基于转录组及WGCNA的甘蔗干旱响应调控网络分析

doi:10.3724/SP.J.1006.2022.14121

作物学报 ›› 2022, Vol. 48 ›› Issue (7): 1583-1600.doi: 10.3724/SP.J.1006.2022.14121

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

基于转录组及WGCNA的甘蔗干旱响应调控网络分析

李佩婷¹(), 赵振丽¹, 黄潮华¹, 黄国强¹, 徐良年¹, 邓祖湖¹, 张玉²^,^*(), 赵新旺¹^,³^,⁴^,^*()

¹福建农林大学国家甘蔗工程技术研究中心, 福建福州 350002
²福建农林大学生命科学学院 / 福建省植物功能生物学与绿色农业重点实验室, 福建福州 350002
³广西大学广西甘蔗生物学重点实验室, 广西南宁 530004
⁴福建农林大学 / 农业农村部福建甘蔗生物学与遗传育种重点实验室, 福建福州 350002

收稿日期:2021-07-13 接受日期:2021-10-19 出版日期:2022-07-12 网络出版日期:2021-11-25
通讯作者: 张玉,赵新旺
作者简介:E-mail: lipeiting147258@163.com
基金资助:
国家自然科学基金青年基金项目(31801423);国家自然科学基金青年基金项目(32001437)

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^,^*()

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 Published:2022-07-12 Published online:2021-11-25
Contact: ZHANG Yu,ZHAO Xin-Wang
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)

摘要/Abstract

摘要：

干旱是制约甘蔗产业发展的重要因素之一。前人研究表明, 斑茅具有良好的抗性基因, 可以通过远缘杂交遗传给后代。本研究以斑茅与甘蔗杂交F₁代无性系YCE96-40为材料, 对苗期干旱处理0 h和24 h后的叶和根进行转录组测序分析, 比较了根和叶在转录水平上响应干旱的差异, 鉴定出21,885个(DR vs CR:10176, DL vs CL:7907)差异表达基因(DEGs), 根中差异表达基因多于叶中, 说明根对干旱胁迫响应更为剧烈。GO功能富集分析发现, 根和叶中DEGs均富集到与脱水反应相关及激素信号转导过程相关的条目, 比如“对渗透胁迫生物过程的响应”和“对缺水生物过程的反应”等。与叶不同的是, 根中大量DEGs显著富集到与细胞膜相关的条目。在根中鉴定出多个木质素相关DEGs, 表明木质素参与了根的干旱响应。通过对所有DEGs进行WGCNA分析, 共鉴定出11个基因共表达模块, 其中与干旱处理后的根显著相关有5个模块, 与干旱处理后的叶显著相关的有2个模块。进一步筛选出了26个转录因子为甘蔗干旱响应的候选转录因子, 构建了调控网络。研究结果为进一步理解甘蔗抗旱性的分子机制及甘蔗抗旱性育种提供了理论指导。

关键词: 甘蔗, 抗旱性, 转录组, 加权基因共表达网络, 转录因子

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

李佩婷, 赵振丽, 黄潮华, 黄国强, 徐良年, 邓祖湖, 张玉, 赵新旺. 基于转录组及WGCNA的甘蔗干旱响应调控网络分析[J]. 作物学报, 2022, 48(7): 1583-1600.

LI Pei-Ting, ZHAO Zhen-Li, HUANG Chao-Hua, HUANG Guo-Qiang, XU Liang-Nian, DENG Zu-Hu, ZHANG Yu, ZHAO Xin-Wang. Analysis of drought responsive regulatory network in sugarcane based on transcriptome and WGCNA[J]. Acta Agronomica Sinica, 2022, 48(7): 1583-1600.

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链接本文: https://zwxb.chinacrops.org/CN/10.3724/SP.J.1006.2022.14121

https://zwxb.chinacrops.org/CN/Y2022/V48/I7/1583

图/表 22

表1

附表1

图1

图2

附表2

根中显著富集的GO条目"

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

附表2

附表3

叶片中显著富集的GO条目"

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

附表3

图3

附表4

根中显著富集的KEGG通路"

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

附表4

附表5

叶中显著富集的KEGG通路"

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

附表5

附表6

木质素生物合成过程涉及的DEGs"

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

附表6

图4

图5

附表7

激素信号转导涉及的DEGs"

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

附表7

图6

附表8

附表9

图7

附表10

表2

抗旱相关特异性模块中核心转录因子的功能注释"

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.

表2

图8

附表11

图9

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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

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

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

基于转录组及WGCNA的甘蔗干旱响应调控网络分析

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

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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

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

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

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