Integrated Transcriptome and Metabolome Analysis to Explore the Carotenoid Synthesis and Metabolism Mechanism in Anoectochilus roxburghii under Different Shading Conditions

doi:10.13560/j.cnki.biotech.bull.1985.2024-1007

Abstract

Abstract:

Objective To explore the effects of different shading conditions on the biosynthesis and metabolism of carotenoids in Anoectochilus roxburghii and to decipher the molecular mechanisms underlying carotenoid accumulation. Method Anoectochilus roxburghii was used as the experimental material, and the leaves from different shading treatments (T1: 25% shading, T2: 50% shading, T3: 75% shading) were selected. High-throughput RNA sequencing technology (RNA-Seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were employed to obtain transcriptomic and metabolomic data of A. roxburghii. Bioinformatics analysis was conducted to identify and quantify differentially expressed genes and metabolites, and to explore their relationships. Result Under different shading conditions, a total of 20 differentially expressed genes and 21 differential metabolites were identified. The significant expressions of key enzyme genes such as ZEP, LUT5, LUT1, LCYE, and NCED1 regulated the changes in metabolites like zeaxanthin, neoxanthin, and violaxanthin, with the highest content under the 75% shading treatment. Additionally, 22 transcription factors were predicted to regulate 14 differentially expressed genes, including ZEP, ZDS, and CYP707A, with 15 transcription factors responding to abscisic acid, gibberellins, and other plant hormone elements involved in the regulation of carotenoid biosynthesis. Eight differentially expressed genes involved in carotenoid biosynthesis were selected for RT-qPCR validation, and the results indicated that the expression trends of these 8 genes were consistent with the sequencing results. Conclusion Under different shading conditions, a total of 15 transcription factors in the leaves of A. roxburghii responded to five types of plant hormone elements, thereby regulating the expression of differentially expressed genes such as ZEP, NCED1, and CCD7, leading to significant accumulation of carotenoid-related metabolites such as zeaxanthin and lutein under 75% shading treatment.

Key words: Anoectochilus roxburghii, shading, carotenoids, transcriptome, metabolome, transcription factors, plant hormone elements

HU Ruo-qun, ZENG Jing-jing, LIANG Wan-feng, CAO Jia-yu, HUANG Xiao-wei, LIANG Xiao-ying, QIU Ming-yue, CHEN Ying. Integrated Transcriptome and Metabolome Analysis to Explore the Carotenoid Synthesis and Metabolism Mechanism in Anoectochilus roxburghii under Different Shading Conditions[J]. Biotechnology Bulletin, 2025, 41(5): 231-243.

Figures/Tables 10

References 51

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基因名称Gene name	基因ID Gene ID	正向引物 Forward primer （5′-3′）	反向引物 Revese primer（5′-3′）
Actin	Reference gene	AGCATGAAGATTAAGGTGGTTG	CTGAGAGAAGCAAGGATGGA
CYP707A	TRINITY_DN8883_c0_g1	TCCAGCGCGGAGAATATCAC	GTGTTGATGAGGCGGCTTTC
CCD7	TRINITY_DN10188_c0_g1	CGATGCTGAAAGAACAGCCG	CCAAAGGCAGAACAACCTGC
NCED1	TRINITY_DN9311_c2_g1	TTCAGACTACTCGCCGCTTC	TGGTTCAGGCCGTCTTTCTC
LUT5	TRINITY_DN2482_c0_g1	CCTGTTGAAAGCTCAGAGGC	ATGCAGAATGGAACCCAGGTG
LUT1	TRINITY_DN1083_c0_g1	ATCCCAGTGGCTAATGCTCG	TGATGACGACGAAGTCACGG
ZEP	TRINITY_DN5360_c0_g1	GGCGACGAGCTCAGGAATAA	CTCAACTGCACGGACTTCCT
AOG	TRINITY_DN513_c0_g1	TCGGCTATGCCATGTATCCG	TGATATGCCTCTGAACCGCC
ZDS	TRINITY_DN1558_c1_g1	GCAGGACTACATCGACAGCA	CTCATTGGCTAGTGCCTCGT

基因名称Gene name	基因ID Gene ID	正向引物 Forward primer （5′-3′）	反向引物 Revese primer（5′-3′）
Actin	Reference gene	AGCATGAAGATTAAGGTGGTTG	CTGAGAGAAGCAAGGATGGA
CYP707A	TRINITY_DN8883_c0_g1	TCCAGCGCGGAGAATATCAC	GTGTTGATGAGGCGGCTTTC
CCD7	TRINITY_DN10188_c0_g1	CGATGCTGAAAGAACAGCCG	CCAAAGGCAGAACAACCTGC
NCED1	TRINITY_DN9311_c2_g1	TTCAGACTACTCGCCGCTTC	TGGTTCAGGCCGTCTTTCTC
LUT5	TRINITY_DN2482_c0_g1	CCTGTTGAAAGCTCAGAGGC	ATGCAGAATGGAACCCAGGTG
LUT1	TRINITY_DN1083_c0_g1	ATCCCAGTGGCTAATGCTCG	TGATGACGACGAAGTCACGG
ZEP	TRINITY_DN5360_c0_g1	GGCGACGAGCTCAGGAATAA	CTCAACTGCACGGACTTCCT
AOG	TRINITY_DN513_c0_g1	TCGGCTATGCCATGTATCCG	TGATATGCCTCTGAACCGCC
ZDS	TRINITY_DN1558_c1_g1	GCAGGACTACATCGACAGCA	CTCATTGGCTAGTGCCTCGT

代谢物 Metabolite	分子式 Molecular formula	KEGG注释编号 KEGG annotation number
二氢菜豆酸 Dihydrophaseic acid	C₁₅H₂₂O₅	C15971
植物预黄质二磷酸 Prephytoene diphosphate	C₄₀H₆₈O₇P₂	C03427
黄质醛酸 Xanthoxic acid	C₁₅H₂₂O₄	C13454
圆酵母素Torulene	C₄₀H₅₄	C08613
念珠藻黄素 Nostoxanthin	C₄₀H₅₆O₄	C16284
羟基氯菌烯葡萄糖苷 Hydroxychlorobactene glucoside	C₄₆H₆₄O₆	C15914
环氧玉米黄质 Antheraxanthin	C₄₀H₅₆O₃	C08579
辣椒玉红素 Capsorubin	C₄₀H₅₆O₄	C08585
角黄素 Canthaxanthin	C₄₀H₅₂O₂	C08583
金盏花黄质 Adonixanthin	C₄₀H₅₄O₃	C15968
新黄质 Neoxanthin	C₄₀H₅₆O₄	C08606
9-顺式-10'-Apo-β-胡萝卜素 9-cis-10'-Apo-beta-Carotenal	C₂₇H₃₆O	C20692
玉米黄质二葡萄糖苷 Zeaxanthin diglucoside	C₅₂H₇₆O₁₂	C15969
脱落酸葡萄糖酯 Abscisic acid glucose ester	C₂₁H₃₀O₉	C15970
独脚金内酯 ABC-环 Strigolactone ABC-rings	C₁₄H₁₈O₃	C18036
4，4'-二聚苯二醛 4，4'-Diapolycopenedial	C₃₀H₃₆O₂	C19798
葡萄球菌黄质 Staphyloxanthin	C₅₁H₇₈O₈	C16148
羟基氯菌烯 Hydroxychlorobactene	C₄₀H₅₄O	C15911
玉米黄质 Zeaxanthin	C₄₀H₅₆O₂	C06098
3-羟基海胆酮 3-Hydroxyechinenone	C₄₀H₅₄O₂	C15966
（3S，2'S）-4-酮米索2'-α-L-岩藻糖苷（3S，2'S）-4-Ketomyxol 2'-alpha-L-fucoside	C₄₆H₆₄O₈	C15942

代谢物 Metabolite	分子式 Molecular formula	KEGG注释编号 KEGG annotation number
二氢菜豆酸 Dihydrophaseic acid	C₁₅H₂₂O₅	C15971
植物预黄质二磷酸 Prephytoene diphosphate	C₄₀H₆₈O₇P₂	C03427
黄质醛酸 Xanthoxic acid	C₁₅H₂₂O₄	C13454
圆酵母素Torulene	C₄₀H₅₄	C08613
念珠藻黄素 Nostoxanthin	C₄₀H₅₆O₄	C16284
羟基氯菌烯葡萄糖苷 Hydroxychlorobactene glucoside	C₄₆H₆₄O₆	C15914
环氧玉米黄质 Antheraxanthin	C₄₀H₅₆O₃	C08579
辣椒玉红素 Capsorubin	C₄₀H₅₆O₄	C08585
角黄素 Canthaxanthin	C₄₀H₅₂O₂	C08583
金盏花黄质 Adonixanthin	C₄₀H₅₄O₃	C15968
新黄质 Neoxanthin	C₄₀H₅₆O₄	C08606
9-顺式-10'-Apo-β-胡萝卜素 9-cis-10'-Apo-beta-Carotenal	C₂₇H₃₆O	C20692
玉米黄质二葡萄糖苷 Zeaxanthin diglucoside	C₅₂H₇₆O₁₂	C15969
脱落酸葡萄糖酯 Abscisic acid glucose ester	C₂₁H₃₀O₉	C15970
独脚金内酯 ABC-环 Strigolactone ABC-rings	C₁₄H₁₈O₃	C18036
4，4'-二聚苯二醛 4，4'-Diapolycopenedial	C₃₀H₃₆O₂	C19798
葡萄球菌黄质 Staphyloxanthin	C₅₁H₇₈O₈	C16148
羟基氯菌烯 Hydroxychlorobactene	C₄₀H₅₄O	C15911
玉米黄质 Zeaxanthin	C₄₀H₅₆O₂	C06098
3-羟基海胆酮 3-Hydroxyechinenone	C₄₀H₅₄O₂	C15966
（3S，2'S）-4-酮米索2'-α-L-岩藻糖苷（3S，2'S）-4-Ketomyxol 2'-alpha-L-fucoside	C₄₆H₆₄O₈	C15942

基因 Gene	缩写 Abbreviation	基因ID Gene ID	酶编号 EC number	KO号 Enzyme KO
（+）-脱落酸8'-羟化酶（+）-abscisic acid 8'-hydroxylase	CYP707A	TRINITY_DN13073_c0_g1	［EC：1.14.14.137］	K09843
		TRINITY_DN1970_c0_g1	［EC：1.14.14.137］	K09843
		TRINITY_DN8883_c0_g2	［EC：1.14.14.137］	K09843
		TRINITY_DN25069_c0_g1	［EC：1.14.14.137］	K09843
		TRINITY_DN5389_c0_g1	［EC：1.14.14.137］	K09843
		TRINITY_DN8883_c0_g1	［EC：1.14.14.137］	K09843
玉米黄质环氧化酶 Zeaxanthin epoxidase	ZEP	TRINITY_DN5360_c0_g1	［EC：1.14.15.21］	K09838
玉米黄质环氧化酶 Zeaxanthin epoxidase	ZEP	TRINITY_DN11443_c0_g1	［EC：1.14.15.21］	K09838
9-顺式-β-胡萝卜素9'，10'-裂解双加氧酶 10-9-cis-beta-carotene 9'，10'-cleaving dioxygenase	CCD7	TRINITY_DN10188_c0_g1	［EC：1.13.11.68］	K17912
	CCD7	TRINITY_DN8303_c0_g1	［EC：1.13.11.68］	K17912
β-胡萝卜素异构酶 Beta-carotene isomerase	DWARF27	TRINITY_DN5387_c0_g1	［EC：5.2.1.14］	K17911
β-胡萝卜素异构酶 Beta-carotene isomerase	DWARF27	TRINITY_DN840_c0_g1	［EC：5.2.1.14］	K17911
9-顺式环氧类胡萝卜素双加氧酶 9-cis-epoxycarotenoid dioxygenase	NCED1	TRINITY_DN1390_c0_g1	［EC：1.13.11.51］	K09840
		TRINITY_DN562_c3_g1	［EC：1.13.11.51］	K09840
		TRINITY_DN9311_c2_g1	［EC：1.13.11.51］	K09840
ε-胡萝卜素羟化酶 Carotenoid epsilon hydroxylase	LUT1	TRINITY_DN1083_c0_g1	［EC：1.14.14.158］	K09837
β-胡萝卜素环羟化酶 Beta-ring hydroxylase	LUT5	TRINITY_DN2482_c0_g1	［EC：1.14.-.-］	K15747
胡萝卜素去饱和酶 Zeta-carotene desaturase	ZDS	TRINITY_DN1558_c1_g1	［EC：1.3.5.6］	K00514
番茄红素ε环化酶 Lycopene epsilon-cyclase	LCYE	TRINITY_DN29073_c0_g1	［EC：5.5.1.18］	K06444
脱落酸β-葡萄糖基转移酶 Abscisate beta-glucosyltransferase	AOG	TRINITY_DN513_c0_g1	［EC：2.4.1.263］	K14595