Integrated Transcriptomic and Metabolomic Analysis of Flavonoid Biosynthesis in the Leaves of Ailanthus altissima‘Chaoyang’

doi:10.16420/j.issn.0513-353x.2025-0011

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (11): 2913-2930.doi: 10.16420/j.issn.0513-353x.2025-0011

• Genetic & Breeding · Germplasm Resources · Molecular Biology • Previous Articles Next Articles

Integrated Transcriptomic and Metabolomic Analysis of Flavonoid Biosynthesis in the Leaves of Ailanthus altissima‘Chaoyang’

ZHENG Conghui¹^,², XU Zhenhua¹^,⁴^,^*(), ZHANG Manman²^,³, WANG Yuzhong¹^,², LI Xiangjun¹^,², DU Kejiu³, SUN Ran¹^,², and LI Ya¹^,²

¹ Hebei Academy of Forestry and Grassland Sciences， Shijiazhuang 050061， China
² Hebei Technical Innovation Center for Forest Improved Variety， Shijiazhuang 050061， China
³ College of Forestry， Hebei Agricultural University，Baoding， Hebei 071001， China
⁴ Hebei Forest City Construction Technology Innovation Center， Shijiazhuang 050061， China

Received:2025-06-20 Revised:2025-08-02 Online:2025-11-27 Published:2025-11-27
Contact: XU Zhenhua

Abstract

Abstract:

The leaves from the upper，middle，and lower positions of Ailanthus altissima‘Chaoyang’and common A. altissima were utilized as experimental materials in the study. Ultra- performance liquid chromatography-tandem mass spectrometry（UPLC-MS/MS）and high-throughput RNA sequencing were employed to determine the flavonoid metabolome and transcriptome，respectively. The flavonoid components and their content changes responsible for coloration in the leaves of the two types of A. altissima at different leaf positions were analyzed. Pearson correlation analysis was used to identify potential regulatory genes of key flavonoid metabolites. The results indicated that two chalcone metabolites and four flavonol metabolites were the key flavonoids directly responsible for the yellow coloration in‘Chaoyang’leaves. Two CHSs and one PGT1 were identified as key candidate structural genes regulating chalcone metabolites，while two FLSs，one FG2，and one FG3 were found to be key candidate structural genes catalyzing the synthesis of flavonol metabolites. Cyanidin-3-O-rutinoside was identified as the key anthocyanin that makes the upper leaves of both types of A. altissima redder than the middle and lower leaves，and‘Chaoyang’leaves redder than those of common A. altissima. Two CHSs，three F3Hs，two DFRs，and one CHI were the main candidate structural genes that positively regulated the synthesis of cyanidin-3-O-rutinoside. Regulatory genes encoding transcription factors（two MYBs and one bHLH）are highly likely to activate these above-mentioned positively regulating structural genes，while one MYB and one bHLH are extremely likely to have inhibitory effects.

Key words: Ailanthus altissima, leaf color, flavonoid, metabolome, transcriptome

ZHENG Conghui, XU Zhenhua, ZHANG Manman, WANG Yuzhong, LI Xiangjun, DU Kejiu, SUN Ran, and LI Ya. Integrated Transcriptomic and Metabolomic Analysis of Flavonoid Biosynthesis in the Leaves of Ailanthus altissima‘Chaoyang’[J]. Acta Horticulturae Sinica, 2025, 52(11): 2913-2930.

Figures/Tables 16

References 42

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材料 Material	叶位 Leaf position	样品组代号 Sample group	颜色 Color	颜色代码 Color code
朝阳椿 Chaoyang	1	Y1	中度红橙Moderate reddish orange	N34D
	2	Y2	浅绿黄Light greenish yellow	6D
	3	Y3	亮黄绿Brilliant yellow green	149B
普通臭椿 Common Ailanthus altissima	1	G1	中度橄榄棕色Moderate olive brown	199A
	2	G2	中绿Moderate green	131C
	3	G3	深绿Dark green	136A

材料 Material	叶位 Leaf position	样品组代号 Sample group	颜色 Color	颜色代码 Color code
朝阳椿 Chaoyang	1	Y1	中度红橙Moderate reddish orange	N34D
	2	Y2	浅绿黄Light greenish yellow	6D
	3	Y3	亮黄绿Brilliant yellow green	149B
普通臭椿 Common Ailanthus altissima	1	G1	中度橄榄棕色Moderate olive brown	199A
	2	G2	中绿Moderate green	131C
	3	G3	深绿Dark green	136A

类别 Type	对照组—试验组 Control group— test group	差异代谢物数 Number of differential metabolites		差异基因数 Number of differentially expressed genes
类别 Type	对照组—试验组 Control group— test group	下调 Down-regulated	上调 Up-regulated	下调 Down-regulated	上调 Up-regulated
朝阳椿 Chaoyang	Y1-Y2	50	63	4 266	5 617
	Y1-Y3	69	67	12 219	11 431
	Y2-Y3	39	35	6 763	4 828
普通臭椿 Common Ailanthus altissima	G1-G2	42	117	7 968	8 265
	G1-G3	55	112	13 997	10 841
	G2-G3	56	58	7 932	6 036
普通臭椿和‘朝阳椿’ Common A. altissima and Chaoyang	G1-Y1	51	102	4 969	4 558
	G2-Y2	55	57	6 720	8 249
	G3-Y3	62	55	7 970	10 096

类别 Type	对照组—试验组 Control group— test group	差异代谢物数 Number of differential metabolites		差异基因数 Number of differentially expressed genes
类别 Type	对照组—试验组 Control group— test group	下调 Down-regulated	上调 Up-regulated	下调 Down-regulated	上调 Up-regulated
朝阳椿 Chaoyang	Y1-Y2	50	63	4 266	5 617
	Y1-Y3	69	67	12 219	11 431
	Y2-Y3	39	35	6 763	4 828
普通臭椿 Common Ailanthus altissima	G1-G2	42	117	7 968	8 265
	G1-G3	55	112	13 997	10 841
	G2-G3	56	58	7 932	6 036
普通臭椿和‘朝阳椿’ Common A. altissima and Chaoyang	G1-Y1	51	102	4 969	4 558
	G2-Y2	55	57	6 720	8 249
	G3-Y3	62	55	7 970	10 096

数据库 Database	基因数 Number of genes	百分比/% Percentage
KEGG	68 246	41.33
Nr	93 228	56.45
SwissProt	66 292	40.14
TrEMBL	92 691	56.13
KOG	55 423	33.56
GO	77 384	46.86
Pfam	60 460	36.61
至少在一个数据库中有注释的基因 Annotated in at least one database	94 616	57.30
基因总数 Total unigenes	165 137	100.00

Integrated Transcriptomic and Metabolomic Analysis of Flavonoid Biosynthesis in the Leaves of Ailanthus altissima‘Chaoyang’

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类目 Category	代谢物 Metabolites	结构基因 Structual genes	转录因子基因 TF encoding genes
花青素 Anthocyanidins	矢车菊素-3-O-芸香糖苷 Cyanidin-3-O-rutinoside；飞燕草素-3-O-葡萄糖苷^* Delphinidin-3-O-glucoside	CHS-5；CHS-8；F3H-1；F3H-2；F3H-3；DFR-2；DFR-1；CHI-6	MYB-4；bHLH-2；MYB-6；MYB-5；bHLH-3
查尔酮Chalcones	柚皮素查尔酮 Naringenin chalcone；根皮苷 Phlorizin	CHS5；CHS8；PGT1-1	-
黄酮醇 Flavonols	紫云英苷* Astragalin；异槲皮苷 Isoquercitrin；芦丁* Rutin；白麻苷 Baimaside	FLS-1；FLS-2；FG2-1；FG3-2	-

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[2]	YU Cannan, GUO Anfang, LU Chun, MIAO Hongjun, HOU Xiaoyu, YUAN Tianyi, LIU Guoyuan, WEI Hui, ZHANG Jian, and YU Chunmei. Identification and Development of SNP Markers for Lagerstroemia indica Leaf Color Based on Transcriptome and Genome Analysis [J]. Acta Horticulturae Sinica, 2025, 52(7): 1803-1816.
[3]	YANG Chunmei, YU Yang, DING Yuge, XIA Jing, ZHOU Ling, and PENG Lei. Joint Transcription-Metabolism Analysis of Starch and Sucrose Metabolic Pathways in the Transformation of Axillary Buds into Flower Buds of ‘Guifei’Mango [J]. Acta Horticulturae Sinica, 2025, 52(6): 1412-1426.
[4]	GUO Xinmiao, TIAN Luyao, CAO Jiaqi, XIE Yan, GAO Yanxia, and SUN Zhichao. Preliminary Research on the Molecular Mechanism of Color Loss in White Mulberry Fruit [J]. Acta Horticulturae Sinica, 2025, 52(6): 1451-1462.
[5]	LI Ziyan, CHEN Weixi, LI Zihan, LI Yin, LIANG Fengming, ZENG Xiangli, JIAN Hongju, and LÜ Dianqiu. Screening Candidate Genes Controlling Potato Maturation Time Based on RNA-Seq [J]. Acta Horticulturae Sinica, 2025, 52(6): 1505-1518.
[6]	ZHANG Yue, FENG Yiliao, WANG Bei, REN Wenjing, JIANG Chunyu, ZHAO Xinyu, WANG Caihong, YANG Limei, ZHUANG Mu, LÜ Honghao, WANG Yong, ZHANG Yangyong, JI Jialei. Preliminary Transcriptome Analysis of Folate Synthesis and Metabolism in Cabbage [J]. Acta Horticulturae Sinica, 2025, 52(5): 1301-1316.
[7]	YUAN Juanwei, JIA Li, WANG Han, YAN Congsheng, ZHANG Qi’an, YU Feifei, GAN Defang, JIANG Haikun. Screening of Resistant Germplasm and Identifying Candidate Gene for Phytophthora capsici Resistance in Pepper Germplasm Resources [J]. Acta Horticulturae Sinica, 2025, 52(4): 857-871.
[8]	ZHANG Yiying, ZHANG Yu, CHU Yunxia, CHEN Hairong, DENG Shan, LI Aiai, ZHAO Hong, LIU Kun, HAN Ruixi, REN Li. Color Characteristics of Broccoli and Cauliflower Leaves Based on the Colorimeter Parameters [J]. Acta Horticulturae Sinica, 2025, 52(4): 872-882.
[9]	TANG Lingli, HE Yuhua, WANG Qingtao, AN Lulu, XU Yongyang, ZHANG Jian, KONG Weihu, HU Keyun, ZHAO Guangwei. Hormonal and Transcriptome Analysis of Ripe Fruits of Non-Climacteric and Climacteric Melon [J]. Acta Horticulturae Sinica, 2025, 52(4): 883-896.
[10]	SHAO Yifan, ZHU Baoqing, WANG Tongxin, LIAO Jianhe, WU Fanhua, YANG Siyi, FENG Jianhang, YU Xudong. Research of Genetic Regulation of Bombax ceiba Prickle Based on Hormone，Transcriptome and Metabolome [J]. Acta Horticulturae Sinica, 2025, 52(4): 933-946.
[11]	LIN Ruxue, WANG Fei, ZHANG Yanjie, MA Li, LIU Xiaofeng, LI Shuran, LIU Yalong, WANG Chen, JIANG Shuling, OU Chunqing. Transcriptome Screening and Functional Analysis of Dwarf Related Genes in Pear [J]. Acta Horticulturae Sinica, 2025, 52(3): 545-560.
[12]	FENG Kezheng, WANG Kang, WANG Yongkang, ZHAO Longlong, LIAO Na, TANG Xiaoyan, WANG Wenjie, WANG Chenggang, YUAN Lingyun, HOU Jinfeng, WU Jianqiang, and CHEN Guohu. Identification and Functional Analysis of Key Gene for Male Sterility in Wucai [J]. Acta Horticulturae Sinica, 2025, 52(11): 2876-2888.
[13]	FAN Amei, JIN Yaxin, HE Longjiao, LI Qi, ZHANG Yanqing, SHAO Qi, SONG Yun, NIU Yanbing, and QIAO Yonggang. Effects of Gibberellin on the Growth and Development of Forsythia suspensa Heterostyly [J]. Acta Horticulturae Sinica, 2025, 52(11): 3016-3030.
[14]	LI Hui, KAN Jialiang, LI Xiaogang, WANG Zhonghua, LIN Jing, YANG Qingsong. Effect of Gibberellin on Wizened Flower Buds Formation of Pyrus pyrifolia Cultivar‘Sucui 1’During the Growing Season [J]. Acta Horticulturae Sinica, 2025, 52(10): 2713-2726.
[15]	LI Jie, WU Chao, JIA Xiangqian, WANG Juan. Screening of Ziziphus jujuba‘Hupingzao’Fruit Coloring Substances and Their Related Genes [J]. Acta Horticulturae Sinica, 2024, 51(8): 1728-1742.