短日照诱导白花泡桐顶芽死亡过程相关基因的表达

doi:10.11707/j.1001-7488.20220215

摘要/Abstract

摘要：

目的: 对短日照诱导的白花泡桐顶芽进行转录组测序分析，探究其顶芽死亡的分子机制，为解决泡桐“冠大干低”提供理论依据。方法: 在25 ℃恒温条件下，对白花泡桐1年生苗进行短日照(SD)处理，在高生长期(SDa)、高生长停止期(SDb)、顶芽死亡发生期(SDc)3个时期进行转录组测序，并利用荧光定量PCR(qRT-PCR)测定11个差异基因的表达量，同时结合转录组信息进行验证。结果: 白花泡桐顶芽3个时期转录组测序共得到57.47 Gb数据，使用DESeq2软件进行3个时期样品间比较，共筛选出差异基因44 397条，其中注释到7大数据库(NR、NT、GO、EggNOG、KEGG、UniProt、Pfam)的基因为37 076条(83.51%)。3个时期的差异基因在KEGG上主要富集在植物激素信号通路，对顶芽死亡发生的SDc时期植物激素信号通路上差异基因的分析得出：脱落酸(ABA)激素信号的响应因子ABF下调表达，乙烯(ETH)激素信号的响应因子ERF1上调表达，油菜素内酯(BR)激素信号上编码木葡聚糖内糖基转移酶的TCH4和细胞周期特异蛋白基因CYCD3上调表达，这些基因与大多数植物芽休眠过程中表达情况不同。qRT-PCR与转录组测序结果在基因表达量差异倍数上存在偏差，但整体趋势一致，可以证明转录组结果的可靠准确。结论: 白花泡桐顶芽死亡发生期的植物激素信号转导通路中ABF、ERF1、TCH4和CYCD3基因的表达情况，使其在高生长停止后顶端分生组织细胞分裂活动仍在继续进行，此时顶端分生组织分化的叶原基展开的幼叶脱落而无法形成芽鳞包裹，导致顶芽未向休眠芽方向发展而死亡。

关键词: 白花泡桐, 顶芽死亡, 短日照, 激素信号转导通路, 转录组

Abstract:

Objective: The transcriptome sequencing analysis of Paulownia fortunei terminal bud induced by short days was carried out to explore the molecular mechanism of terminal bud death, so as to provide a theoretical basis for solving the problem of Paulownia "crown big stem low" Method: Under the condition of constant temperature of 25 ℃, the one-year-old seedlings of P. fortunei were induced by short days (SD) so that the terminal buds were in three periods: growth period (SDa), growth cessation period (SDb), and terminal bud death period (SDc). Terminal buds of each period were tested for transcriptome sequencing, and fluorescent quantitative PCR (qRT-PCR) was used to verify the expression of 11 genes. Result: A total of 57.47 Gb clean data were obtained from the transcriptome sequencing of P. fortunei. A total of 44 397 differentially expressed genes were screened out by comparing the samples of three periods using the software DESeq2. Among them, 37076 genes (83.51%) were annotated into seven databases (NR, NT, GO, EggNOG, KEGG, UniProt, Pfam). KEGG pathway enrichment analysis showed that the main enrichment was in the plant hormone signaling pathway. Through the analysis of the expressed genes in the plant hormone signaling pathway of SDc during the terminal bud death stage, it was concluded that the abscisic acid (ABA) signal transduction factor ABF was down-regulated, the ethylene (ETH) signal transduction factor ERF1 was up-regulated, brassinolide(BR) hormone signal transduction of TCH4 encoding xyloglucan endoglycosyltransferase and cell cycle-specific protein gene CYCD3 were up-regulated, which were different from those in most plants during bud dormancy. The result of qRT-PCR and transcriptome sequencing had deviation, but the overall trend was consistent, which proved that transcriptome sequencing result were correct and reliable. Conclusion: The expression of ABF, ERF1, TCH4 and CYCD3 in the plant hormone signal transduction pathway may lead to the continued division and differentiation of the shoot apical meristem in SDc. At the same time, the young leaves that wrapped the apical meristem fall off, so that the terminal bud of Paulownia fortunei cannot form dormant buds and result in death.

Key words: Paulownia fortunei, terminal bud death, short day, hormone signal transduction, transcriptome

中图分类号:

S718.43

李顺福,王慧敏,房丽莎,刘震. 短日照诱导白花泡桐顶芽死亡过程相关基因的表达[J]. 林业科学, 2022, 58(2): 148-158.

Shunfu Li,Huimin Wang,Lisha Fang,Zhen Liu. Gene Expression Related to Terminal Bud Death Induced by Short-Day in Paulownia fortunei[J]. Scientia Silvae Sinicae, 2022, 58(2): 148-158.

图/表 10

图1

表1

表2

图2

图3

表3

差异表达基因KEGG富集通路分析"

通路名称 Pathway	上调基因数 UP regulated genes	下调基因数 Down regulated genes	校正P值 Corrected P value	通路位置 Pathway ID
SDb vs SDa
植物激素信号转导Plant hormone signal transduction	36	59	1.06×10^-10	map04075
角质、木栓质和蜡的合成Cutin, suberine and wax biosynthesis	19	7	2.56×10^-7	map00073
光合作用天线蛋白Photosynthesis-antenna proteins	0	18	5.07×10^-6	map00196
苯丙烷类合成Phenylpropanoid biosynthesis	36	20	8.72×10^-6	map00940
MAPK信号通路MAPK signaling pathway-plant	46	21	9.74×10^-5	map04016
乙醛酸和二羧酸代谢Glyoxylate and dicarboxylate metabolism	64	11	0.000 2	map00630
光合作用Photosynthesis	1	19	0.000 7	map00195
碳代谢作用Carbon metabolism	175	12	0.007 1	map01200
SDc vs SDb
植物激素信号转导Plant hormone signal transduction	26	84	0.000 2	map04075
氨基酸合成Biosynthesis of amino acids	197	76	0.001 5	map01230
淀粉和蔗糖代谢Starch and sucrose metabolism	95	58	0.001 9	map00500
苯丙氨酸等合成Phenylalanine, tyrosine and tryptophan biosynthesis	40	15	0.004 6	map00400
SDc vs SDa
植物激素信号转导Plant hormone signal transduction	59	93	3.94×10^-11	map04075
淀粉和蔗糖代谢Starch and sucrose metabolism	146	67	1.25×10^-10	map00500
苯丙烷类合成Phenylpropanoid biosynthesis	59	42	1.94×10^-9	map00940
MAPK信号通路MAPK signaling pathway-plant	72	44	9.89×10^-5	map04016
氰氨基酸代谢Cyanoamino acid metabolism	48	21	1.77×10^-5	map00460
吲哚生物碱生物合成Indole alkaloid biosynthesis	9	13	5.27×10^-5	map00901
角质、木栓质和蜡的合成Cutin, suberine and wax biosynthesis	17	14	0.000 2	map00073
苯丙氨酸等合成Phenylalanine, tyrosine and tryptophan biosynthesis	45	19	0.001 6	map00400
乙醛酸和二羧酸代谢Glyoxylate and dicarboxylate metabolism	103	19	0.001 9	map00630
氨基糖核苷酸糖代谢Amino sugar and nucleotide sugar metabolism	103	56	0.007 3	map00520

表3

图4

表4

富集到植物激素信号转导KEGG通路上差异基因及功能描述①"

植物激素 Hormone	基因编号 Gene number	KO ID	基因功能描述 Function description
生长素Auxin	DN80863_c0_g1 DN81206_c0_g2 DN64977_c0_g1 DN70584_c2_g2 DN77909_c1_g1 DN79226_c1_g1 DN67543_c0_g1 DN63863_c0_g1	K13946 K14485 K14484 K14486 K14487 K14488	生长输入载体AUX1 Auxin influx carrier AUX1(AUX1) 转运响应抑制因子1 Transport inhibitor response 1 (TIR1) 生长素响应蛋白IAA Auxin responsive protein (IAA) 生长素响应因子 Auxin response factor (ARF) 生长素响应GH3基因家族 Auxin responsive GH3 gene family (GH3) SAUR家族蛋白SAUR family protein(SAUR)
细胞分裂素Cytokinin	DN68870_c1_g5	K14491	双组分响应调节器ARR-B家族 Two component response regulator ARR-B family (ARR-B)
赤霉素Gibberellin	DN82220_c1_g1 DN82158_c1_g2 DN81860_c1_g1 DN81860_c1_g2	K14493 K14494	赤霉素受体GID1 Gibberellin receptor GID1 (GID1) DELLA蛋白 DELLA protein (DELLA)
脱落酸Abscisic acid	DN67794_c1_g1 DN59959_c0_g1 DN81200_c0_g1 DN79605_c0_g2 DN79605_c0_g3 DN83661_c2_g2	K14496 K14497 K14498 K14432	脱落酸受体PYR/PYL蛋白家族Abscisic acid receptor PYR/PYL family (PYL) 蛋白磷酸酶2C Protein phosphatase 2C (PP2C) 蔗糖非酵解型蛋白激酶2 Sucrose non-fermenting1-related protein kinase 2 (SNRK2) ABA反应元件结合因子 ABA responsive element binding factor (ABF)
乙烯Ethylene	DN75732_c0_g1 DN75455_c0_g1 DN82109_c0_g1 DN72495_c1_g1 DN72737_c2_g4	K14510 K14513 K14514 K14516	丝氨酸/苏氨酸蛋白激酶CTR1 Serine/threonine-protein kinase CTR1 (CTR1) 乙烯不敏感蛋白2 Ethylene insensitive protein 2 (EIN2) 乙烯不敏感蛋白3 Ethylene insensitive protein 3 (EIN3) 乙烯应答转录因子1 Ethylene responsive transcription factor 1 (ERF1)
油菜素内酯Brassinolide	DN80256_c0_g5	K13416	油菜素内酯不敏感相关受体激酶1 Brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1)
	DN74700_c1_g1	K14499	BRI1激酶抑制子1 BRI1 kinase inhibitor 1 (BKI1)
	DN80006_c0_g7	K14500	BR信号激酶BR signaling kinase (BSK)
	DN78469_c0_g1	K14503	油菜素内酯抗性因子1/2 Brassinosteroid resistant 1/2 (BZR1/2)
	DN80006_c0_g7	K14504	木糖葡萄糖基转移酶TCH4 Xyloglucosyl transferase TCH4 (TCH4)
	DN78469_c0_g1	K14505	细胞周期蛋白D3 Cyclin D3 (CYCD3)

表4

表5

图5

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样品 Sample	原始数据 Raw reads	有效数据 Clean reads	有效碱基数 Clean bases/Gb	Q30(%)	有效读数比例 Clean reads ratio (%)
SDa-1	47 170 900	46 155 682	6.45	93.51	97.85
SDa-2	47 296 568	46 028 158	6.43	93.84	97.32
SDa-3	47 694 770	46 368 244	6.48	93.96	97.22
SDb-1	48 454 868	47 249 798	6.60	92.85	97.51
SDb-2	45 454 586	44 452 908	6.21	93.76	97.80
SDb-3	45 592 110	44 391 996	6.20	93.77	97.37
SDc-1	49 038 356	47 567 810	6.64	94.58	97.00
SDc-2	48 460 682	46 921 468	6.55	93.50	96.82
SDc-3	44 069 318	42 734 802	6.01	93.71	96.97

被注释基因 Annotated genes	总数 Total	数据库 Databases							总体 Overall
被注释基因 Annotated genes	总数 Total	NR	NT	GO	EggNOG	KEGG	UniProt	Pfam	总体 Overall
数目 Number	44 937	33 810	20 559	22 111	13 328	12 540	25 396	19 101	37 076
百分比 Percentage(%)	100	75.24	45.75	49.20	29.66	27.91	56.51	42.51	83.51

基因编号 Gene number	基因功能描述 Function description	引物序列 Primer sequence (5’- 3’)	KO ID
DN82158_c1_g1	赤霉素受体GID1 Gibberellin receptor GID1 (GID1)	F: TGCGGGGTGAAAACAATAG R: TCAGAGTAACACGGGAAGAAAT	K14493
DN81200_c0_g1	蔗糖非酵解型蛋白激酶2 Sucrose non-fermenting1-related protein kinase 2 (SNRK2)	F: TGTTTTGCCTCTTTGATTGTTC R: CTCACCTTCTTGCCCCTCT	K14498
DN81546_c5_g3	光系统Ⅰ亚单位F Photosystem I subunit F (PSI-F)	F: AGTGAGGCAAACCATCAGAAC R: CGAGAAGCAGGAGATCAAGAA	K02694
DN67975_c4_g7	茉莉酸氨基合成酶JAR1 Jasmonic acid resistant 1 (JAR1)	F: GCTTGGCTGCTGCTTCTACA R: TCAAGGGTTCCACAACTCCAC	K14506
DN68587_c3_g1	采光复合物II叶绿素a/b结合蛋白2 Light harvesting complex II chlorophyll a/b binding protein 2 (LHCB2)	F: GCCTCCTCCAACTCTGTATCC R: CGTCTTCCCCGAAATCCT	K08913
DN74090_c1_g2	采光复合物II叶绿素a/b结合蛋白4 Light harvesting complex II chlorophyll a/b binding protein 4 (LHCB4)	F: CTGGATGGCTCCCTCGTT R: GCTGTAAGGCTGGAATGGC	K08915
DN68271_c1_g1	采光复合物II叶绿素a/b结合蛋白6 Light harvesting complex II chlorophyll a/b binding protein 6 (LHCB6)	F: GTTGCTTTTCCTACTCGGTTTA R: GCTTCTGGACTCTGGCACTAT	K08917
DN80256_c0_g5	油菜素内酯不敏感相关受体激酶1 Brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1)	F: CGCTGCCCTTCTATTTGCT R: GAACTTCGGGGTCCTCCTC	K13416
DN67597_c0_g3	光系统Ⅰ亚单位D Photosystem I subunit D (PSI-D)	F: GAGAATTGTGCAAGGGACTGT R: CCACCCCTCCGAACTCAT	K02692
DN68054_c0_g4	TGA转录因子TGA transcription factor (TGA)	F: TGCTTGCTTTCGGGGAGT R: GCTGCTTGTGCCATTTTGTAG	K14431
DN81860_c1_g2	DELLA蛋白DELLA protein (DELLA)	F: TTGCATATCTGCCTCCCTAAAT R: AATGAACCCGAAAATCGTGAC	K14494
18S rRNA	18S核糖体RNA 18S ribosomal RNA	F: ACATAGTAAGGATTGACAGA R: TAACGGAATTAACCAGACA

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