Identification of key genes associated with secondary metabolites biosynthesis by system network analysis in Valeriana officinalis

Bolhassani, Mohammad; Niazi‎, Ali; Tahmasebi, Ahmad; Moghadam, Ali

doi:10.1007/s10265-021-01277-5

Cited by 14 publications

(12 citation statements)

References 56 publications

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“…In both networks modeled, we found that the CAMK CDPK subfamily had the highest hub score, suggesting the importance of calcium signals over Hbr PK activities, as already reported in soybean (Liu et al, 2015). Members of the RLK-Pelle group were also identified as hubs in both networks, reinforcing the primary and secondary metabolic functions of this group (Bolhassani et al, 2021). Additionally, TKL-Pl-4 was among the hubs in the stress-related network, corroborating the already described upregulation of members of this subfamily in stress conditions (Yan et al, 2017) and reinforcing the potential of biological inferences over the network structure.…”

Section: Discussionsupporting

confidence: 80%

The rubber tree kinome: genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

Santos

Aono

Francisco

et al. 2022

Preprint

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The protein kinase (PK) superfamily constitutes one of the largest and most conserved protein families in eukaryotic genomes, comprising core components of signaling pathways in cell regulation. Despite its remarkable relevance, only a few kinase families have been studied in Hevea brasiliensis. A comprehensive characterization and global expression analysis of the PK superfamily, however, is currently lacking. In this study, we identified and characterized the entire set of PKs, also known as the kinome, present in the Hevea genome. A total of 1,809 PK genes were identified using the current reference genome assembly at the scaffold level, and 1,379 PK genes were identified using the latest chromosome-level assembly and combined into a single set of 2,842 PKs. These proteins were further classified into 20 different groups and 122 families, exhibiting high compositional similarities among family members and with two phylogenetically close species (Manihot esculenta and Ricinus communis). Different RNA-sequencing datasets were employed to identify tissue-specific expression patterns and potential correspondences between different rubber tree genotypes. In addition, coexpression networks under several abiotic stress conditions, such as cold, drought and latex overexploitation, were employed to elucidate associations between families and tissues/stresses. Through the joint investigation of tandemly duplicated kinases, transposable elements, gene expression patterns, and coexpression events, we provided insights into the understanding of the cell regulation mechanisms in response to several conditions, which can often lead to a significant reduction in rubber yield.

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Section: Discussionsupporting

confidence: 80%

The rubber tree kinome: genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

Santos

Aono

Francisco

et al. 2022

Preprint

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“…Interestingly, other subfamilies in the vulnerable edges of the control network (TKL-Pl-8, CMGC CDK-PITSLRE, and Group-Pl-4) were disconnected elements in the stress network. This demonstrates that the existent vulnerabilities become more pronounced in adverse conditions, and also reinforces the importance of the RLK-Pelle group (Bolhassani et al, 2021). By contrasting the other subfamilies present in the high betweenness edges in the stress related network with their connection profile in the control network, we can visualize that AGC RSK-2, AGC PKA-PKG, and NEK presented median hub scores, i.e.…”

Section: Discussionsupporting

confidence: 71%

Section: Gene Expression Estimationsupporting

confidence: 69%

Genome-wide characterization of the common bean kinome: catalog and insights into expression patterns and genetic organization

Aono

Pimenta

Kuroshu

et al. 2022

Preprint

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The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinome of common bean (Phaseolus vulgaris) has not been profiled yet. Here, we identified and characterised the complete set of kinases of common bean, performing an in-depth investigation with phylogenetic analyses and measurements of gene distribution, structural organization, protein properties, and expression patterns over a large set of RNA-Sequencing data. Being composed of 1,203 PKs distributed across all P. vulgaris chromosomes, this set represents 3.25% of all predicted proteins for the species. These PKs could be classified into 20 groups and 119 subfamilies, with a more pronounced abundance of subfamilies belonging to the receptor-like kinase (RLK)-Pelle group. In addition to provide a vast and rich reservoir of data, our study supplied insights into the compositional similarities between PK subfamilies, their evolutionary divergences, highly variable functional profile, structural diversity, and expression patterns, modeled with coexpression networks for investigating putative interactions associated with stress response.

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“…Gene expression studies using qRT-PCR have been used across numerous research studies to unravel the molecular mechanisms behind the biosynthetic pathways of various medicinal and aromatic plants [ 6 , 28 , 29 , 30 , 31 ]. With substantial progress, many genes and gene families have been identified that are directly or indirectly responsible for the synthesis of economically important secondary metabolites [ 31 , 32 , 33 ]. To identify these genes, selecting suitable reference genes for qRT-PCR analyses is crucial to avoid misleading results.…”

Section: Discussionmentioning

confidence: 99%

Systematic Identification of Suitable Reference Genes for Quantitative Real-Time PCR Analysis in Melissa officinalis L

Bharati

Sen

Kumar

et al. 2023

Plants

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Melissa officinalis L. is well known for its lemon-scented aroma and various pharmacological properties. Despite these valuable properties, the genes involved in the biosynthetic pathways in M. officinalis are not yet well-explored when compared to other members of the mint family. For that, gene expression studies using quantitative real-time PCR (qRT-PCR) are an excellent tool. Although qRT-PCR can provide accurate results, its accuracy is highly reliant on the expression and stability of the reference gene used for normalization. Hence, selecting a suitable experiment-specific reference gene is very crucial to obtain accurate results. However, to date, there are no reports for experiment-specific reference genes in M. officinalis. Therefore, in the current study, ten commonly used reference genes were assessed for their suitability as optimal reference genes in M. officinalis under various abiotic stress conditions and different plant organs. The candidate genes were ranked based on BestKeeper, comparative ΔCt, geNorm, NormFinder, and RefFinder. Based on the results, we recommend the combination of EF-1α and GAPDH as the best reference genes to normalize gene expression studies in M. officinalis. On the contrary, HLH71 was identified as the least-performing gene. Thereafter, the reliability of the optimal gene combination was assessed by evaluating the relative gene expression of the phenylalanine ammonia lyase (PAL) gene under two elicitor treatments (gibberellic acid and jasmonic acid). PAL is a crucial gene involved directly or indirectly in the production of various economically important secondary metabolites in plants. Suitable reference genes for each experimental condition are also discussed. The findings of the current study form a basis for current and future gene expression studies in M. officinalis and other related species.

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Identification of key genes associated with secondary metabolites biosynthesis by system network analysis in Valeriana officinalis

Cited by 14 publications

References 56 publications

The rubber tree kinome: genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

The rubber tree kinome: genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

Genome-wide characterization of the common bean kinome: catalog and insights into expression patterns and genetic organization

Systematic Identification of Suitable Reference Genes for Quantitative Real-Time PCR Analysis in Melissa officinalis L

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