新疆阿魏不同部位转录组特征分析及倍半萜合成相关基因挖掘

doi:10.13560/j.cnki.biotech.bull.1985.2025-0452

生物技术通报 ›› 2025, Vol. 41 ›› Issue (12): 280-293.doi: 10.13560/j.cnki.biotech.bull.1985.2025-0452

新疆阿魏不同部位转录组特征分析及倍半萜合成相关基因挖掘

司旭鹏¹^,²(), 崔秀文¹^,², 欧阳荔枝³, 房丹丹¹^,², 裴龙英¹^,², 方贵平¹^,², 濮希蕾¹^,², 马艺沔³, 张争³()

^1.新疆理工学院食品安全与营养实验教学示范中心，阿克苏 843100
^2.新疆黑木耳工程技术研究中心，阿克苏 843100
^3.中国医学科学院北京协和医学院药用植物研究所，北京 100193

收稿日期:2025-05-01 出版日期:2025-12-26 发布日期:2026-01-06
通讯作者: 张争，男，博士，研究员，研究方向：药用植物次生代谢调控；E-mail: zhangzheng@implad.ac.cn
作者简介:司旭鹏，男，硕士，讲师，研究方向：药用植物次生代谢调控；E-mail: sixupeng0527@163.com
崔秀文同为本文第一作者
基金资助:
新疆理工学院校级科研项目(ZZ202403);国家重点研发计划项目(2022YFC3501502);中国医学科学院医学与健康科技创新工程项目(2022-I2M-1-017)

Transcriptome Analysis of Different Parts of Ferula Sinkiangensis K. M. Shen and Exploration of Genes Related to Sesquiterpene Synthesis

SI Xu-peng¹^,²(), CUI Xiu-wen¹^,², OUYANG Li-zhi³, FANG Dan-dan¹^,², PEI Long-ying¹^,², FANG Gui-ping¹^,², PU Xi-lei¹^,², MA Yi-mian³, ZHANG Zheng³()

^1.Experimental Teaching Demonstration Center of Food Safety and Nutrition, Xinjiang Institute of Technology, Akesu 843100
^2.Xinjiang Auricularia Engineering Technology Research Center, Akesu 843100
^3.Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193

Received:2025-05-01 Published:2025-12-26 Online:2026-01-06

摘要/Abstract

摘要：

目的分析新疆阿魏不同部位的转录组信息，发掘倍半萜类成分生物合成关键代谢通路和调控基因，为新疆阿魏分子育种和资源开发提供基因资源。方法通过转录组测序获得新疆阿魏根茎叶不同部位的Unigenes序列，并进行生物信息学分析。结果经过转录组测序共获得116 517个transcripts，共有44 896条Unigenes序列被注释，新疆阿魏与胡萝卜亚种（Daucus carota subsp. sativus）具有的同源序列匹配度比例最高。19 290个Unigenes被注释于生物过程、细胞组成和分子功能。通过KEGG富集到萜类和聚酮化合物代谢通路（11个通路，204条Unigenes）和其他次生代谢产物合成通路（17个通路，233条Unigenes），进一步研究发现，与倍半萜类合成相关的Unigenes为57个，涉及9个关键酶基因的34条全长转录本。差异表达基因主要富集在MEP途径，6个表达趋势变化明显的酶基因RT-qPCR结果与RNA-seq结果呈现相似的表达模式。表达分析显示倍半萜合成下游关键基因P450和TPS在根中相对表达量最高，DXS和HMGR在叶中的表达量最高，AACT和DXR在茎中表达量最高。同时，转录组共预测到28 017个CDS序列，18 86个转录因子，14 277个SSR位点及9 844对相应引物。结论通过转录组分析明确了新疆阿魏倍半萜类物质的生物合成途径，推测根中P450和TPS为倍半萜合成下游关键基因。

关键词: 新疆阿魏, 转录组, 次生代谢, 代谢通路, SSR

Abstract:

Objective By analyzing the transcriptome information of different parts of Ferula sinkiangensis, we aim to explore the key metabolic pathways and regulatory genes involved in the biosynthesis of sesquiterpenes, providing genetic resources for molecular breeding and resource development of F. sinkiangensis Method The Unigene sequences of different parts of the roots, stems and leaves of F. sinkiangensis were obtained by transcriptome sequencing, and bioinformatics analysis was carried out. Result A total of 116 517 transcripts were obtained by transcriptome sequencing, and a total of 44 896 Unigene sequences were annotated. F. sinkiangensis has the highest proportion of homologous sequence matching with Daucus carota subsp. sativus. A total of 19 290 Unigenes were annotated in biological processes, cell composition and molecular function. The metabolic pathways of terpenoids and polyketides (11 pathways, 204 Unigenes) and other secondary metabolite synthesis pathways (17 pathways, 233 Unigenes) were enriched by KEGG. Further studies showed that 57 Unigenes were related to sesquiterpene synthesis, involving 34 full-length transcripts of 9 key enzyme genes. The differentially expressed genes were mainly enriched in the MEP pathway, and the RT-qPCR results of six enzyme genes with obvious expression trends showed similar expression patterns with the RNA-seq results. The expression analysis showed that the relative expressions of P450 and TPS, the key genes downstream of sesquiterpene synthesis, were the highest in the roots, the expressions of DXS and HMGR were the highest in the leaves, and the expressions of AACT and DXR were the highest in the stems. Meanwhile, a total of 28 017 CDS sequences, 1 886 transcription factors, 14 277 SSR loci and 9 844 pairs of corresponding primers were predicted in the transcriptome. Conclusion Through transcriptome analysis, the biosynthetic pathway of sesquiterpenes in F. sinkiangensis is clarified, and it is speculated that P450 and TPS in the roots are the key downstream genes of sesquiterpene synthesis.

Key words: Ferula sinkiangensis K. M. Shen, transcriptome, secondary metabolism, metabolic pathway, SSR

司旭鹏, 崔秀文, 欧阳荔枝, 房丹丹, 裴龙英, 方贵平, 濮希蕾, 马艺沔, 张争. 新疆阿魏不同部位转录组特征分析及倍半萜合成相关基因挖掘[J]. 生物技术通报, 2025, 41(12): 280-293.

SI Xu-peng, CUI Xiu-wen, OUYANG Li-zhi, FANG Dan-dan, PEI Long-ying, FANG Gui-ping, PU Xi-lei, MA Yi-mian, ZHANG Zheng. Transcriptome Analysis of Different Parts of Ferula Sinkiangensis K. M. Shen and Exploration of Genes Related to Sesquiterpene Synthesis[J]. Biotechnology Bulletin, 2025, 41(12): 280-293.

图/表 14

参考文献 37

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基因名 Gene name	基因ID Gene ID	引物序列 Primer sequence （5′-3′）
P450	Cluster-8529.5884-F	CGGTCCGAGAAGTTATGGGG
	Cluster-8529.5884-R	TGGCAACCACCCTCTTCATC
DXS	Cluster-8529.15434-F	GCTGGACATGGGTGTATGCT
	Cluster-8529.15434-R	CTGGAGTTTTGCTCCCCCAT
AACT	Cluster-8529.15178-F	CTGCGGTTAAATCTGCTGGT
	Cluster-8529.15178-R	GTTACTCCCAAAGGATGCCCC
TPS	Cluster-8529.5582-F	TACTGGATGATGAGGGAGCGA
	Cluster-8529.5582-R	ACAATACGAGTGGAGCCGC
HMGR	Cluster-8529.7778-F	TTCGAGACGCTTGCACTCAT
	Cluster-8529.7778-R	TTGCATCCCCAGTGCTACAG
DXR	Cluster-8529.20686-F	TGTCAGAAGCACCAAGACGA
	Cluster-8529.20686-R	TACAAGAGCGGGACTCAAGC
Actin	Actin-F	TGGTATTGTGCTGGATTCTGGT
	Actin-R	TGAGATCACCACCAGCAAGG

基因名 Gene name	基因ID Gene ID	引物序列 Primer sequence （5′-3′）
P450	Cluster-8529.5884-F	CGGTCCGAGAAGTTATGGGG
	Cluster-8529.5884-R	TGGCAACCACCCTCTTCATC
DXS	Cluster-8529.15434-F	GCTGGACATGGGTGTATGCT
	Cluster-8529.15434-R	CTGGAGTTTTGCTCCCCCAT
AACT	Cluster-8529.15178-F	CTGCGGTTAAATCTGCTGGT
	Cluster-8529.15178-R	GTTACTCCCAAAGGATGCCCC
TPS	Cluster-8529.5582-F	TACTGGATGATGAGGGAGCGA
	Cluster-8529.5582-R	ACAATACGAGTGGAGCCGC
HMGR	Cluster-8529.7778-F	TTCGAGACGCTTGCACTCAT
	Cluster-8529.7778-R	TTGCATCCCCAGTGCTACAG
DXR	Cluster-8529.20686-F	TGTCAGAAGCACCAAGACGA
	Cluster-8529.20686-R	TACAAGAGCGGGACTCAAGC
Actin	Actin-F	TGGTATTGTGCTGGATTCTGGT
	Actin-R	TGAGATCACCACCAGCAAGG

序号 Serial number	通路ID Pathway ID	代谢通路 Metabolic pathway	数量 Quantity
1	ko00523	Polyketide sugar unit biosynthesis	3
2	ko00900	Terpenoid backbone biosynthesis	59
3	ko00902	Monoterpenoid biosynthesis	7
4	ko00903	Limonene degradation	12
5	ko00904	Diterpenoid biosynthesis	24
6	ko00905	Brassinosteroid biosynthesis	18
7	ko00906	Carotenoid biosynthesis	33
8	ko00908	Zeatin biosynthesis	34
9	ko00909	Sesquiterpenoid and triterpenoid biosynthesis	15
10	ko01051	Biosynthesis of ansamycins	2
11	ko01053	Biosynthesis of siderophore group nonribosomal peptides	1

序号 Serial number	通路ID Pathway ID	代谢通路 Metabolic pathway	数量 Quantity
1	ko00523	Polyketide sugar unit biosynthesis	3
2	ko00900	Terpenoid backbone biosynthesis	59
3	ko00902	Monoterpenoid biosynthesis	7
4	ko00903	Limonene degradation	12
5	ko00904	Diterpenoid biosynthesis	24
6	ko00905	Brassinosteroid biosynthesis	18
7	ko00906	Carotenoid biosynthesis	33
8	ko00908	Zeatin biosynthesis	34
9	ko00909	Sesquiterpenoid and triterpenoid biosynthesis	15
10	ko01051	Biosynthesis of ansamycins	2
11	ko01053	Biosynthesis of siderophore group nonribosomal peptides	1

骨架 Skeleton	名称 Name	数量 Quantity	FPKM （Fragments Per）
萜类骨架 Terpenoid skeleton（59）ko00900	Geranylgeranyl pyrophosphate synthase	3	6.62-14.69
	Farnesol kinase	1	4.79-7.41
	2-C-methyl-D-erythritol 2，4-cyclodiphosphate synthase （MDS）	1	5.3-6.11
	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase （MCT）	3	10.67-29.75
	Prenyl protein peptidase	1	3.66-6.47
	Diphosphomevalonate decarboxylase （MVD）	2	4.33-10.76
	Hydroxymethylglutaryl-CoA synthase （HMGCS）	2	6.53-37.72
	Farnesylcysteine lyase	1	39-45.25
	Geranylgeranyl diphosphate reductase	2	3.17-46.74
	Acetyl-CoA C-acetyltransferase （ACAT）	1	23.22-41.51
	Polycis-polyprenyl diphosphate synthase	2	2.29-22.71
	Geranyl diphosphate synthase （GPS）	3	0.39-14.17
	4-Hydroxy-3-methylbut-2-enyl diphosphate reductase （HDR）	5	0.1-25.06
	Hypothetical protein	1	0.38-1.52
	1-Deoxy-D-xylulose-5-phosphate synthase （DXS）	3	3.58-43.29
	3-Hydroxy-3-methylglutaryl-coenzyme A reductase （HMGR）	3	0.43-60.75
	4-Hydroxy-3-methylbut-2-enyl-diphosphate synthase （HXS）	1	25.93-42.74
	CAAX prenyl protease	1	60.08-65.9
	Mevalonate kinase （MK）	1	16.24-18.02
	Phosphomevalonate kinase （MVK2）	1	8.52-11.37
	Isopentenyl-diphosphate Delta-isomerase	1	75.21-102.72
	Acetyl-CoA C-acetyltransferase	4	0.16-83.75
	Protein-S-isoprenylcysteine O-methyltransferase （STE14）	1	10.42-17.69
	Isopentenyl phosphate kinase	1	8.28-10.05
	Farnesyl diphosphate synthase （FDPS）	1	5.67-7.64
	Dihydroflavonol-4-reductase	3	0.42-18.19
	Prenylcysteine alpha-carboxyl methylesterase	1	3.53-4.22
	Protein farnesyltransferase/geranylgeranyltransferase	1	13.1-14.01
	Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase	1	6.66-8.04
	4-Diphosphocytidyl-2-C-methyl-D-erythritol kinase （CMK）	1	12.65-15.84
	Solanesyl-diphosphate synthase	1	2.35-3.24
	Protein farnesyltransferase subunit beta （FNTB）	1	8.47-9.76
	Ditrans，polycis-polyprenyl diphosphate synthase	1	11.54-14.64
	Prenyl protease	1	12.7-13.94
倍半萜及三萜生物合成 Biosynthesis of sesquiterpenes and triterpenes（15）ko00909	Sesquiterpene synthase	3	0.33-10.01
	Beta-amyrin synthase	2	1.05-3.53
	Squalene epoxidase	4	0.14-32.06
	Dihydroflavonol-4-reductase	3	0.16-18.19
	Squalene synthase	2	0.42-58.1
	（3S， 6E）-Nerolidol synthase	1	1.97-3.91

新疆阿魏不同部位转录组特征分析及倍半萜合成相关基因挖掘

Transcriptome Analysis of Different Parts of Ferula Sinkiangensis K. M. Shen and Exploration of Genes Related to Sesquiterpene Synthesis

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参考文献 37

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重复基序数目 Number of repeated motifs	SSR位点数目 Number of SSR loci						总数量 Total quantity
重复基序数目 Number of repeated motifs	单核苷酸 Single nucleotide	二核苷酸 Dinucleotide	三核苷酸 Trinucleotide	四核苷酸 Tetranucleotide	五核苷酸 Pentanucleotide	六核苷酸 Hexanucleotide	总数量 Total quantity
5	0	0	844	96	27	41	1 008
6	0	1800	371	36	8	5	2 220
7	0	1208	181	18	0	4	1 411
8	0	939	83	5	0	3	1 030
9	0	757	60	1	0	0	818
10	5	534	42	0	0	0	581
11	6	338	3	0	0	0	347
12	7	280	9	1	0	0	297
13	8	202	9	0	0	0	219
14	9	227	6	0	0	0	242
15	15	153	5	1	0	0	174
16	17	66	1	0	0	0	84
17	19	72	1	0	0	1	93
18	21	86	3	0	0	0	110
19	23	51	2	0	0	0	76
20	30	54	2	0	0	0	86
＞20	198	125	6	0	0	0	329
总数量	358	6 892	1 628	158	35	54	9 125

[1]	刘建国, 刘格儿, 郭颖欣, 王斌, 王玉昆, 卢金凤, 黄文庭, 朱云娜. 转录组和代谢组联合解析‘桂柚1号’和‘沙田柚’果实品质差异[J]. 生物技术通报, 2025, 41(9): 168-181.
[2]	刘泽洲, 段乃彬, 岳丽昕, 王清华, 姚行浩, 高莉敏, 孔素萍. 大蒜叶片蜡质成分分析及蜡质缺失基因Ggl-1筛选[J]. 生物技术通报, 2025, 41(9): 219-231.
[3]	闫梦阳, 梁晓阳, 戴君昂, 张妍, 关团, 张辉, 刘良波, 孙志华. 阿莫西林降解菌的筛选及降解机制研究[J]. 生物技术通报, 2025, 41(9): 314-325.
[4]	卢瑶, 袁平平, 金鑫, 毛向红, 范向斌, 白小东. 基于SSR标记的马铃薯野生种和地方种遗传多样性分析和指纹图谱构建[J]. 生物技术通报, 2025, 41(9): 94-104.
[5]	白雨果, 李婉迪, 梁建萍, 石志勇, 卢庚龙, 刘红军, 牛景萍. 哈茨木霉T9131对黄芪幼苗的促生机理[J]. 生物技术通报, 2025, 41(8): 175-185.
[6]	柴军发, 洪波, 贾彦霞. 转录组和代谢组联合分析三株蜡蚧轮枝菌菌株毒力差异[J]. 生物技术通报, 2025, 41(8): 311-321.
[7]	裴红霞, 汪露瑶, 李生梅, 高晶霞. 基于SCoT、SRAP和SSR分子标记的220份辣椒种质资源遗传多样性分析[J]. 生物技术通报, 2025, 41(8): 165-174.
[8]	王月琛, 韩鑫骐, 魏文敏, 崔兆兰, 罗阳美, 陈鹏如, 王海岗, 刘龙龙, 张莉, 王纶. 黍稷落粒的生物学基础研究及落粒调控基因的鉴定[J]. 生物技术通报, 2025, 41(7): 164-171.
[9]	张越, 毕钰, 慕雪男, 郑子薇, 王志刚, 徐伟慧. 小麦赤霉病拮抗菌JB7的生防特性[J]. 生物技术通报, 2025, 41(7): 261-271.
[10]	段敏杰, 李怡斐, 王春萍, 黄任中, 黄启中, 张世才. 辣椒果实颜色性状与SSR分子标记的关联分析及指纹图谱构建[J]. 生物技术通报, 2025, 41(7): 81-94.
[11]	李成花, 豆飞飞, 任毓昭, 刘彩霞, 刘凤楼, 王掌军, 李清峰. 外施水杨酸对白粉菌侵染小麦的影响及白粉菌转录组分析[J]. 生物技术通报, 2025, 41(7): 272-280.
[12]	郭秀娟, 冯宇, 吴瑞香, 王利琴, 杨建春. Ca²⁺处理对胡麻种子萌发影响的转录组分析[J]. 生物技术通报, 2025, 41(7): 139-149.
[13]	段永红, 杨欣, 于冠群, 夏俊俊, 宋陆帅, 白小东, 彭锁堂. 125份马铃薯种质资源遗传多样性及主成分分析[J]. 生物技术通报, 2025, 41(6): 130-143.
[14]	胡若群, 曾菁菁, 梁婉凤, 曹佳玉, 黄小苇, 梁晓英, 仇明月, 陈莹. 转录组和代谢组联合分析探究不同遮光条件下金线莲类胡萝卜素合成代谢机制[J]. 生物技术通报, 2025, 41(5): 231-243.
[15]	唐游, 赵俊伟, 孙兰茜, 李翔. 多组学技术在植物代谢通路解析中的联合应用[J]. 生物技术通报, 2025, 41(4): 76-87.