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Abstract Background Ratoon sugarcane is susceptible to chlorosis, characterized by chlorophyll loss, poor growth, and a multitude of nutritional deficiency mainly occurring at young stage. Chlorosis would significantly reduce the cane production. The molecular mechanism underlying this phenomenon remains unknown. We analyzed the transcriptome and metabolome of chlorotic and non-chlorotic sugarcane leaves of the same age from the same field to gain molecular insights into this phenomenon. Results The agronomic traits, such as plant height and the number of leaf, stalk node, and tillers declined in chlorotic sugarcane. Chlorotic leaves had substantially lower chlorophyll content than green leaves. A total of 11,776 differentially expressed genes (DEGs) were discovered in transcriptome analysis. In the KEGG enriched chlorophyll metabolism pathway, sixteen DEGs were found, eleven of which were down-regulated. Two photosynthesis pathways were also enriched with 32 genes downregulated and four genes up-regulated. Among the 81 enriched GO biological processes, there were four categories related to metal ion homeostasis and three related to metal ion transport. Approximately 400 metabolites were identified in metabolome analysis. The thirteen differentially expressed metabolites (DEMs) were all found down-regulated. The phenylpropanoid biosynthesis pathway was enriched in DEGs and DEMs, indicating a potentially vital role for phenylpropanoids in chlorosis. Conclusions Chlorophyll production, metal ion metabolism, photosynthesis, and some metabolites in the phenylpropanoid biosynthesis pathway were considerably altered in chlorotic ratoon sugarcane leaves. Our finding revealed the relation between chlorosis and these pathways, which will help expand our mechanistic understanding of ratoon sugarcane chlorosis.

Background: Ratoon sugarcane is susceptible to chlorosis, characterized by chlorophyll loss, poor growth, and a multitude of nutritional deficiency mainly occurring at young stage. Chlorosis would significantly reduce the cane production. The molecular mechanism underlying this phenomenon remains unknown. We analyzed the transcriptome and metabolome of chlorotic and non-chlorotic sugarcane leaves of the same age from the same field to gain molecular insights into this phenomenon. Results: The agronomic traits, such as plant height and the number of leaf, stalk node, and tillers declined in chlorotic sugarcane. Chlorotic leaves had substantially lower chlorophyll content than green leaves. A total of 11,776 differentially expressed genes (DEGs) were discovered in transcriptome analysis. In the KEGG enriched chlorophyll metabolism pathway, sixteen DEGs were found, eleven of which were down-regulated. Two photosynthesis pathways were also enriched with 32 genes downregulated and four genes up-regulated. Among the 81 enriched GO biological processes, there were four categories related to metal ion homeostasis and three related to metal ion transport. Approximately 400 metabolites were identified in metabolome analysis. The thirteen differentially expressed metabolites (DEMs) were all found down-regulated. The phenylpropanoid biosynthesis pathway was enriched in DEGs and DEMs, indicating a potentially vital role for phenylpropanoids in chlorosis. Conclusions: Chlorophyll production, metal ion metabolism, photosynthesis, and some metabolites in the phenylpropanoid biosynthesis pathway were considerably altered in chlorotic ratoon sugarcane leaves. Our finding revealed the relation between chlorosis and these pathways, which will help expand our mechanistic understanding of ratoon sugarcane chlorosis. [ABSTRACT FROM AUTHOR]

The aerial parts of Agastache rugosa are rich in essential oils containing monoterpenoids, phenylpropanoids, and aromatic compounds. These are used as herbs, perfume plants, and ornamental plants. Based on the difference in the constituents of the essential oil, A. rugosa is divided into pulegone and estragole chemotypes, but the mechanism of key metabolite biosynthesis in these two A. rugosa chemotypes remains unclear. In this study, we compared the morphological differences, metabolite constituents, and transcriptomic data between the two chemotypes of A. rugosa. Monoterpenoid was the main compound in the pulegone chemotype, and phenylpropanoid was the main compound in the estragole chemotype; however, limonene was detected in both chemotypes. Furthermore, 46 genes related to pulegone and estragole biosynthesis were identified. Limonene synthase , limonene-3-hydroxylase , and isopiperitenol dehydrogenase were upregulated in the pulegone chemotype, while phenylalanine ammonia-lyase , 4-coumarate: CoA ligase , CYP73A , coumaroyl-aldehyde dehydrogenase , and eugenol synthase were downregulated in the pulegone chemotype. We identified chavicol methyl transferase and limonene-3-hydroxylase in A. rugosa. This work not only provides the difference in morphology and metabolites in pulegone and estragole chemotypes, but also offers a molecular mechanism of volatile oil biosynthesis, which could be a basis for specialized metabolites in specialized chemotypes. [ABSTRACT FROM AUTHOR]

The aerial parts of Agastache rugosa are rich in essential oils containing monoterpenoids, phenylpropanoids, and aromatic compounds. These are used as herbs, perfume plants, and ornamental plants. Based on the difference in the constituents of the essential oil, A. rugosa is divided into pulegone and estragole chemotypes, but the mechanism of key metabolite biosynthesis in these two A. rugosa chemotypes remains unclear. In this study, we compared the morphological differences, metabolite constituents, and transcriptomic data between the two chemotypes of A. rugosa. Monoterpenoid was the main compound in the pulegone chemotype, and phenylpropanoid was the main compound in the estragole chemotype; however, limonene was detected in both chemotypes. Furthermore, 46 genes related to pulegone and estragole biosynthesis were identified. Limonene synthase, limonene-3-hydroxylase, and isopiperitenol dehydrogenase were upregulated in the pulegone chemotype, while phenylalanine ammonia-lyase, 4-coumarate: CoA ligase, CYP73A, coumaroyl-aldehyde dehydrogenase, and eugenol synthase were downregulated in the pulegone chemotype. We identified chavicol methyl transferase and limonene-3-hydroxylase in A. rugosa. This work not only provides the difference in morphology and metabolites in pulegone and estragole chemotypes, but also offers a molecular mechanism of volatile oil biosynthesis, which could be a basis for specialized metabolites in specialized chemotypes.

Phellinus gilvus (Schwein.) Pat, a species of ‘Sanghuang’, has been well-documented for various medicinal uses, but the genome information and active constituents are largely unknown. Here, we sequenced the whole-genome of P. gilvus, identified phenylpropanoids as its key anti-cancer components, and deduced their biosynthesis pathways. A 41.11-Mb genome sequence was assembled and the heatmap created with high-throughput chromosome conformation capture techniques data suggested all bins could be clearly divided into 11 pseudochromosomes. Cellular experiments showed that P. gilvus fruiting body was more effective to inhibit hepatocellular carcinoma cells than mycelia. High resolution electrospray ionization mass spectroscopy (HR-ESI-MS) analysis revealed P. gilvus fruiting body was rich in phenylpropanoids, and several unique phenylpropanoids in Phellinus spp. exhibited potent anti-carcinogenesis activity. Based on genomic, HR-ESI-MS information and differentially expressed genes in transcriptome analysis, we deduced the biosynthesis pathway of four major phenylpropanoids in P. gilvus. Transcriptome analysis revealed the deduced genes expressions were synergistically changed with the production of phenylpropanoids. The optimal candidate genes of phenylpropanoids’ synthesis pathway were screened by molecular docking analysis. Overall, our results provided a high-quality genomic data of P. gilvus and inferred biosynthesis pathways of four phenylpropanoids with potent anti-carcinogenesis activities. These will be a valuable resource for further genetic improvement and effective use of the P. gilvus.

Phellinus gilvus (Schwein.) Pat, a species of 'Sanghuang', has been well-documented for various medicinal uses, but the genome information and active constituents are largely unknown. Here, we sequenced the whole-genome of P. gilvus , identified phenylpropanoids as its key anti-cancer components, and deduced their biosynthesis pathways. A 41.11-Mb genome sequence was assembled and the heatmap created with high-throughput chromosome conformation capture techniques data suggested all bins could be clearly divided into 11 pseudochromosomes. Cellular experiments showed that P. gilvus fruiting body was more effective to inhibit hepatocellular carcinoma cells than mycelia. High resolution electrospray ionization mass spectroscopy (HR-ESI-MS) analysis revealed P. gilvus fruiting body was rich in phenylpropanoids, and several unique phenylpropanoids in Phellinus spp. exhibited potent anti-carcinogenesis activity. Based on genomic, HR-ESI-MS information and differentially expressed genes in transcriptome analysis, we deduced the biosynthesis pathway of four major phenylpropanoids in P. gilvus. Transcriptome analysis revealed the deduced genes expressions were synergistically changed with the production of phenylpropanoids. The optimal candidate genes of phenylpropanoids' synthesis pathway were screened by molecular docking analysis. Overall, our results provided a high-quality genomic data of P. gilvus and inferred biosynthesis pathways of four phenylpropanoids with potent anti-carcinogenesis activities. These will be a valuable resource for further genetic improvement and effective use of the P. gilvus. [ABSTRACT FROM AUTHOR]

• Two NtWRKY41 genes were identified from Nicotiana tabacum , among which NtWRKY41a exhibited stronger transcriptional activity. • Knock-out or overexpression of the NtWRKY41a gene significantly changed the content of phenylpropanoids in tobacco leaves. • NtWRKY41a induced the transcription of NtCCoAOMT and NtHST , but repressed those of NtF6'H1 and NtGT3 genes. • ChIP-qPCR and Dual-Luc assays further indicated that NtWRKY41a could bind to the promoter regions of these four genes. Phenylpropanoids are important secondary metabolites that have multifaceted effects on plant growth, development, and environmental adaptation. WRKY41 has been shown to repress anthocyanins synthesis in Arabidopsis, but its full roles in regulating plant phenylpropanoids metabolism still remains to be further studied. Here, we cloned two NtWRKY41 genes from N. tabacum genome, and NtWRKY41a showed higher expression levels than NtWRKY41b genes in all the tobacco tissues examined. Overexpression and knock-out of NtWRKY41a gene revealed that NtWRKY41a promoted the biosynthesis of Chlorogenic acid (CGA) and lignin, but repressed the accumulation of scopoletin and flavonoids in tobacco. Transcriptome analysis found 7 phenylpropanoids related differentially expressed genes (DEGs) between WT and NtWRKY41a -OE plants, among which the transcription of NtCCoAOMT and NtHST was significantly induced by posttranslational activation of NtWRKY41a, while those of NtF 6' H1 and NtGT3 was significantly repressed by NtWRKY41a. Chromatin immunoprecipitation and Dual-Luc assays further indicated that NtWRKY41a could bind to the promoter regions of these four genes to regulate their transcription. Moreover, ectopic expression of NtWRKY41a also promoted the transcription of several NtLOX and NtHPL genes, which encode key enzymes involved in the oxylipin pathway. Our findings revealed new functions of NtWRKY41a in modulating the distribution of metabolism flux in phenylpropanoids pathway, and provided a promising target for manipulating phenylpropanoids contents in tobacco. [ABSTRACT FROM AUTHOR]

• Transcriptome and metabolomics analysis of two Cinnamomum cassia Presl varieties was performed. • Cinnamomum cassia Presl var. macrophyllum Chu has high levels of cinnamaldehyde, coumarin, and flavonoids. • 30 differentially expressed genes in phenylpropanoid metabolic pathway were discovered. • 73 photosynthesis genes were upregulated in Cinnamomum cassia Presl var. macrophyllum Chu. Essential oil content is the major component of Cinnamomum cassia Presl quality. In this research, an analysis of transcriptome and metabolite profiles between Cinnamomum cassia Presl (CK) and Cinnamomum cassia Presl var. macrophyllum Chu (Var) was performed to investigate the molecular mechanisms underlying the difference of active components content in the barks, branches, and leaves. Results revealed that higher contents of flavonoids were present in the barks, branches, and leaves of Var, and higher levels of cinnamaldehyde and coumarine were present in the barks of Var, but lower in the leaves when compared with CK. Transcriptome analysis revealed that genes related to photosynthesis and flavonoid biosynthesis were upregulated in Var relative to CK. Differences in essential oil contents between the two varieties could be attributed to the differential expression of genes related to the two branches of the phenylpropanoid metabolic pathway, i.e., one controls flavonoid metabolism and was highly active in Var, whereas the other regulates the synthesis of cinnamaldehyde and coumarine and was only upregulated in the barks of Var, but downregulated in the leaves. The findings of this study provide insights into the mechanism behind the phenylpropanoid metabolic pathway of Cinnamomum cassia Presl. [ABSTRACT FROM AUTHOR]