
GO:0004601 过氧化物酶活性Peroxidase activity MF 4.02E-34 185
GO:0046906 四吡咯结合Tetrapyrrole binding MF 2.48E-33 449
GO:0016491 氧化还原酶活性Oxidoreductase activity MF 2.32E-32 1658
GO:0016684 氧化还原酶活性,作用于过氧化物作为受体
Oxidoreductase activity, acting on peroxide as acceptor		 MF 7.59E-29 186
GO:0001071 核酸结合转录因子活性
Nucleic acid binding transcription factor activity		 MF 1.08E-27 692
GO:0003700 转录因子活性,序列特异性DNA结合
Transcription factor activity, sequence-specific DNA binding		 MF 1.08E-27 692
GO:0016705 氧化还原酶活性,作用于成对供体,分子氧掺入或减少
Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen		 MF 6.14E-27 452
GO:0003824 催化活性Catalytic activity MF 2.78E-22 7173
GO:0005506 铁离子结合Iron ion binding MF 7.16E-22 395
GO:0016209 抗氧化活性Antioxidant activity MF 3.69E-19 212
GO:0051213 双加氧酶活性Dioxygenase activity MF 6.87E-16 163
GO:0004553 水解酶活性,水解邻糖基化合物
Hydrolase activity, hydrolyzing O-glycosyl compounds		 MF 1.19E-15 421
GO:0043169 阳离子结合Cation binding MF 3.65E-15 2408
GO:0016798 水解酶活性,作用于糖基键
Hydrolase activity, acting on glycosyl bonds		 MF 6.31E-15 454
GO:0004497 单加氧酶活性Monooxygenase activity MF 1.22E-13 229
GO:0016161 β-淀粉酶活性Beta-amylase activity MF 1.29E-13 32
GO:0005509 钙离子结合Calcium ion binding MF 1.78E-13 313
GO:0046872 金属离子结合Metal ion binding MF 3.49E-13 2295
GO:0043565 序列特异性DNA结合Sequence-specific DNA binding MF 2.5E-12 375

Table S3

GO terms significantly enriched in leafs"

GO条目GO_trem 描述
Description		 条目类型
Term_type		 P值矫正值FDR DEGs数量
DEGs number
GO:0015979 光合作用Photosynthesis BP 4.87E-29 201
GO:0055114 氧化还原法Oxidation-reduction process BP 5.7E-24 946
GO:0015995 叶绿素生物合成过程Chlorophyll biosynthetic process BP 7.37E-18 44
GO:0009628 对非生物刺激的反应Response to abiotic stimulus BP 7.85E-16 295
GO:0044699 单生物过程Single-organism process BP 4.78E-14 3540
GO:0009725 对激素的反应Response to hormone BP 6.56E-14 203
GO:0009409 对寒冷的反应Response to cold BP 2.02E-13 87
GO:0009719 对内源性刺激的反应Response to endogenous stimulus BP 2.33E-13 207
GO:0009416 对光刺激的反应Response to light stimulus BP 8.04E-13 119
GO:0009737 脱落酸反应Response to abscisic acid BP 9.82E-13 103
GO:0009637 对蓝光的反应Response to blue light BP 7.79E-12 26
GO:0010033 对有机物的反应Response to organic substance BP 9.31E-12 233
GO:0046148 色素生物合成过程Pigment biosynthetic process BP 9.39E-12 98
GO:0009415 对水的反应Response to water BP 1.08E-11 76
GO:0001101 对酸性化学物质的反应Response to acid chemical BP 1.12E-11 156
GO:0009314 对辐射的反应Response to radiation BP 1.78E-11 119
GO:1901700 对含氧化合物的反应
Response to oxygen-containing compound		 BP 1.78E-11 193
GO:0097305 对酒精的反应Response to alcohol BP 1.82E-11 109
GO:0010114 对红灯的反应Response to red light BP 3.16E-11 23
GO:0008152 代谢过程Metabolic process BP 4.1E-11 4395
GO:0042651 类囊体膜Thylakoid membrane CC 1.86E-54 199
GO:0044436 类囊体部分Thylakoid part CC 3.33E-41 267
GO:0009535 叶绿体类囊体膜Chloroplast thylakoid membrane CC 8.11E-41 138
GO:0055035 质体类囊体膜Plastid thylakoid membrane CC 8.11E-41 138
GO:0044434 叶绿体部分Chloroplast part CC 2.83E-40 329
GO:0009579 类囊体Thylakoid CC 3.32E-40 280
GO:0034357 光合膜Photosynthetic membrane CC 3.64E-40 246
GO:0009534 叶绿体类囊体Chloroplast thylakoid CC 6.45E-40 144
GO:0031976 质体类囊体Plastid thylakoid CC 6.45E-40 144
GO:0044435 质体部分Plastid part CC 1.09E-39 332
GO:0031984 细胞器小室Organelle subcompartment CC 1.61E-36 154
GO:0009507 叶绿体Chloroplast CC 7.17E-32 520
GO:0009536 质体Plastid CC 1.27E-30 547
GO:0009941 叶绿体包膜Chloroplast envelope CC 2.35E-19 156
GO:0009526 质体包膜Plastid envelope CC 4.84E-19 161
GO:0009654 光系统II析氧复合体
Photosystem II oxygen evolving complex		 CC 1.37E-16 51
GO:0009532 质体基质Plastid stroma CC 7.47E-16 158
GO:0009521 光系统Photosystem CC 1.45E-14 122
GO:0009570 叶绿体基质Chloroplast stroma CC 1.76E-14 151
GO:0031977 类囊体腔Thylakoid lumen CC 7.77E-13 39
GO:0016491 氧化还原酶活性Oxidoreductase activity MF 2.17E-25 934
GO:0048037 辅因子结合Cofactor binding MF 1.16E-14 364
GO:0003824 催化活性Catalytic activity MF 1.86E-12 3817
GO:0016705 氧化还原酶活性,作用于成对供体,分子氧掺入或减少
Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen		 MF 5.66E-12 233
GO:0001071 核酸结合转录因子活
性Nucleic acid binding transcription factor activity		 MF 8.34E-12 356
GO:0003700 转录因子活性,序列特异性DNA结合
Transcription factor activity, sequence-specific DNA binding		 MF 8.34E-12 356
GO:0003959 NADPH脱氢酶活性NADPH dehydrogenase activity MF 3.16E-11 13
GO:0050662 辅酶结合Coenzyme binding MF 2.01E-10 287
GO:0005506 铁离子结合Iron ion binding MF 3.4E-10 205
GO:0016851 镁螯合酶活性Magnesium chelatase activity MF 8.95E-09 12
GO:0051002 连接酶活性,形成氮金属键
Ligase activity, forming nitrogen-metal bonds		 MF 8.95E-09 12
GO:0051003 连接酶活性,形成氮金属键,形成配合物
Ligase activity, forming nitrogen-metal bonds, forming coordination complexes		 MF 8.95E-09 12
GO:0004497 单加氧酶活性Monooxygenase activity MF 1.82E-08 127
GO:0043565 序列特异性DNA结合Sequence-specific DNA binding MF 1.85E-08 210
GO:0003883 CTP合成酶活性CTP synthase activity MF 2.32E-08 24
GO:0004753 糖精嘌呤脱氢酶活性Saccharopine dehydrogenase activity MF 4.17E-07 7
GO:0047130 糖精嘌呤脱氢酶(NADP+,L-赖氨酸形成)活性
Sccharopine dehydrogenase (NADP+, L-lysine-forming) activity		 MF 4.17E-07 7
GO:0050661 NADP结合NADP binding MF 4.63E-07 52
GO:0004553 水解酶活性,水解邻糖基化合物
Hydrolase activity, hydrolyzing O-glycosyl compounds		 MF 5.58E-07 217
GO:0004471 苹果酸脱氢酶(脱羧)(NAD+)活性
Malate dehydrogenase (decarboxylating) (NAD+) activity		 MF 5.58E-07 22

Fig. 3

Top 20 pathways of KEGG enrichment of DEGs in sugarcane roots and leaves A: DR vs CR DEGs enriched KEGG pathway; B: DL vs CL DEGs enriched KEGG pathway. The vertical axis represents the enriched KEGG pathway, the horizontal axis represents the ratio of enriched genes, the point size represents the number of enriched genes in the pathway, and the color represents the P-value (FDR) corrected by multiple tests. CL: untreated leaves; DL: drought treated leaves; CR: untreated roots; DR: drought treated roots."

Table S4

KEGG pathway significantly enriched in roots"

通路编号
Pathway ID		 通路
Pathway		 DEGs数量
DEGs number		 p值矫正值
FDR
DR vs CR UP
ko04075 植物激素信号转导Plant hormone signal transduction 206 3.16E-20
ko00052 半乳糖代谢Galactose metabolism 114 2.82E-16
ko00906 类胡萝卜素生物合成Carotenoid biosynthesis 63 1.25E-15
ko00592 α-亚麻酸代谢α-Linolenic acid metabolism 86 1.67E-15
ko00591 亚油酸Linoleic acid metabolism 41 6.81E-11
ko00500 淀粉和蔗糖代谢Starch and sucrose metabolism 182 5.68E-09
ko00564 甘油磷脂代谢Glycerophospholipid metabolism 120 4.38E-07
ko00250 丙氨酸、天冬氨酸和谷氨酸代谢Alanine, aspartate and glutamate metabolism 77 1.84E-06
ko00561 甘油酯代谢Glycerolipid metabolism 84 2.57E-06
ko00600 鞘脂代谢Sphingolipid metabolism 50 1.35E-05
ko00910 氮代谢Nitrogen metabolism 46 1.46E-05
ko00480 谷胱甘肽代谢Glutathione metabolism 102 0.000107079
ko00760 烟酸和烟酰胺代谢Nicotinate and nicotinamide metabolism 32 0.00017074
ko00945 二苯乙烯类、二芳基庚烷类和姜辣素生物合成
Stilbenoid, diarylheptanoid and gingerol biosynthesis		 34 0.000260611
ko00710 光合生物的固碳作用Carbon fixation in photosynthetic organisms 85 0.000380085
ko00010 糖酵解/糖异生Glycolysis / Gluconeogenesis 132 0.00063726
ko00590 花生四烯酸代谢Arachidonic acid metabolism 23 0.001180007
ko00562 磷酸肌醇代谢Inositol phosphate metabolism 62 0.001180007
ko00330 精氨酸和脯氨酸代谢Arginine and proline metabolism 58 0.001345202
ko00430 牛磺酸和低牛磺酸代谢Taurine and hypotaurine metabolism 21 0.002349213
ko00565 乙醚脂质代谢Ether lipid metabolism 39 0.002572574
ko00410 β-丙氨酸代谢beta-Alanine metabolism 48 0.002572574
ko00904 β-丙氨酸代谢Diterpenoid biosynthesis 31 0.002789186
ko04626 植物-病原相互作用Plant-pathogen interaction 141 0.002931207
ko00603 鞘糖脂生物合成-globo系列Glycosphingolipid biosynthesis - globo series 17 0.007304209
ko00280 缬氨酸、亮氨酸和异亮氨酸降解Valine, leucine and isoleucine degradation 49 0.015423467
ko00402 苯并恶嗪类生物合成Benzoxazinoid biosynthesis 5 0.020686992
ko01040 不饱和脂肪酸的生物合成Biosynthesis of unsaturated fatty acids 33 0.025968338
ko00400 苯丙氨酸、酪氨酸和色氨酸生物合成
Phenylalanine, tyrosine and tryptophan biosynthesis		 44 0.025968338
ko00908 玉米素生物合成Zeatin biosynthesis 20 0.026518753
DR vs CR DOWN
ko00940 苯丙烷生物合成Phenylpropanoid biosynthesis 124 1.19E-31
ko00195 光合作用Photosynthesis 39 4.25E-13
ko00196 光合作用天线蛋白Photosynthesis - antenna proteins 18 4.61E-09
ko00630 乙醛酸和二羧酸代谢Glyoxylate and dicarboxylate metabolism 43 0.00000338
ko00460 氰基氨基酸代谢Cyanoamino acid metabolism 36 0.00000901
ko00730 硫胺素代谢Thiamine metabolism 12 0.000256332
ko04075 植物激素信号转导Plant hormone signal transduction 54 0.000477217
ko00941 类黄酮生物合成Flavonoid biosynthesis 19 0.006976581
ko00260 甘氨酸、丝氨酸和苏氨酸代谢Glycine, serine and threonine metabolism 29 0.007551386
ko00860 卟啉与叶绿素代谢Porphyrin and chlorophyll metabolism 18 0.012474933
ko00905 油菜素类固醇生物合成Brassinosteroid biosynthesis 8 0.030624012

Table S5

KEGG pathway significantly enriched in leafs"

通路编号
Pathway ID		 通路
Pathway		 DEGs数量
DEGs_Num		 p值矫正值
FDR
DL vs CL UP
ko04075 植物激素信号转导Plant hormone signal transduction 141 5.93E-31
ko00052 半乳糖代谢Galactose metabolism 63 2.57E-13
ko00603 鞘糖脂生物合成-globo系列Glycosphingolipid biosynthesis - globo series 24 1.61E-11
ko00500 淀粉和蔗糖代谢Starch and sucrose metabolism 96 3.42E-08
ko00561 甘油酯代谢Glycerolipid metabolism 52 4.28E-08
ko00600 鞘脂代谢Sphingolipid metabolism 33 2.72E-07
ko00250 丙氨酸、天冬氨酸和谷氨酸代谢Alanine, aspartate and glutamate metabolism 43 3.16E-06
ko00906 类胡萝卜素生物合成Carotenoid biosynthesis 25 3.20E-06
ko00430 牛磺酸和低牛磺酸代谢Taurine and hypotaurine metabolism 17 1.23E-05
ko00280 缬氨酸、亮氨酸和异亮氨酸降解Valine, leucine and isoleucine degradatio 36 1.23E-05
ko00330 精氨酸和脯氨酸代谢Arginine and proline metabolism 35 0.000131771
ko00100 甾体生物合成Steroid biosynthesis 31 0.000139675
ko00592 α-亚麻酸代谢alpha-Linolenic acid metabolism 30 0.000209326
ko00909 倍半萜和三萜生物合成Sesquiterpenoid and triterpenoid biosynthesis 16 0.002175606
ko00650 丁酸代谢Butanoate metabolism 17 0.002261337
ko00904 二萜生物合成Diterpenoid biosynthesis 18 0.002565069
ko00760 烟酸和烟酰胺代谢Nicotinate and nicotinamide metabolism 16 0.003174526
ko00402 苯并恶嗪类生物合成Benzoxazinoid biosynthesis 4 0.00822359
ko00232 咖啡因代谢Caffeine metabolism 6 0.014517862
ko00590 花生四烯酸代谢Arachidonic acid metabolism 11 0.020800302
ko00564 甘油磷脂代谢Glycerophospholipid metabolism 46 0.026196513
ko00071 脂肪酸降解Fatty acid degradation 27 0.039857743
ko00620 丙酮酸代谢Pyruvate metabolism 36 0.043040988
DL vs CL DOWN
ko00195 光合作用Photosynthesis 77 4.61E-52
ko00860 卟啉与叶绿素代谢Porphyrin and chlorophyll metabolism 59 3.90E-35
ko00196 光合作用天线蛋白Photosynthesis - antenna proteins 34 2.00E-28
ko00710 光合生物的固碳作用Carbon fixation in photosynthetic organisms 48 9.80E-13
ko00910 氮代谢Nitrogen metabolism 19 2.05E-05
ko00630 乙醛酸和二羧酸代谢Glyoxylate and dicarboxylate metabolism 33 4.86E-05
ko04712 植物昼夜节律Circadian rhythm - plant 19 9.61E-05
ko00740 核黄素代谢Riboflavin metabolism 9 0.000113929
ko00030 戊糖磷酸途径Pentose phosphate pathway 25 0.000347306
ko00902 单萜生物合成Monoterpenoid biosynthesis 10 0.00191122
ko00960 托烷、哌啶和吡啶生物碱的生物合成Tropane, piperidine and pyridine alkaloid biosynthesis 11 0.01412646
ko00190 氧化磷酸化Oxidative phosphorylation 30 0.02482389
ko00480 谷胱甘肽代谢Glutathione metabolism 27 0.0322657

Table S6

DEGs involved in lignin biosynthesis process"

基因编号
Gene ID		 CL DL CR DR 注释
Annotation
Cluster-14906.71489 3.070 9.323 14.043 29.253 苯丙氨酸解氨酶Phenylalanine ammonia-lyase
Cluster-14906.139395 0.553 0.923 3.330 6.990 苯丙氨酸解氨酶Phenylalanine ammonia-lyase
Cluster-14906.56879 1.883 1.333 16.627 55.193 苯丙氨酸解氨酶Phenylalanine ammonia-lyase
Cluster-14906.98337 26.197 79.867 63.683 102.497 苯丙氨酸解氨酶Phenylalanine ammonia-lyase
Cluster-14906.76036 0.907 1.157 7.933 24.347 苯丙氨酸解氨酶Phenylalanine ammonia-lyase
Cluster-14906.166499 3.867 30.673 31.877 78.123 反式肉桂酸4-单加氧酶Trans-cinnamate 4-monooxygenase
Cluster-14906.161634 1.840 17.440 10.913 33.137 反式肉桂酸4-单加氧酶Trans-cinnamate 4-monooxygenase
Cluster-14906.183751 2.063 17.230 9.277 20.610 反式肉桂酸4-单加氧酶Trans-cinnamate 4-monooxygenase
Cluster-14906.205461 1.340 32.647 5.007 16.92 反式肉桂酸4-单加氧酶Trans-cinnamate 4-monooxygenase
Cluster-14906.183750 1.547 9.180 3.297 12.877 反式肉桂酸4-单加氧酶Trans-cinnamate 4-monooxygenase
Cluster-14906.161532 12.513 111.977 74.997 213.130 反式肉桂酸4-单加氧酶Trans-cinnamate 4-monooxygenase
Cluster-14906.182827 19.500 159.120 117.697 293.707 反式肉桂酸4-单加氧酶Trans-cinnamate 4-monooxygenase
Cluster-14906.104971 1.913 6.293 4.903 9.997 反式肉桂酸4-单加氧酶Trans-cinnamate 4-monooxygenase
Cluster-14906.135776 2.060 10.270 5.010 14.483 反式肉桂酸4-单加氧酶Trans-cinnamate 4-monooxygenase
Cluster-14906.41002 0.090 0.660 3.777 8.323 4 -香豆酸-辅酶A连接酶4-coumarate--CoA ligase
Cluster-14906.172556 2.697 6.117 7.847 11.320 4 -香豆酸-辅酶A连接酶4-coumarate--CoA ligase
Cluster-14906.244214 0.250 0.320 3.243 8.450 4 -香豆酸-辅酶A连接酶4-coumarate--CoA ligase
Cluster-14906.98045 1.410 1.550 7.030 11.090 4 -香豆酸-辅酶A连接酶4-coumarate--CoA ligase
Cluster-14906.159381 27.833 62.880 74.293 109.827 4 -香豆酸-辅酶A连接酶4-coumarate--CoA ligase
Cluster-14906.35439 0.940 27.317 30.183 60.867 4 -香豆酸-辅酶A连接酶4-coumarate--CoA ligase
Cluster-14906.123210 1.273 0.233 8.260 2.420 4 -香豆酸-辅酶A连接酶4-coumarate--CoA ligase
Cluster-14906.159383 0.007 0.000 1.207 0.233 4 -香豆酸-辅酶A连接酶4-coumarate--CoA ligase
Cluster-14906.60211 0.150 0.507 1.057 6.523 肉桂酰辅酶A还原酶Cinnamoyl-CoA reductase
Cluster-14906.172984 0.070 0.300 0.523 1.110 肉桂酰辅酶A还原酶Cinnamoyl-CoA reductase
Cluster-14906.60213 1.100 4.167 6.277 34.983 肉桂酰辅酶A还原酶Cinnamoyl-CoA reductase
Cluster-14906.172314 1.140 11.927 9.780 35.253 肉桂酰辅酶A还原酶Cinnamoyl-CoA reductase
Cluster-35239.0 0.020 0.023 1.727 3.883 肉桂酰辅酶A还原酶Cinnamoyl-CoA reductase
Cluster-14906.60210 0.040 0.253 0.147 0.873 肉桂酰辅酶A还原酶Cinnamoyl-CoA reductase
Cluster-14906.60209 0.053 0.543 0.433 5.577 肉桂酰辅酶A还原酶Cinnamoyl-CoA reductase
Cluster-14906.42614 0.000 1.003 20.833 3.030 肉桂酰辅酶A还原酶Cinnamoyl-CoA reductase
Cluster-14561.1 0.000 0.000 0.037 2.430 肉桂醇脱氢酶Cinnamyl-alcohol dehydrogenase
Cluster-14561.0 0.000 0.000 0.333 2.470 肉桂醇脱氢酶Cinnamyl-alcohol dehydrogenase
Cluster-14906.55023 0.220 0.290 505.470 115.510 肉桂醇脱氢酶Cinnamyl-alcohol dehydrogenase
Cluster-14906.52428 0.000 0.000 5.457 0.263 肉桂醇脱氢酶Cinnamyl-alcohol dehydrogenase
Cluster-14906.52638 0.000 0.090 55.993 11.630 肉桂醇脱氢酶Cinnamyl-alcohol dehydrogenase
Cluster-14906.48450 0.000 0.000 26.770 5.013 肉桂醇脱氢酶Cinnamyl-alcohol dehydrogenase
Cluster-14906.122136 0.500 0.253 133.550 27.537 肉桂醇脱氢酶Cinnamyl-alcohol dehydrogenase
Cluster-14906.151146 337.100 109.617 58.610 21.810 肉桂醇脱氢酶Cinnamyl-alcohol dehydrogenase
Cluster-14906.148566 0.030 0.730 58.430 11.743 肉桂醇脱氢酶Cinnamyl-alcohol dehydrogenase
Cluster-14906.162254 17.813 166.080 79.383 705.197 过氧化物酶Peroxidase
Cluster-14906.99962 1.957 1.903 251.467 363.743 过氧化物酶Peroxidase
Cluster-14906.51580 0.107 1.793 103.743 314.013 过氧化物酶Peroxidase
Cluster-14906.163436 24.420 148.720 140.720 196.070 过氧化物酶Peroxidase
Cluster-14906.112155 26.703 127.633 111.990 171.277 过氧化物酶Peroxidase
Cluster-14906.162250 7.010 52.423 19.460 158.550 过氧化物酶Peroxidase
Cluster-14906.167188 14.620 104.527 41.543 140.513 过氧化物酶Peroxidase
Cluster-14906.51123 0.407 2.883 34.840 126.203 过氧化物酶Peroxidase
Cluster-14906.75719 0.000 3.357 7.083 121.560 过氧化物酶Peroxidase
Cluster-14906.149942 241.280 43.240 75.630 12.810 过氧化物酶Peroxidase
Cluster-14906.96512 1.513 46.580 54.063 5.037 过氧化物酶Peroxidase
Cluster-14906.122006 1.790 0.703 6.870 1.363 过氧化物酶Peroxidase
Cluster-14906.180977 0.000 1.697 25.100 8.317 过氧化物酶Peroxidase
Cluster-14906.51983 0.000 0.000 16.220 0.277 过氧化物酶Peroxidase
Cluster-14906.242928 0.000 0.000 6.163 1.570 过氧化物酶Peroxidase
Cluster-14906.38206 0.000 0.000 12.043 0.470 过氧化物酶Peroxidase
Cluster-14906.237061 0.303 2.687 284.187 118.177 过氧化物酶Peroxidase
Cluster-14906.60176 2.130 21.483 36.497 2.127 过氧化物酶Peroxidase
Cluster-14906.48834 0.303 9.257 9.500 35.240 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.234705 0.463 1.297 0.083 2.147 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.234707 1.097 2.443 1.410 5.907 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.84135 0.327 2.637 3.597 9.643 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.234709 0.053 0.510 0.317 3.823 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.33828 0.310 2.977 0.703 6.697 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.235478 3.173 1.997 12.850 4.297 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.52653 0.640 0.037 1.370 0.033 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.246300 1.347 0.000 4.387 0.343 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.236102 0.237 0.157 2.400 0.433 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-19452.0 0.013 1.097 2.707 0.757 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.186135 0.000 0.073 6.267 0.997 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.183828 1.253 1.263 1.163 0.070 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.183825 1.657 0.703 8.633 0.897 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.77787 1.153 0.597 2.630 0.257 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase
Cluster-14906.77785 4.030 2.130 19.020 7.520 莽草酸O-邻羟基肉桂酰转移酶
Shikimate O-hydroxycinnamoyltransferase

Fig. 4

Relative expression analysis of DEGs involved in lignin biosynthesis Red blocks and blue blocks indicates up regulation and down regulation in the relative expression levels; yellow squares represent the order of comparison groups. CL: untreated leaves; DL: drought treated leaves; CR: untreated roots; DR: drought treated roots."

Fig. 5

Hormone signal transduction related DEGS expression pattern Red indicates up regulation and blue indicates down regulation. CL: untreated leaves; DL: drought treated leaves; CR: untreated roots; DR: drought treated roots."

Table S7

DEGs involved in hormone signal transduction process"

基因编号
Gene ID		 CL DL CR DR 注释
Annotation
Cluster-14906.221505 0.557 1.390 1.167 3.040 DELLA蛋白DELLA protein
Cluster-14906.251505 0.250 1.577 1.577 4.297 DELLA蛋白DELLA protein
Cluster-14906.212188 0.790 2.627 2.263 6.180 DELLA蛋白DELLA protein
Cluster-14906.36214 0.213 0.893 0.387 1.240 DELLA蛋白DELLA protein
Cluster-14906.136410 7.867 103.147 43.327 94.863 赤霉素受体GID1 Gibberellin receptor GID1
Cluster-14906.159942 4.393 72.967 27.303 66.610 赤霉素受体GID1 Gibberellin receptor GID1
Cluster-14906.136409 14.547 322.227 75.783 180.640 赤霉素受体GID1 Gibberellin receptor GID1
Cluster-14906.175210 19.627 493.157 104.097 319.060 赤霉素受体GID1 Gibberellin receptor GID1
Cluster-14906.175209 2.593 55.220 20.887 63.517 赤霉素受体GID1 Gibberellin receptor GID1
Cluster-14906.245283 0.767 0.023 0.370 0.233 F-box蛋白GID2 F-box protein GID2
Cluster-14906.85071 0.590 2.543 1.283 4.213 光敏色素相互作用因子3
Phytochrome-interacting factor 3
Cluster-14906.245085 1.693 8.603 4.467 11.933 光敏色素相互作用因子3
Phytochrome-interacting factor 3
Cluster-14906.171581 2.620 6.073 1.313 0.120 光敏色素相互作用因子3
Phytochrome-interacting factor 3
Cluster-14906.84753 0.657 1.453 2.650 0.227 光敏色素相互作用因子4
phytochrome-interacting factor 4
Cluster-14906.196922 2.823 5.563 2.803 0.527 光敏色素相互作用因子3
Phytochrome-interacting factor 3
Cluster-14906.100642 0.217 0.670 0.317 1.140 光敏色素相互作用因子3
Phytochrome-interacting factor 3
Cluster-14906.94012 0.133 0.430 0.160 1.100 光敏色素相互作用因子3
Phytochrome-interacting factor 3
Cluster-14906.87877 0.547 2.797 0.820 0.300 光敏色素相互作用因子3
Phytochrome-interacting factor 3
Cluster-14906.104785 1.133 1.300 1.580 0.253 光敏色素相互作用因子4
Phytochrome-interacting factor 4
Cluster-14906.156785 51.100 3.237 1.983 0.543 光敏色素相互作用因子4
Phytochrome-interacting factor 4
Cluster-14906.150558 46.077 4.493 2.690 0.983 光敏色素相互作用因子4
Phytochrome-interacting factor 4
Cluster-14906.190884 0.430 0.273 0.447 0.047 生长素反应因子Auxin response factor
Cluster-14906.108900 4.437 12.997 7.723 14.110 生长素反应因子Auxin response factor
Cluster-14906.97388 3.767 3.137 14.040 23.287 生长素内流载体(AUX1-LAX家族)
Auxin influx carrier (AUX1 LAX family)
Cluster-14906.167834 4.077 5.457 17.403 29.683 生长素内流载体(AUX1-LAX家族)
Auxin influx carrier (AUX1 LAX family)
Cluster-14906.118371 1.780 2.737 10.503 18.667 生长素内流载体(AUX1-LAX家族)
Auxin influx carrier (AUX1 LAX family)
Cluster-14906.167832 1.733 2.737 7.550 16.573 生长素内流载体(AUX1-LAX家族)
Auxin influx carrier (AUX1 LAX family)
Cluster-14906.124564 1.593 2.467 6.840 16.883 生长素内流载体(AUX1-LAX家族)
Auxin influx carrier (AUX1 LAX family)
Cluster-14906.192689 0.120 0.690 1.370 3.903 生长素内流载体(AUX1-LAX家族)
Auxin influx carrier (AUX1 LAX family)
Cluster-14906.193369 0.460 2.440 2.243 6.810 生长素内流载体(AUX1-LAX家族)
Auxin influx carrier (AUX1 LAX family)
Cluster-14906.11436 0.017 0.217 0.947 0.130 生长素反应性GH3基因家族
Auxin responsive GH3 gene family
Cluster-14906.42600 0.000 0.537 8.167 14.530 生长素反应性GH3基因家族
Auxin responsive GH3 gene family
Cluster-14906.50539 0.260 1.067 7.483 29.600 生长素反应性GH3基因家族
Auxin responsive GH3 gene family
Cluster-14906.50538 0.037 0.253 1.813 7.353 生长素反应性GH3基因家族
Auxin responsive GH3 gene family
Cluster-14906.50540 0.033 0.317 1.067 4.763 生长素反应性GH3基因家族
Auxin responsive GH3 gene family
Cluster-14906.92468 0.087 0.237 0.793 3.657 生长素反应性GH3基因家族
Auxin responsive GH3 gene family
Cluster-14906.213311 1.277 6.033 2.257 19.243 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.205367 2.700 13.417 26.930 84.550 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.140785 11.743 78.487 34.137 237.477 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.140784 5.783 47.150 18.533 138.790 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.175488 0.627 5.257 2.377 9.377 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.209309 0.073 0.620 1.483 0.140 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.69886 1.063 10.667 7.183 41.047 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.214614 0.760 10.533 10.563 89.317 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.52693 0.087 1.150 0.087 0.733 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.234130 0.423 7.470 0.350 3.190 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.181232 0.447 8.980 1.613 5.237 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.175039 0.237 6.097 0.733 3.297 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.95904 0.173 4.337 0.200 1.607 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.181231 1.123 31.097 5.303 19.280 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.28541 0.133 4.007 1.117 6.690 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.211052 0.787 25.223 1.893 9.567 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.171815 0.417 14.793 2.193 8.610 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.211051 1.017 36.383 2.087 14.030 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.83296 0.100 4.510 0.237 2.447 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.37981 0.050 2.787 2.807 55.770 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.101613 11.710 13.753 24.937 44.163 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.30073 0.190 5.890 2.510 4.873 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.123161 1.320 4.520 4.563 9.457 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.261113 0.083 0.643 1.003 2.327 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.104522 1.497 5.473 10.070 26.157 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.205368 3.603 8.410 17.550 49.360 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.55479 4.720 2.567 12.250 36.047 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.104520 1.233 4.450 6.840 22.983 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.66377 0.670 4.227 2.167 8.437 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.51751 0.047 0.167 0.220 0.830 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.236180 0.330 1.427 1.627 6.770 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.224347 0.000 0.480 0.867 4.703 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.84443 0.310 4.580 1.033 9.260 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.252340 0.880 0.427 0.193 1.953 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.3150 0.000 0.110 2.310 28.077 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.3151 0.000 0.057 0.580 9.260 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.175040 0.000 1.167 0.037 0.870 生长素反应蛋白IAA Auxin-responsive protein IAA
Cluster-14906.89778 1.313 8.323 2.383 14.960 SAUR家族蛋白SAUR family protein
Cluster-14906.74371 1.107 25.770 3.400 17.370 SAUR家族蛋白SAUR family protein
Cluster-14906.74563 0.887 3.477 4.590 9.077 SAUR家族蛋白SAUR family protein
Cluster-14906.74564 2.703 2.243 4.177 10.027 SAUR家族蛋白SAUR family protein
Cluster-14906.74562 3.727 6.370 8.090 21.447 SAUR家族蛋白SAUR family protein
Cluster-14906.61729 2.470 4.837 6.120 19.717 SAUR家族蛋白SAUR family protein
Cluster-14906.61742 2.210 6.630 4.213 16.503 SAUR家族蛋白SAUR family protein
Cluster-14906.60146 4.073 30.210 6.277 43.960 SAUR家族蛋白SAUR family protein
Cluster-14906.243068 1.013 31.953 4.980 51.570 SAUR家族蛋白SAUR family protein
Cluster-14906.216156 1.837 0.753 0.080 0.970 SAUR家族蛋白SAUR family protein
Cluster-14906.2322 0.040 0.047 0.077 1.673 SAUR家族蛋白SAUR family protein
Cluster-14906.121117 7.640 6.140 6.117 9.467 调节蛋白NPR1 Regulatory protein NPR1
Cluster-14906.121119 3.090 3.567 3.033 5.747 调节蛋白NPR1 Regulatory protein NPR1
Cluster-14906.96141 0.993 1.450 0.677 1.667 调节蛋白NPR1 Regulatory protein NPR1
Cluster-14906.91484 4.457 19.817 7.900 21.490 调节蛋白NPR1 Regulatory protein NPR1
Cluster-14906.174587 0.063 0.113 30.947 2.330 致病相关蛋白1 Pathogenesis-related protein 1
Cluster-14906.189409 0.000 0.160 28.003 3.120 致病相关蛋白1 Pathogenesis-related protein 1
Cluster-14906.129257 3.483 3.117 61.843 11.880 致病相关蛋白1 Pathogenesis-related protein 1
Cluster-14906.35029 0.000 0.007 0.833 0.017 转录因子TGA Transcription factor TGA
Cluster-14906.35028 0.000 0.000 1.623 0.210 转录因子TGA Transcription factor TGA
Cluster-14906.58847 0.113 0.153 1.743 0.227 转录因子TGA Transcription factor TGA
Cluster-14906.235475 0.437 0.970 1.680 0.287 转录因子TGA Transcription factor TGA
Cluster-14906.204994 0.640 0.147 3.060 0.647 转录因子TGA Transcription factor TGA
Cluster-14906.51255 0.000 0.007 2.253 0.520 转录因子TGA Transcription factor TGA
Cluster-14906.77294 0.407 0.613 1.957 0.463 转录因子TGA Transcription factor TGA
Cluster-14906.213586 1.370 1.773 4.797 1.300 转录因子TGA Transcription factor TGA
Cluster-14906.69390 2.027 3.407 8.877 2.373 转录因子TGA Transcription factor TGA
Cluster-14906.126707 3.753 1.147 25.537 6.910 转录因子TGA Transcription factor TGA
Cluster-14906.126704 4.027 1.530 17.170 4.670 转录因子TGA Transcription factor TGA
Cluster-14906.213952 0.497 0.170 7.107 1.987 转录因子TGA Transcription factor TGA
Cluster-14906.214468 2.427 3.947 9.313 3.327 转录因子TGA Transcription factor TGA
Cluster-14906.184928 0.740 3.387 7.423 5.863 转录因子TGA Transcription factor TGA
Cluster-14906.156973 0.783 4.343 3.070 2.990 转录因子TGA Transcription factor TGA
Cluster-14906.80433 0.657 6.800 18.270 10.683 转录因子TGA Transcription factor TGA
Cluster-14906.17984 0.033 1.503 0.603 1.437 丝氨酸/苏氨酸蛋白激酶
CTR1Serine/threonine-protein kinase CTR1
Cluster-14906.88790 0.113 1.777 1.197 1.940 丝氨酸/苏氨酸蛋白激酶
CTR1Serine/threonine-protein kinase CTR1
Cluster-14906.88795 0.313 3.543 1.733 3.230 丝氨酸/苏氨酸蛋白激酶
CTR1Serine/threonine-protein kinase CTR1
Cluster-14906.243327 0.650 9.103 4.270 8.493 丝氨酸/苏氨酸蛋白激酶
CTR1Serine/threonine-protein kinase CTR1
Cluster-14906.88794 0.643 12.410 4.250 8.900 丝氨酸/苏氨酸蛋白激酶
CTR1Serine/threonine-protein kinase CTR1
Cluster-14906.89642 0.540 2.887 1.983 4.750 丝氨酸/苏氨酸蛋白激酶
CTR1Serine/threonine-protein kinase CTR1
Cluster-14906.163398 4.007 16.237 39.750 9.367 EIN3结合F-box蛋白EIN3-binding F-box protein
Cluster-14906.255933 0.070 0.000 0.030 0.253 乙烯不敏感蛋白2 Ethylene-insensitive protein 2
Cluster-14906.76809 2.777 27.703 7.583 26.123 乙烯不敏感蛋白3 Ethylene-insensitive protein 3
Cluster-14906.39924 0.023 1.180 0.160 0.050 乙烯不敏感蛋白3 Ethylene-insensitive protein 3
Cluster-14906.45915 0.420 0.633 1.433 3.353 乙烯反应转录因子1
Ethylene-responsive transcription factor 1
Cluster-14906.76670 0.067 0.230 1.003 0.073 乙烯受体Ethylene receptor
Cluster-14906.123629 3.440 6.847 17.543 6.620 乙烯受体Ethylene receptor

Fig. 6

Relative expression profiles of transcription factor family in each sample The transcription factors appeared in the text were selected for expression pattern heat map display, and log2 (Fold Change) was used for mapping. Red blocks and blue blocks indicate up regulation and down regulation in the relative expression levels. The data are row standardized and row clustered and the gene family to which the gene belongs is in parentheses. CL: untreated leaves; DL: drought treated leaves; CR: untreated roots; DR: drought treated roots."

Table S8

DEGs in transcription factors"

基因编号
Gene ID		 CL DL CR DR 注释
Annotation
Cluster-14906.196840 0.000 10.697 0.047 19.380 DREB1C, AP2-EREBP
Cluster-14906.17595 0.107 13.857 1.057 18.227 ERF027, AP2-EREBP
Cluster-14906.14127 0.000 3.050 0.047 15.543 bZIP60, bZLP
Cluster-14906.26480 0.000 15.983 0.463 106.220 ABI4, AP2-EREBP
Cluster-14906.17611 0.840 5.330 2.497 16.907 LBD4, LOB
Cluster-14906.44675 0.567 14.780 2.590 42.597 TIFY3, Tify
Cluster-14906.81425 0.420 7.670 1.930 20.953 MYBR13, MYB
Cluster-14906.47480 0.000 3.107 7.757 30.450 ERF054, AP2-EREBP
Cluster-14906.117403 0.293 2.217 2.930 11.377 MYBS3, MYB
Cluster-14906.214614 0.760 10.533 10.563 89.317 IAA24, AUX/IAA
Cluster-14906.45120 0.000 10.573 9.077 46.850 RAP2-13, AP2-EREBP
Cluster-14906.231981 0.070 2.330 1.720 8.390 ERF1, AP2-EREBP
Cluster-14906.82449 1.070 7.210 4.790 27.327 ERF8, AP2-EREBP
Cluster-14906.257000 0.377 2.343 1.367 4.593 NAC71, NAC
Cluster-14906.198691 0.323 4.170 2.593 10.763 BIM1, bHLH
Cluster-14906.47622 0.183 1.800 32.773 80.773 HOX29, HB
Cluster-14906.44261 0.717 0.750 2.337 327.897 MYB2, MYB
Cluster-14906.146281 0.410 1.570 6.573 52.243 NAC92, NAC
Cluster-14906.209309 0.073 0.620 1.483 0.140 IAA25, AUX/Laa
Cluster-14906.106436 0.170 19.527 0.233 8.913 ERF061, AP2-EREBP
Cluster-14906.111752 0.593 30.990 0.237 5.283 HSF C-1b, HSF
Cluster-14906.182530 1.333 10.267 0.000 0.393 MDA-box 51, MADS
Cluster-14906.123506 0.260 5.080 0.400 1.080 ERF5, AP2-EREBP
Cluster-14906.41976 0.053 30.537 0.127 2.207 ODORANT1, MYB

Table S9

Number of transcription factors"

转录因子家族
Transcription factor family		 基因数量
Genes number		 DEGs数量DEGs number 转录因子家族Transcription factor family 基因数量
Genes number		 DEGs数量
DEGs number
MYB 555 144 Alfin-like 40 4
bHLH 426 87 CPP 40 4
Orphans 416 116 TAZ 40 8
AP2-EREBP 394 117 PLATZ 39 7
WRKY 376 84 IWS1 38 2
bZIP 364 116 BSD 37 4
NAC 339 77 ARID 34 0
C2H2 317 30 GeBP 33 3
FAR1 305 10 zf-HD 33 8
C3H 290 29 EIL 27 10
GRAS 253 56 BES1 25 6
HB 236 53 Sigma70-like 25 11
AUX/IAA 234 50 Rcd1-like 24 0
ABI3VP1 221 22 C2C2-YABBY 21 1
G2-like 208 23 SRS 21 2
TRAF 203 23 TIG 20 1
SET 193 12 CSD 19 4
CCAAT 175 29 DBP 17 10
PHD 169 8 GRF 17 1
SNF2 164 5 PBF-2-like 14 0
GNAT 146 27 SWI/SNF-SWI3 14 2
mTERF 130 0 ARR-B 13 4
ARF 128 13 LUG 13 2
MADS 125 22 MED6 13 11
TUB 112 25 MBF1 12 1
C2C2-GATA 104 10 SOH1 12 1
HSF 90 37 DDT 10 0
Jumonji 87 18 Pseudo ARR-B 10 4
LOB 87 13 C2C2-CO-like 8 1
C2C2-Dof 85 20 CAMTA 8 2
FHA 85 14 VOZ 8 1
Trihelix 83 13 LIM 7 0
Tify 82 39 Coactivator p15 6 0
SBP 81 12 HRT 6 0
OFP 76 12 ULT 6 6
HMG 73 10 RB 5 0
SWI/SNF-BAF60b 67 9 BBR/BPC 4 0
E2F-DP 61 10 MED7 4 0
TCP 56 17 Zn-clus 2 0
RWP-RK 41 3 S1Fa-like 1 0

Fig. 7

Heat map of the correlation between modules and traits Each row represents a module, and each column represents a trait. The number in the rectangular box represents the correlation coefficient and corresponding P-value between the module and the trait. Red block represents the positive correlation between the module and the trait, and blue represents the negative correlation. The module with positive correlation is defined as the module with positive correlation with the sample if the correlation coefficient is greater than 0.65 and P < 0.05. CL: untreated leaves; DL: drought treated leaves; CR: untreated roots; DR: drought treated roots."

Table S10

Number of genes in different modules"

模块
Module		 DEGs数量
DEGs number
green 1476
cyan 96
greenyellow 260
magenta 1097
salmon 216
red 601
blue 978
brown 813
black 569
midnightblue 39
pink 264

Table 2

Functional annotation of core transcription factors in drought related specific modules"

样本
Sample		 模块
Module		 甘蔗基因ID
Gene ID in sugarcane		 基因名称
Gene name		 基因功能
Gene function
根Root red Cluster-14906.26480 ABI4 编码一个包含AP2结构域的假定转录因子。对ABA、渗透胁迫、糖胁迫和干旱响应。
Encodes a putative transcription factor containing an AP2 domain. Expressed in response to ABA, osmotic stress, sugar stress and drought.
Cluster-14906.49886 ABR1 编码ERF/AP2转录因子家族的ERF (乙烯反应因子)亚家族B-6的一个成员。
Encodes a member of the ERF (ethylene response factor) subfamily B-6 of ERF/AP2 transcription factor family.
Cluter-14906.198691 BIM1 编码基本螺旋-环-螺旋(bHLH)家族蛋白BIM1 (BES1-相互作用的MYC-LIKE 1), 参与油菜素类固醇信号传导。
Encodes a basic helix-loop-helix (bHLH) family protein BIM1 (BES1-INTERACTING MYC-LIKE 1), involved in brassinosteroid signaling.
Cluster-14906.14127 bZIP60 bZIP60由一个bZIP DNA结合域和一个假定的跨膜域组成, 在盐胁迫中发挥作用, 但这种反应通过一个信号通路进行。
bZIP60 consists of a bZIP DNA binding domain followed by a putative transmembrane domain, play a role in salt stress but this response goes through a signaling pathway.
Cluster-14906.17595 ERF27 编码ERF/AP2转录因子家族的ERF (乙烯反应因子)亚家族的一个成员。
Encodes a member of the ERF (ethylene response factor) subfamily of ERF/AP2 transcription factor family.
Cluster-14906.82449 ERF8 编码ERF/AP2转录因子家族的ERF (乙烯反应因子)亚家族成员, 参与ABA和免疫信号传导。
Encodes a member of the ERF (ethylene response factor) subfamily of ERF/AP2 transcription factor family, involved in both ABA and immune signaling.
Cluster-14906.17611 LOB4 植物特异性LATERAL ORGAN BOUNDARIES (LOB)结构域基因家族的成员, 参与土壤中植物根系形态的形成。
Members of the plant-specific LATERAL ORGAN BOUNDARIES (LOB) domain gene family, participate in the formation of root morphology of plants in soil.
Cluter-14906.257000 NAC71 NAC转录因子家族的成员, 通过上调脱落酸(ABA)信号基因的表达来增强对干旱和盐胁迫的抗性。
A member of NAC transcription factor family, which enhances the resistance to drought and salt stress by up regulating the expression of abscisic acid (ABA) signal gene.
样本
Sample		 模块
Module		 甘蔗基因ID
Gene ID in sugarcane		 基因名称
Gene name		 基因功能
Gene function
根Root red Cluster-14906.44675 TIFY 11c-like 它包含一种由非生物胁迫诱导的锌指结构域tify。
It contains tify domain, a kind of zinc-finger domain, which is induced by abiotic stress.
Cluster-14906.17972 TIFY9 它包含一种由非生物胁迫诱导的锌指结构域tify。
It contains tify domain, a kind of zinc-finger domain, which is induced by abiotic stress.
Cluster-14906.81425 DIVARICATA MYB转录因子的一个成员。
A member of MYB transcription factor.
Cluster-14906.86529 C2H2-1 C2H2型锌指转录因子。
C2H2 type of zinc finger transcription factors.
根Root pink Cluter-14906.231981 ERF1 编码ERF/AP2转录因子家族的ERF (乙烯反应因子)亚家族的一个成员。
Encodes a member of the ERF (ethylene response factor) subfamily of ERF/AP2 transcription factor family.
Cluter-14906.214614 IAA24 与生长素反应元件结合的转录因子。
A transcription factor that binds to an auxin response element.
Cluter-14906.117403 MYBS3 一种单一的DNA结合重复序列MYB转录因子, 参与植物对冷胁迫的反应。
A single DNA-binding repeat MYB transcription factor, it is involved in plant response to cold stress.
Cluster-14906.45120 RAP2-13 作为AP2/ERF转录因子的一员, 与缺氧、氧化和渗透胁迫有关。
A member of AP2 / ERF transcription factors, it is related to hypoxia, oxidation and osmotic stress.
根Root brown Cluster-14906.37143 CSA 油菜素类固醇诱导的MYB结构域蛋白CSA参与花粉和种子发育。
The MYB domain protein CSA, induced by brassinosteroid, participates in pollen and seed development.
Cluster-14906.47480 DREB2B 编码脱水反应元件结合(DREB)转录因子的基因。
Genes encoding the dehydration-responsive element-binding (DREB) transcription factors.
Cluster-14906.47622 HOX29 同源结构域亮氨酸拉链家族成员。
Member of homeodomain-leucine zipper family.
Cluter-14906.146281 NAC92 NAC转录因子家族的成员。
Member of NAC transcription factor family.
叶Leaf greenyellow Cluter-14906.136592 WRKY50 WRKY蛋白。
WRKY proteins.
Cluter-14906.182530 MADS51 MADS-box基因, 与植物根系发育有关。
MADS-box genes, it is related to the development of plant root system.
Cluter-14906.111752 Hsf C-1b 热应激转录因子C-1b。
Heat stress transcription factor C-1b.
Cluter-14906.123506 ERF5 编码ERF/AP2转录因子家族的ERF (乙烯反应因子)亚家族成员, 参与ABA和免疫信号传导。
Encodes a member of the ERF (ethylene response factor) subfamily of ERF/AP2 transcription factor family, involved in both ABA and immune signaling.
Cluster-14906.17935 HSB1 热休克因子结合蛋白1。
Heat shock factor-binding protein 1.
Cluster-14906.41976 ODORANT1 R2R3型MYB家族的成员。
A member of the R2R3-type MYB family.

Fig. 8

Co-expression network of drought related core transcription factors with kME value of top 150 The red dot is the core transcription factor and the yellow dot is other genes. The networks from left to right are the co-expression network of genes in green yellow module, the co-expression network of genes in red module, the coexpression network of genes in pink module, and the co-expression network of genes in brown module."

Table S11

Drought resistance related core transcription factors with top 150 KME values"

基因编号
Gene ID		 连通性
kME		 模块
Module
Cluster-14906.26480 0.994853 red
Cluster-14906.49886 0.9924 red
Cluster-14906.14127 0.9841 red
Cluster-14906.231981 0.9881 pink
Cluster-14906.47622 0.9801 brown
Cluster-14906.117403 0.9730 pink
Cluster-14906.146281 0.9802 brown
Cluster-14906.45120 0.9729 pink
Cluster-14906.44675 0.9779 red
Cluster-14906.136592 0.961263 greenyellow
Cluster-14906.41976 0.973491 greenyellow
Cluster-14906.123506 0.958913 greenyellow

Fig. 9

Real-time quantitative PCR and RNA-seq analysis of 12 genes The left Y-axis represents the relative expression of RT-qPCR, the right Y-axis represents the FPKM value of RNA-seq, the gray column is the RT-qPCR result, and the gray broken line is the RNA seq result. Different lowercase letters above the bar indicate significant differences at the 0.05 probability level. CL: untreated leaves; DL: drought treated leaves; CR: untreated roots; DR: drought treated roots."

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