Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook

Sharma, Balraj; Seth, Romit; Thakur, Sapna; Parmar, Rajni; Masand, Mamta; Devi, A. Kanchana; Singh, Gopal; Dhyani, Praveen; Choudhary, Sonal; Sharma, Ram Kumar

doi:10.1016/j.phytochem.2021.112772

Cited by 23 publications

(16 citation statements)

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“…In this study, we identified a couple of candidate transcription factors, belonging to AP2/ERF, MYB, C2H2, and bHLH families, that were highly expressed in BFC. These transcription factors have been shown to directly or indirectly regulate the biosynthesis of alkaloids in Fritillaria roylei Hook [17,18,47,48].…”

Section: Discussionmentioning

confidence: 99%

“…Kumar et al identified the essential genes and regulatory transcription factors (TFs) of imperialine biosynthesis in Fritillaria roylei Hook using comparative de novo transcriptome analysis [17]. The molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in F. roylei Hook was investigated by transcriptome analysis [18]. In the current study, we conducted the first metabolomics and transcriptomics combined analysis to systematically investigate the characteristics of steroidal alkaloids synthesis in the five species of BFC and BFT, another Fritillaria species distributed in the lower altitude areas.…”

Section: Introductionmentioning

confidence: 99%

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Integrative analysis of the steroidal alkaloids distribution and biosynthesis of bulbs Fritillariae Cirrhosae through metabolome and transcriptome analyses

Liao

et al. 2022

BMC Genomics

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Background Bulbus Fritillariae Cirrhosae (BFC) is an endangered high-altitude medicine and food homology plant with anti-tumor, anti-asthmatic, and antitussive activities as it contains a variety of active ingredients, especially steroidal alkaloids. Bulbus Fritillariae Thunbergia (BFT) is another species of Fritillaria that grows at lower altitude areas. Production of plant-derived active ingredients through a synthetic biology strategy is one of the current hot topics in biological research, which requires a complete understanding of the related molecular pathways. Our knowledge of the steroidal alkaloid biosynthesis in Fritillaria species is still very limited. Results To promote our understanding of these pathways, we performed non-target metabolomics and transcriptome analysis of BFC and BFT. Metabolomics analysis identified 1288 metabolites in BFC and BFT in total. Steroidal alkaloids, including the proposed active ingredients of Fritillaria species peimine, peimisine, peiminine, etc., were the most abundant alkaloids detected. Our metabolomics data also showed that the contents of the majority of the steroidal alkaloids in BFC were higher than in BFT. Further, our comparative transcriptome analyses between BFC and BFT identified differentially expressed gene sets among these species, which are potentially involved in the alkaloids biosynthesis of BFC. Conclusion These findings promote our understanding of the mechanism of steroidal alkaloids biosynthesis in Fritillaria species.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Integrative analysis of the steroidal alkaloids distribution and biosynthesis of bulbs Fritillariae Cirrhosae through metabolome and transcriptome analyses

Liao

et al. 2022

BMC Genomics

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“…CYPs catalyze many oxidative reactions, such as epoxidation, dehydration, hydroxylation and dealkylation. In secondary metabolic pathways such as phenylpropanoids, alkaloids and terpenoids, CYPs oxidize metabolites with an oxygen atom ( Yao et al., 2020 ; Sharma et al, 2021 ; Wang et al, 2021 ). At the final steps of anthraquinone biosynthesis, CYPs modify the framework of anthraquinones ( Furumoto and Sato, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative transcriptome analysis of different tissues of Rheum tanguticum Maxim. ex Balf. (Polygonaceae) reveals putative genes involved in anthraquinone biosynthesis

Hu¹,

Zhang

Sun

et al. 2022

Genet. Mol. Biol.

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Rheum tanguticum is a perennial herb and an important medicinal plant, with anthraquinones as its main bioactive compounds. However, the specific pathway of anthraquinone biosynthesis in rhubarb is still unclear. The accumulation of anthraquinones in different tissues (root, leaf, stem and seed) of R. tanguticum revealed considerable variation, suggesting possible differences in metabolite biosynthetic pathways and accumulation among various tissues. To better illustrate the biosynthetic pathway of anthraquinones, we assembled transcriptome sequences from the root, leaf, stem and seed tissues yielding 157,564 transcripts and 88,142 unigenes. Putative functions could be assigned to 56,911 unigenes (64.57%) based on BLAST searches against annotation databases, including GO, KEGG, Swiss-Prot, NR, and Pfam. In addition, putative genes involved in the biosynthetic pathway of anthraquinone were identified. The expression profiles of nine unigenes involved in anthraquinone biosynthesis were verified in different tissues of R. tanguticum by qRT-PCR. Various transcription factors, including bHLH, MYB_related, and C2H2, were identified by searching unigenes against plantTFDB. This is the first transcriptome analysis of different tissues of R. tanguticum and can be utilized to describe the genes involved in the biosynthetic pathway of anthraquiones, understanding the molecular mechanism of active compounds in R. tanguticum .

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“…In another study, Kumar et al (2021) identified 30 unigenes specific to sipeimine biosynthesis and inferred that F. cirrhosa bulbs derived from in vitro cultures were a promising source for sipeimine biosynthesis. Recently, Sharma et al obtained 82,848 unigenes and 31,061 isoforms from F. roylei using the Nova-Seq 6000 platform (Sharma et al, 2021). Moreover, full-length transcriptome analysis has been used to discover genes involved in the flavonoid biosynthesis pathway of F. hupehensis (Guo et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…With its outstanding advantages of high throughput, high accuracy, high sensitivity, and relatively low cost, next‐generation sequencing has become an attractive choice for non‐model organisms without genomic sequences (Ozsolak & Milos, 2011; Wang et al, 2009). Recently, a number of transcriptome analyses of Fritillaria species have been reported, namely F. cirrhosa , Fritillaria imperialis , Fritillaria hupehensis , and Fritillaria roylei (Chao et al, 2011; Eshaghi et al, 2019; Guo et al, 2021; Kumar et al, 2021; Sharma et al, 2021; Zhao et al, 2018). By contrast, there is no reference genome or transcriptome available for F. anhuiensis , which severely limits the development and utilization of this medicinal herb.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis reveals candidate genes related to steroid alkaloid biosynthesis in Fritillaria anhuiensis

Shan

Shi

et al. 2022

Physiologia Plantarum

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Fritillaria anhuiensis (F. anhuiensis), a traditional medicinal herb of the Liliaceae family, has various pharmacological effects, including anti‐tussive, anti‐asthmatic, and expectorant activities. Peimine, a steroidal alkaloid, is a major active constituent of F. anhuiensis. Although steroidal alkaloids of F. anhuiensis have been explored chemically and pharmacologically, the molecular basis of their biosynthesis remains unknown due to a lack of genomic and transcriptomic information. In this study, peimine was detected in bulbs, stems, and leaves of F. anhuiensis, with the highest content in the bulbs. We analyzed the transcriptomes of the bulbs, stems, and leaves of F. anhuiensis using an Illumina HiSeq 4000 platform. A total of 92,829 unigenes with a mean length of 804 base pairs (bp) and an N50 value of 1354 bp were assembled from a total of 30.56 Gb high‐quality reads. Based on the Kyoto Encyclopedia of Genes and Genomes annotation, 83 unigenes were found to be related to the steroid biosynthesis pathway, while 155 unigenes were related to the terpenoid backbone biosynthesis pathway. Numerous transcription factors are involved in the regulation of alkaloid biosynthesis. A putative steroidal alkaloid biosynthesis pathway in F. anhuiensis was constructed, providing a novel understanding of peimine biosynthesis. We performed extensive bioinformatics and phylogenetic analyses to investigate the functional characteristics and evolutionary history of cycloartenol synthase. This study is the first to report transcriptome data from F. anhuiensis and extends our knowledge of the molecular mechanisms of steroid alkaloid biosynthesis.

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Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook

Cited by 23 publications

References 53 publications

Integrative analysis of the steroidal alkaloids distribution and biosynthesis of bulbs Fritillariae Cirrhosae through metabolome and transcriptome analyses

Integrative analysis of the steroidal alkaloids distribution and biosynthesis of bulbs Fritillariae Cirrhosae through metabolome and transcriptome analyses

Comparative transcriptome analysis of different tissues of Rheum tanguticum Maxim. ex Balf. (Polygonaceae) reveals putative genes involved in anthraquinone biosynthesis

Transcriptome analysis reveals candidate genes related to steroid alkaloid biosynthesis in Fritillaria anhuiensis

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