Comparative analysis of root anatomical structure, chemical components and differentially expressed genes between early bolting and unbolting in Peucedanum praeruptorum Dunn
“…2 ). These results indicate that numerous genes in P. praeruptorum are involved in biological processes such as growth and development, signal transduction, environmental stress, and secondary metabolism [ 6 ]. In addition, we also detected alternative splicing events in these new transcripts, and different splicing patterns may be closely associated with the formation of truncated genes and the novel functions.…”
Section: Discussionmentioning
confidence: 99%
“…Genes involved in transmembrane transport, ion channels, cytokinin synthesis, hexose phosphate metabolism, inositol phosphate metabolism, DNA-binding, phosphatidylinositol signaling, fatty acid metabolism, the peroxisome, and autophagy were significantly enriched in this study. These results indicated that many genes associated with material and energy metabolism were triggered after bolting [ 6 ]. Fig.…”
Section: Discussionmentioning
confidence: 99%
“…Some key genes involved in the biosynthesis and transport of P. praeruptorum coumarins have been successfully identified using transcriptome and metabolome techniques. It was believed that CYP450 family genes and MDR transporters were involved in the biosynthesis and transport of coumarins [ 5 , 6 ]. Many studies have proved that PAL , 4CL , C2’H , BMT , COMT , AS , PS , etc.…”
Background
Peucedanum praeruptorum Dunn, a traditional Chinese herbal medicine, contains coumarin and volatile oil components that have clinical application value. However, early bolting often occurs in the medicinal materials of Apiaceae plants. The rhizomes of the medicinal parts are gradually lignified after bolting, resulting in a sharp decrease in the content of coumarins. At present, the link between coumarin biosynthesis and early bolting in P. praeruptorum has not been elucidated.
Results
Combining the genome sequencing and the previous transcriptome sequencing results, we reanalyzed the differential transcripts of P. praeruptorum before and after bolting. A total of 62,088 new transcripts were identified, of which 31,500 were unknown transcripts. Functional classification and annotation showed that many genes were involved in the regulation of transcription, defense response, and carbohydrate metabolic processes. The main domains are the pentatricopeptide repeat, protein kinase, RNA recognition motif, leucine-rich repeat, and ankyrin repeat domains, indicating their pivotal roles in protein modification and signal transduction. Gene structure analysis showed that skipped exon (SE) was the most dominant alternative splicing, followed by the alternative 3’ splice site (A3SS) and the alternative 5’ splice site (A5SS). Functional enrichment of differentially expressed genes showed that these differentially expressed genes mainly include transmembrane transporters, channel proteins, DNA-binding proteins, polysaccharide-binding proteins, etc. In addition, genes involved in peroxisome, hexose phosphate pathway, phosphatidylinositol signaling system, and inositol phosphate metabolism pathway were greatly enriched. A protein-protein interaction network analysis discoverd 1,457 pairs of proteins that interact with each other. The expression levels of six UbiA genes, three UGT genes, and four OMT genes were higher during the bolting stage. This observation suggests their potential involvement in the catalytic processes of prenylation, glycosylation, and methylation of coumarins, respectively. A total of 100 peroxidase (PRX) genes were identified being involved in lignin polymerization, but only nine PRX genes were highly expressed at the bolting stage. It is worth noting that 73 autophagy-related genes (ATGs) were first identified from the KEGG pathway-enriched genes. Some ATGs, such as BHQH00009837, BHQH00013830, and novel8944, had higher expression levels after bolting.
Conclusions
Comparative transcriptome analysis and large-scale genome screening provide guidance and new opinions for the identification of bolting-related genes in P. praeruptorum.
“…2 ). These results indicate that numerous genes in P. praeruptorum are involved in biological processes such as growth and development, signal transduction, environmental stress, and secondary metabolism [ 6 ]. In addition, we also detected alternative splicing events in these new transcripts, and different splicing patterns may be closely associated with the formation of truncated genes and the novel functions.…”
Section: Discussionmentioning
confidence: 99%
“…Genes involved in transmembrane transport, ion channels, cytokinin synthesis, hexose phosphate metabolism, inositol phosphate metabolism, DNA-binding, phosphatidylinositol signaling, fatty acid metabolism, the peroxisome, and autophagy were significantly enriched in this study. These results indicated that many genes associated with material and energy metabolism were triggered after bolting [ 6 ]. Fig.…”
Section: Discussionmentioning
confidence: 99%
“…Some key genes involved in the biosynthesis and transport of P. praeruptorum coumarins have been successfully identified using transcriptome and metabolome techniques. It was believed that CYP450 family genes and MDR transporters were involved in the biosynthesis and transport of coumarins [ 5 , 6 ]. Many studies have proved that PAL , 4CL , C2’H , BMT , COMT , AS , PS , etc.…”
Background
Peucedanum praeruptorum Dunn, a traditional Chinese herbal medicine, contains coumarin and volatile oil components that have clinical application value. However, early bolting often occurs in the medicinal materials of Apiaceae plants. The rhizomes of the medicinal parts are gradually lignified after bolting, resulting in a sharp decrease in the content of coumarins. At present, the link between coumarin biosynthesis and early bolting in P. praeruptorum has not been elucidated.
Results
Combining the genome sequencing and the previous transcriptome sequencing results, we reanalyzed the differential transcripts of P. praeruptorum before and after bolting. A total of 62,088 new transcripts were identified, of which 31,500 were unknown transcripts. Functional classification and annotation showed that many genes were involved in the regulation of transcription, defense response, and carbohydrate metabolic processes. The main domains are the pentatricopeptide repeat, protein kinase, RNA recognition motif, leucine-rich repeat, and ankyrin repeat domains, indicating their pivotal roles in protein modification and signal transduction. Gene structure analysis showed that skipped exon (SE) was the most dominant alternative splicing, followed by the alternative 3’ splice site (A3SS) and the alternative 5’ splice site (A5SS). Functional enrichment of differentially expressed genes showed that these differentially expressed genes mainly include transmembrane transporters, channel proteins, DNA-binding proteins, polysaccharide-binding proteins, etc. In addition, genes involved in peroxisome, hexose phosphate pathway, phosphatidylinositol signaling system, and inositol phosphate metabolism pathway were greatly enriched. A protein-protein interaction network analysis discoverd 1,457 pairs of proteins that interact with each other. The expression levels of six UbiA genes, three UGT genes, and four OMT genes were higher during the bolting stage. This observation suggests their potential involvement in the catalytic processes of prenylation, glycosylation, and methylation of coumarins, respectively. A total of 100 peroxidase (PRX) genes were identified being involved in lignin polymerization, but only nine PRX genes were highly expressed at the bolting stage. It is worth noting that 73 autophagy-related genes (ATGs) were first identified from the KEGG pathway-enriched genes. Some ATGs, such as BHQH00009837, BHQH00013830, and novel8944, had higher expression levels after bolting.
Conclusions
Comparative transcriptome analysis and large-scale genome screening provide guidance and new opinions for the identification of bolting-related genes in P. praeruptorum.
“…[20], Angelica sinensis (Oliv.) Diels [21,22], and K. praeruptora [23]. During early bolting, endogenous hormones will change to regulate growth and development, which has a greater impact on the root structure and coumarin content of K. praeruptora.…”
Kitagawia praeruptora (Dunn) Pimenov, commonly known as Qianhu in China, is a widely used folk Chinese herbal medicine. This article reviews its botanical traits, ethnopharmacology, cultivation techniques, identification, phytochemical compositions, and pharmacological effects. Over 70 coumarin compounds, including simple coumarins, pyranocoumarins, and furanocoumarins, have been isolated within this plant. Additionally, K. praeruptora contains other components such as flavonoids, fatty acids, benzoic acids, and sterols. This information highlights the importance of utilizing active ingredients and excavating pharmacological effects. With its remarkable versatility, K. praeruptora exhibits a wide range of pharmacological effects. It has been found to possess expectorant and bronchodilator properties, cardiovascular protection, antimicrobial and antioxidant activities, anti-tumor effects, and even antidiabetic properties. It is recommended to focus on the development of new drugs that leverage the active ingredients of K. praeruptora and explore its potential for new clinical applications and holistic utilization.
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