Combined Metabolomic and Transcriptomic Analysis in Different Parts of Paphiopedilum purpuratum

doi:10.13560/j.cnki.biotech.bull.1985.2025-0927

Abstract

Abstract:

Objective This study elucidated the functional differentiation mechanism across Paphiopedilum purpuratum tissues and systematically revealed its metabolite distribution characteristics, gene expression patterns, and metabolism-gene co-regulation network through multi-omics strategies, which may provide a molecular basis for understanding species environmental adaptability. Method Non-targeted metabolomic analysis (UHPLC-MS/MS) were used to compare metabolites differences in leaves (SL), flowers (SF), and roots (SR) of P. purpuratum. Transcriptome sequencing was used to identify differentially expressed genes, followed by metabolite-gene co-expression network construction. Result The 2 164 metabolites (1 471 positive ion mode, 693 negative ion mode) were identified in metabolomics, with significant inter-group differences: SL vs. SF (499 positive and 193 negative ion mode metabolites), SL vs. SR (534 and 243), SF vs. SR (433 and 187). KEGG enrichment analysis showed differential metabolite enrichment in phenylpropanoid biosynthesis, flavonoid biosynthesis, and linoleic acid metabolism pathways. Transcriptomic analysis revealed profound tissue-specific gene expression: Photosynthetic genes (e.g., sqdB, DVR) were significantly upregulated in the leaves; second, fragrance/pigment synthesis genes (e.g., FAH, crtZ) were highly expressed in the flowers; and third, stress-responsive genes (e.g., CCR, GPAT) were upregulated in the roots. Key regulators were identified via co-expression network analysis: such as INO80B (regulating flavonoid synthesis), CCT1 (regulating terpene metabolism), and CCR (involved in root defense), revealing core metabolite synthesis regulatory mechanisms. Conclusion Integrated metabolomic and transcriptomic analysis demonstrates that P. purpuratum forms its ecological adaptability molecular mechanism through three tissue-specific “metabolism-gene” coordinated regulatory networks: The synergy of photosynthesis and stress resistance in its leaves, the attraction of pollination in its flowers, and the stress defense in its roots.

Key words: Paphiopedilum purpuratum, functional differentiation, transcriptome, metabolome, correlation analysis, multi-omics integration, tissue specificity, coordinated regulation

WANG Jia-bin, HU Yue, CHEN Jia-jie, WANG Meng, HE Xiu-yun, LI Zhi-yong, LI Jian, WANG Mei-na. Combined Metabolomic and Transcriptomic Analysis in Different Parts of Paphiopedilum purpuratum[J]. Biotechnology Bulletin, 2026, 42(6): 279-293.

Figures/Tables 13

References 59

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代谢物类别 Metabolite category	代谢物名称 Metabolite name	SL vs. SF		SL vs. SR		SF vs. SR
代谢物类别 Metabolite category	代谢物名称 Metabolite name	Log₂FC	VIP	Log₂FC	VIP	Log₂FC	VIP
脂质和类脂分子 Lipids and lipid-like molecules	姜糖脂B Gingerglycolipid B	1.95	1.52	6.92	1.19	4.96	1.07
	重楼皂苷 VI Polyphyllin VI	2.51	1.36	6.36	1.63	3.85	1.34
	柴胡皂苷C Saikosaponin C	5.72	1.66	6.06	1.05	/	/
	单酰甘油（18∶3） MAG （18∶3）	/	/	6.01	1.31	5.17	1.71
	海葱苷A Proscillaridin A	5.07	1.68	6.01	1.47	/	/
	知母皂苷A3 Timosaponin A3	/	/	5.95	1.39	5.26	1.50
	脱氧皮质酮21-葡萄糖苷 Deoxycorticosterone 21-glucoside	2.52	1.76	5.76	1.86	3.23	1.25
	羟基积雪草苷 Madecassoside	5.31	1.41	2.78	1.50	/	/
	远志酸 Polygalic acid	3.18	1.60	5.20	1.79	/	/
	香叶基丙酮 Geranylacetone	4.55	1.66	5.13	1.07	/	/
	二十二碳六烯酸 Docosahexaenoic acid	4.93	1.00	3.80	1.17	/	/
	20-羟基蜕皮酮 20-Hydroxyecdysone	4.05	1.43	4.88	1.14	/	/
	二氢玫瑰苷 Dihydroroseoside	4.58	1.84	4.67	1.12	/	/
	茯苓酸B Poricoic acid B	/	/	4.67	1.01	3.84	1.52/
	草乌甲素A Bulleyaconi cine A	/	/	-3.66	1.18	-4.85	2.10
	拉帕醇 Lapachol	-2.75	1.07	-3.81	2.68	/	/
	丹参酚C Danshenol C	/	/	-4.06	1.54	-4.14	1.74
	桦木酮酸 Betulonic acid	2.34	1.17	/	/	-4.32	2.24
	乙酰哈帕苷 Acetylharpagide	/	/	-3.59	1.47	-4.41	1.06
	毒毛旋花苷 Ouabain	/	/	-4.54	1.38	-4.34	1.66
	竹节参皂苷 IVa Chikusetsusponin IVa	3.69	1.67	-1.98	1.69	-4.80	1.10
	8-异前列腺素A2 8-iso Prostaglandin A2	/	/	-4.86	1.73	-5.02	1.72
	马鞭草苷 Verbenalin	1.16	1.04	-5.09	1.15	-6.25	2.02
	亚油酸 Linoleic acid	/	/	-4.58	1.53	-5.61	2.07
	玫瑰苷 Roseoside	/	/	4.67	1.12	-6.34	1.30
	（±）-脱落酸（±）-Abscisic acid	/	/	-6.28	1.49	-6.46	1.47
苯丙类和聚酮类 Phenylpropanoids and polyketides	槲皮素-3β-D-葡萄糖苷 Quercetin-3β-D-glucoside	-7.65	1.84	/	/	8.26	1.31
	山奈酚 Kaempferol	/	/	7.27	1.63	6.60	1.29
	荭草素 Orientin	-1.97	1.13	3.84	1.13	5.81	1.84
	矢车菊素-3-O-葡萄糖苷 Kuromanin	/	/	5.24	1.33	5.15	1.74
	柚皮素 Naringenin	-3.70	1.45	/	/	2.65	1.06
	咖啡酸乙酯 Ethyl caffeate	/	/	-4.13	1.93	-3.10	1.47
	落新妇苷 Astilbin	-1.65	1.30	-4.57	1.48	/	/
	异茴芹素 Isopimpinellin	-4.71	2.03	/	/	4.46	1.00
	曲克芦丁 Troxerutin	-5.37	1.48	-5.72	1.61	/	/
	车前苷 Plantagoside	-6.19	1.28	/	/	3.64	1.32
	毛蕊花糖苷 Verbascoside	/	/	-6.41	1.32	-4.20	1.54
	槲皮素3-O-槐糖苷 Quercetin 3-O-sophoroside	-9.93	1.20	/	/	9.64	1.91

代谢物类别 Metabolite category	代谢物名称 Metabolite name	SL vs. SF		SL vs. SR		SF vs. SR
代谢物类别 Metabolite category	代谢物名称 Metabolite name	Log₂FC	VIP	Log₂FC	VIP	Log₂FC	VIP
脂质和类脂分子 Lipids and lipid-like molecules	姜糖脂B Gingerglycolipid B	1.95	1.52	6.92	1.19	4.96	1.07
	重楼皂苷 VI Polyphyllin VI	2.51	1.36	6.36	1.63	3.85	1.34
	柴胡皂苷C Saikosaponin C	5.72	1.66	6.06	1.05	/	/
	单酰甘油（18∶3） MAG （18∶3）	/	/	6.01	1.31	5.17	1.71
	海葱苷A Proscillaridin A	5.07	1.68	6.01	1.47	/	/
	知母皂苷A3 Timosaponin A3	/	/	5.95	1.39	5.26	1.50
	脱氧皮质酮21-葡萄糖苷 Deoxycorticosterone 21-glucoside	2.52	1.76	5.76	1.86	3.23	1.25
	羟基积雪草苷 Madecassoside	5.31	1.41	2.78	1.50	/	/
	远志酸 Polygalic acid	3.18	1.60	5.20	1.79	/	/
	香叶基丙酮 Geranylacetone	4.55	1.66	5.13	1.07	/	/
	二十二碳六烯酸 Docosahexaenoic acid	4.93	1.00	3.80	1.17	/	/
	20-羟基蜕皮酮 20-Hydroxyecdysone	4.05	1.43	4.88	1.14	/	/
	二氢玫瑰苷 Dihydroroseoside	4.58	1.84	4.67	1.12	/	/
	茯苓酸B Poricoic acid B	/	/	4.67	1.01	3.84	1.52/
	草乌甲素A Bulleyaconi cine A	/	/	-3.66	1.18	-4.85	2.10
	拉帕醇 Lapachol	-2.75	1.07	-3.81	2.68	/	/
	丹参酚C Danshenol C	/	/	-4.06	1.54	-4.14	1.74
	桦木酮酸 Betulonic acid	2.34	1.17	/	/	-4.32	2.24
	乙酰哈帕苷 Acetylharpagide	/	/	-3.59	1.47	-4.41	1.06
	毒毛旋花苷 Ouabain	/	/	-4.54	1.38	-4.34	1.66
	竹节参皂苷 IVa Chikusetsusponin IVa	3.69	1.67	-1.98	1.69	-4.80	1.10
	8-异前列腺素A2 8-iso Prostaglandin A2	/	/	-4.86	1.73	-5.02	1.72
	马鞭草苷 Verbenalin	1.16	1.04	-5.09	1.15	-6.25	2.02
	亚油酸 Linoleic acid	/	/	-4.58	1.53	-5.61	2.07
	玫瑰苷 Roseoside	/	/	4.67	1.12	-6.34	1.30
	（±）-脱落酸（±）-Abscisic acid	/	/	-6.28	1.49	-6.46	1.47
苯丙类和聚酮类 Phenylpropanoids and polyketides	槲皮素-3β-D-葡萄糖苷 Quercetin-3β-D-glucoside	-7.65	1.84	/	/	8.26	1.31
	山奈酚 Kaempferol	/	/	7.27	1.63	6.60	1.29
	荭草素 Orientin	-1.97	1.13	3.84	1.13	5.81	1.84
	矢车菊素-3-O-葡萄糖苷 Kuromanin	/	/	5.24	1.33	5.15	1.74
	柚皮素 Naringenin	-3.70	1.45	/	/	2.65	1.06
	咖啡酸乙酯 Ethyl caffeate	/	/	-4.13	1.93	-3.10	1.47
	落新妇苷 Astilbin	-1.65	1.30	-4.57	1.48	/	/
	异茴芹素 Isopimpinellin	-4.71	2.03	/	/	4.46	1.00
	曲克芦丁 Troxerutin	-5.37	1.48	-5.72	1.61	/	/
	车前苷 Plantagoside	-6.19	1.28	/	/	3.64	1.32
	毛蕊花糖苷 Verbascoside	/	/	-6.41	1.32	-4.20	1.54
	槲皮素3-O-槐糖苷 Quercetin 3-O-sophoroside	-9.93	1.20	/	/	9.64	1.91

比较组 Comparison group	调控方向 Up/Down	基因Gene	Log₂FC	FDR	功能注释 Functional annotation
SL vs. SF	上调 Up	GLDC	15.72	4.40e-32	碳代谢 Carbon metabolism
	上调 Up	LOX1_5	14.59	1.74e-22	脂质代谢和亚油酸代谢 Lipid metabolism and linoleic acid metabolism
	上调 Up	chlH	14.42	4.33e-15	叶绿素合成 Chlorophyll synthesis
	上调 Up	cynT	13.94	1.61e-6	氮代谢 Nitrogen metabolism
	上调 Up	PMA1/PMA2	13.51	4.38e-7	能量代谢 Energy metabolism
	下调 Down	GPAT	-10.00	1.14e-10	脂质代谢 Lipid metabolism
	下调 Down	P5CS	-9.98	1.37e-11	氨基酸代谢 Amino acid metabolism
	下调 Down	pdhC	-9.95	1.23e-7	碳代谢 Carbon metabolism
	下调 Down	ALDH	-9.92	2.47e-9	新陈代谢 Metabolism
	下调 Down	PIP5K	-9.85	5.33e-12	信号转导 Signal transduction
SL vs. SR	上调 Up	nadB	9.99	3.65e-12	新陈代谢 Metabolism
	上调 Up	ALDO	9.30	1.34e-07	新陈代谢 Metabolism
	下调 Down	E1.11.1.7	-14.72	1.04e-22	次生代谢物的生物合成 Biosynthesis of secondary metabolites
	下调 Down	CISZOG	-14.18	2.63e-11	萜类和多酮类化合物的代谢 Terpenoid and polyketide metabolism
	下调 Down	PAL	-13.46	4.69e-9	新陈代谢 Metabolism
	下调 Down	TGA	-11.80	1.37e-7	植物激素信号转导 Plant hormone signal transduction
SF vs. SR	上调 Up	psbS	10.53	1.04e-05	新陈代谢 Metabolism
	上调 Up	FAH	8.10	1.61e-06	脂质代谢 Lipid metabolism
	上调 Up	crtZ	6.94	3.17e-03	次生代谢物的生物合成 Biosynthesis of secondary metabolites
	下调 Down	ROMT	-15.07	1.49e-24	次生代谢物的生物合成 Biosynthesis of secondary metabolites
	下调 Down	HHT1	-14.69	2.42e-23	脂质代谢 Lipid metabolism
	下调 Down	asnB	-13.24	1.58e-07	氨基酸代谢 Amino acid metabolism
	下调 Down	SGT1	-12.89	1.74e-08	聚糖的生物合成与代谢 Glycan biosynthesis and metabolism
	下调 Down	LOX1_5	-8.82	5.84e-09	脂质代谢和亚油酸代谢 Lipid metabolism and linoleic acid metabolism

比较组 Comparison group	调控方向 Up/Down	基因Gene	Log₂FC	FDR	功能注释 Functional annotation
SL vs. SF	上调 Up	GLDC	15.72	4.40e-32	碳代谢 Carbon metabolism
	上调 Up	LOX1_5	14.59	1.74e-22	脂质代谢和亚油酸代谢 Lipid metabolism and linoleic acid metabolism
	上调 Up	chlH	14.42	4.33e-15	叶绿素合成 Chlorophyll synthesis
	上调 Up	cynT	13.94	1.61e-6	氮代谢 Nitrogen metabolism
	上调 Up	PMA1/PMA2	13.51	4.38e-7	能量代谢 Energy metabolism
	下调 Down	GPAT	-10.00	1.14e-10	脂质代谢 Lipid metabolism
	下调 Down	P5CS	-9.98	1.37e-11	氨基酸代谢 Amino acid metabolism
	下调 Down	pdhC	-9.95	1.23e-7	碳代谢 Carbon metabolism
	下调 Down	ALDH	-9.92	2.47e-9	新陈代谢 Metabolism
	下调 Down	PIP5K	-9.85	5.33e-12	信号转导 Signal transduction
SL vs. SR	上调 Up	nadB	9.99	3.65e-12	新陈代谢 Metabolism
	上调 Up	ALDO	9.30	1.34e-07	新陈代谢 Metabolism
	下调 Down	E1.11.1.7	-14.72	1.04e-22	次生代谢物的生物合成 Biosynthesis of secondary metabolites
	下调 Down	CISZOG	-14.18	2.63e-11	萜类和多酮类化合物的代谢 Terpenoid and polyketide metabolism
	下调 Down	PAL	-13.46	4.69e-9	新陈代谢 Metabolism
	下调 Down	TGA	-11.80	1.37e-7	植物激素信号转导 Plant hormone signal transduction
SF vs. SR	上调 Up	psbS	10.53	1.04e-05	新陈代谢 Metabolism
	上调 Up	FAH	8.10	1.61e-06	脂质代谢 Lipid metabolism
	上调 Up	crtZ	6.94	3.17e-03	次生代谢物的生物合成 Biosynthesis of secondary metabolites
	下调 Down	ROMT	-15.07	1.49e-24	次生代谢物的生物合成 Biosynthesis of secondary metabolites
	下调 Down	HHT1	-14.69	2.42e-23	脂质代谢 Lipid metabolism
	下调 Down	asnB	-13.24	1.58e-07	氨基酸代谢 Amino acid metabolism
	下调 Down	SGT1	-12.89	1.74e-08	聚糖的生物合成与代谢 Glycan biosynthesis and metabolism
	下调 Down	LOX1_5	-8.82	5.84e-09	脂质代谢和亚油酸代谢 Lipid metabolism and linoleic acid metabolism