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Omics Approaches in Plants Metabolism
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Omics Approaches in Plants Metabolism

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 8389

Special Issue Editor

Dr. Georgia Tanou

E-Mail Website
Guest Editor
Institute of Soil Science and Water Resources, Hellenic Agricultural Organization-Demeter, Thermi, GR-57001 Thessaloniki, Greece
Interests: fruit tree physiology and nutrition; abiotic stress physiology; proteomics; metabolomics; transcriptomics

Special Issue Information

Dear Colleagues,

This Special Issue aims to elucidate how plants coordinate their metabolic pathways under various environmental and developmental conditions, combining information produced by various omics-based approaches (genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, and beyond) along with the aid of bioinformatics.

The integrated network of gene expression, proteins and metabolite accumulation is disclosed by high-throughput experimenting, providing the essential data, which, following meta-omics data analysis and an integrative approach at systems level, helps us to characterize plant phenotype and behavior.

This Special Issue aims to publish high-quality discoveries in plants using integrated omics technologies.

Dr. Georgia Tanou
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • transcriptomics
  • proteomics
  • metabolomics
  • epigenomics
  • DNA sequencing
  • post-translational modifications

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Published Papers (2 papers)

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Research

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16 pages, 3902 KiB  
Article
Comprehensive Analysis of Metabolome and Transcriptome in Fruits and Roots of Kiwifruit
by Long Zhang, Zhengmin Tang, Hao Zheng, Caihong Zhong and Qiong Zhang
Int. J. Mol. Sci. 2023, 24(2), 1299; https://doi.org/10.3390/ijms24021299 - 9 Jan 2023
Cited by 7 | Viewed by 3154
Abstract
Kiwifruit (Actinidia chinensis) roots instead of fruits are widely used as Chinese medicine, but the functional metabolites remain unclear. In this study, we conducted comparative metabolome analysis between root and fruit in kiwifruit. A total of 410 metabolites were identified in [...] Read more.
Kiwifruit (Actinidia chinensis) roots instead of fruits are widely used as Chinese medicine, but the functional metabolites remain unclear. In this study, we conducted comparative metabolome analysis between root and fruit in kiwifruit. A total of 410 metabolites were identified in the fruit and root tissues, and of them, 135 metabolites were annotated according to the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway. Moreover, 54 differentially expressed metabolites (DEMs) were shared in root and fruit, with 17 DEMs involved in the flavonoid pathway. Of the 17 DEMs, three flavonols (kaempferol-3-rhamnoside, L-Epicatechin and trifolin) and one dihydrochalcone (phloretin) showed the highest differences in the content level, suggesting that flavonols and dihydrochalcones may act as functional components in kiwifruit root. Transcriptome analysis revealed that genes related to flavonols and dihydrochalcones were highly expressed in root. Moreover, two AP2 transcription factors (TFs), AcRAP2-4 and AcAP2-4, were highly expressed in root, while one bHLH TF AcbHLH62 showed extremely low expression in root. The expression profiles of these TFs were similar to those of the genes related to flavonols and dihydrochalcones, suggesting they are key candidate genes controlling the flavonoid accumulation in kiwifruit. Our results provided an insight into the functional metabolites and their regulatory mechanism in kiwifruit root. Full article
(This article belongs to the Special Issue Omics Approaches in Plants Metabolism)
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Review

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13 pages, 247 KiB  
Review
Olive Fruit Development and Ripening: Break on through to the “-Omics” Side
by Christina Skodra, Vaia Styliani Titeli, Michail Michailidis, Christos Bazakos, Ioannis Ganopoulos, Athanassios Molassiotis and Georgia Tanou
Int. J. Mol. Sci. 2021, 22(11), 5806; https://doi.org/10.3390/ijms22115806 - 28 May 2021
Cited by 17 | Viewed by 4494
Abstract
The olive tree (Olea europaea L. subsp. europaea) is the most important perennial crop in the Mediterranean region, producing table olives and oil, both appreciated for their nutraceutical value. Although olive oil quality traits have been extensively studied, much less attention [...] Read more.
The olive tree (Olea europaea L. subsp. europaea) is the most important perennial crop in the Mediterranean region, producing table olives and oil, both appreciated for their nutraceutical value. Although olive oil quality traits have been extensively studied, much less attention has been paid to olive drupe. Olive drupe ripening is an extremely complex process involving numerous physiological and molecular changes that are unique in this fruit crop species. This review underlines the contribution of “-omics” techniques and of the recent advances in bioinformatics and analytical tools, notably next-generation sequencing and mass spectrometry, for the characterization of the olive ripening syndrome. The usage of high-dimensional datasets, such as transcriptomics, proteomics, and metabolomics, will provide a systematical description of the molecular-specific processes regulating olive fruit development and ripening. However, the incomplete sequence of the O. europaea L. reference genome has largely hampered the utilization of omics tools towards olive drupe research. Due to this disadvantage, the most reported -omics studies on fruit trees concern metabolomics and only a few transcriptomics and proteomics. In this review, up-to-date applications of -omics technologies towards olive drupe biology are addressed, and future perspectives in olive fruit research are highlighted. Full article
(This article belongs to the Special Issue Omics Approaches in Plants Metabolism)
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