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

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

Abstract

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

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.

Figures/Tables 14

References 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