Mining Ferula gummosa transcriptome to identify miRNAs involved in the regulation and biosynthesis of terpenes

Najafabadi, Ahmad Sobhani; Naghavi, Mohammad Reza

doi:10.1016/j.gene.2017.12.035

Cited by 48 publications

(19 citation statements)

References 22 publications

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“…Significantly negative MFE and MEFI value stipulated appropriate folding and stable secondary structures of the predicted miRNAs . A good percentage of GC content (> 40%) in the miRNA sequences further specified their stability . When examined terpene biosynthesis, the miRNA families, miR2108, miR4993, miR396, miR5015, and miR414, targeting terpene pathway genes were more or less in agreement with the previous findings on terpene biosynthesis occurring in different plant species, Mentha spp., Z. officinale , Coffea , W. somnifera and Viscum album L. .…”

Section: Discussionsupporting

confidence: 86%

“…However, miRNAs of a family may not be conserved with respect to their sequence and/or secondary structure . Significantly negative MFE and MEFI value stipulated appropriate folding and stable secondary structures of the predicted miRNAs . A good percentage of GC content (> 40%) in the miRNA sequences further specified their stability .…”

Section: Discussionmentioning

confidence: 99%

“…The noncoding high‐quality reads were fed into C‐mii tool (http://www.biotec.or.th/isl/c-mii) for identification of miRNAs. This tool does homology search against the miRBase database, comprised of known plant miRNAs, and evaluates the stability of secondary structures of the predicted precursor miRNAs . The rose‐scented geranium miRNAs were predicted on the default criteria of 18–32 nucleotides length, less than three mismatches, relatively high AU content than GC, and highly negative minimal folding free energy (MFE) and MFE index (MFEI) value.…”

Section: Methodsmentioning

confidence: 99%

“…The miRNAs down‐regulate the target gene through transcript cleavage and translational repression , contributing significant regulatory roles in numerous cellular and metabolic processes. The advent of high throughput RNA sequencing led to identification of a number of miRNAs in plants such as Gossypium arboretum , Cajanus cajan , Typha angustifolia , Mesembryanthemum crystallinum , Marchantia polymorpha , Oenanthe javanica , Zea maize , Camellia sinensis , Asparagus officinalis , Zingiber officinale , Catharanthus roseus , Ferula gummosa , Withania somnifera , Curcuma longa , Cannabis sativa L., and Ocimum basilicum etc. Some aromatic and medicinal plants like Camellia sinensis , Mentha spp., and Z. officinale have also been investigated for identification of miRNAs in gene regulation of terpene biosynthetic pathway .…”

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confidence: 99%

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Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

2019

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This study aimed to explore the noncoding RNAs, which have emerged as key regulatory molecules in biological processes, in rose‐scented geranium. We analyzed RNA‐seq data revealing 26 784 long noncoding RNAs (lncRNAs) and 871 miRNAs in rose‐scented geranium. A total of 466 lncRNAs were annotated using different plant lncRNA public databases. Furthermore, 372 lncRNAs and 99 miRNAs were detected that target terpene and tartarate biosynthetic pathways. An interactome, comprising of lncRNAs, miRNAs, and mRNAs, was constructed that represents a noncoding RNA regulatory network of the target mRNAs. Real‐time quantitative PCR expression validation was done for selected lncRNAs involved in the regulation of terpene and tartaric acid pathways. This study provides the first insights into the regulatory functioning of noncoding RNAs in rose‐scented geranium.

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Section: Discussionsupporting

confidence: 86%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

2019

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“…Transcription factors regulating a variety of terpenes have also been identified; in cotton WRKY1 positively regulates (+)-□-cadinene synthase (CAD1) [65], and in kiwifruit, NAC transcription factors were found to regulate the expression of TPS1 in ripe fruit [66]. Post-transcriptional regulation includes the action of miRNAs, which have been identified in plants such as Ocimum basilicum [67] and Ferula gummosa [68]. The existence of SNPs between transcripts from each chemotype may suggest differences in functionality of each linalool synthase; however, few of the SNPs are shared among linalool-plants, such that the regulation of (R)-(-)-linalool synthase in O. harringtonii may be associated only with upregulation and the allele found in linalool+ individuals.…”

Section: Resultsmentioning

confidence: 99%

Differential gene expression associated with a floral scent polymorphism in the evening primroseOenothera harringtonii(Onagraceae)

Bechen

Johnson

Broadhead

et al. 2021

Preprint

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BackgroundPlant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare. Oenothera harringtonii populations are polymorphic in floral emission of the monoterpene (R)-(-)-linalool; some plants emit (R)-(-)-linalool (linalool+ plants) while others do not (linalool-plants). However, the genes associated with differential production of this floral volatile in Oenothera are unknown. We used RNA-Seq to broadly characterize differential gene expression involved in (R)-(-)-linalool biosynthesis. To identify genes that may be associated with the polymorphism for this trait, we used RNA-Seq to compare gene expression in six different Oenothera harringtonii tissues from each of three linalool+ and linalool-plants.ResultsThree clusters of differentially expressed genes were enriched for terpene synthase activity: two were characterized by tissue-specific upregulation and one by upregulation only in plants with flowers that produce (R)-(-)-linalool. A molecular phylogeny of all terpene synthases identified two putative (R)-(-)-linalool synthase transcripts in Oenothera harringtonii, a single allele of which is found exclusively in linalool+ plants.ConclusionsBy using a naturally occurring polymorphism and comparing different tissues, we were able to identify genes putatively involved in the biosynthesis of (R)-(-)-linalool. Expression of these genes in linalool-plants suggests a regulatory polymorphism, rather than a population-specific loss-of-function allele. Additional terpene biosynthesis-related genes that are up-regulated in plants that emit (R)-(-)-linalool may be associated with herbivore defense, suggesting a potential economy of scale between plant reproduction and defense.

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Progress on the Transcriptome Analysis of Medicinal Plants with Next‐Generation Sequencing Technologies

Luo

Chen

2019

Encyclopedia of Analytical Chemistry

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Most medicinal plants are sources for the production of valuable natural products. Major natural products possessing pharmacological properties are secondary metabolites of medicinal plants. However, transcriptomes/genomes of most medicinal plants are not available, which hinders biological research on the biosynthetic mechanism of these bioactive secondary metabolites. Transcriptome analysis is a promising tool to illustrate biological processes, such as the biosynthesis of bioactive compounds, growth and development and genetic diversity of medicinal plants. Next‐generation sequencing (NGS) technologies, including second‐generation sequencing (SGS) and third‐generation sequencing (TGS) (e.g. PacBio) technologies, are suitable for the transcriptome analysis of medicinal plants. NGS sequencing is advantageous for the identification of gene expression profiling and facilitates reliable discoveries of secondary metabolite biosynthetic pathway‐related genes. Recently, hybrid sequencing strategies integrating the strength of SGS and PacBio sequencing have made much transcriptome information available. Additionally, NGS sequencing technologies aids in the direct detection of genetic markers and alternative splicing events related to the biosynthesis of secondary metabolites, which facilitates fast‐track breeding of medicinal plants.

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Mining Ferula gummosa transcriptome to identify miRNAs involved in the regulation and biosynthesis of terpenes

Cited by 48 publications

References 22 publications

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

Differential gene expression associated with a floral scent polymorphism in the evening primroseOenothera harringtonii(Onagraceae)

Progress on the Transcriptome Analysis of Medicinal Plants with Next‐Generation Sequencing Technologies

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