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Plants
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Plant Synthetic Biology and Plant Transcriptome
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Plant Synthetic Biology and Plant Transcriptome

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Systems and Synthetic Biology".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 7106

Special Issue Editor

Prof. Dr. Pengcheng Fu

E-Mail Website
Guest Editor
State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
Interests: bioengineering; biosystems engineering; chemical engineering; plant science; synthetic biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the advent of multi-omics high-throughput technologies and synthetic biology, the plant research paradigm has shifted to a holistic view of higher plants to understand complex life phenomena and of engineering of biology for the modification of genes, proteins, metabolites, and other cellular components in plants to create a new vista in plant biotechnology. This Special Issue is focused on transcriptomics and synthetic biology for higher plants that are essential for the elucidation of mechanisms in data-intensive approaches and for the design and building of novel or existing photosynthetic systems for improved growth and production of bioactive substances. Original research and review articles covering all aspects of plant transcriptomics for the study of differential gene expression that regulate cell growth and metabolism of plants and resistance to environmental stress with the aid of bioinformatics, and the demonstration of engineering formalism, systematic design, and module assembly in creative reconstruction of plant systems are welcome.

Prof. Dr. Pengcheng Fu
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. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • bioinformatics
  • transcriptomics
  • synthetic biology
  • systems biology
  • plant physiology

Published Papers (4 papers)

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Research

18 pages, 6785 KiB  
Article
Transcriptome-Wide Integrated Analysis of the PgGT25-04 Gene in Controlling Ginsenoside Biosynthesis in Panax ginseng
by Lei Zhu, Jian Hu, Ruiqi Li, Chang Liu, Yang Jiang, Tao Liu, Mingming Liu, Mingzhu Zhao, Yi Wang, Kangyu Wang and Meiping Zhang
Plants 2023, 12(10), 1980; https://doi.org/10.3390/plants12101980 - 15 May 2023
Cited by 2 | Viewed by 1351
Abstract
Panax ginseng is a valuable medicinal herb of the Araliaceae family with various pharmacological activities. The Trihelix transcription factors family is involved in growth and secondary metabolic processes in plants, but no studies have been reported on the involvement of Trihelix genes in [...] Read more.
Panax ginseng is a valuable medicinal herb of the Araliaceae family with various pharmacological activities. The Trihelix transcription factors family is involved in growth and secondary metabolic processes in plants, but no studies have been reported on the involvement of Trihelix genes in secondary metabolic processes in ginseng. In this study, weighted co-expression network analysis, correlation analysis between PgGTs and ginsenosides and key enzyme genes, and interaction network analysis between PgGTs and key enzyme genes were used to screen out the PgGT25-04 gene, which was negatively correlated with ginsenoside synthesis. Using ABA treatment of ginseng hair roots, PgGT genes were found to respond to ABA signals. Analysis of the sequence characteristics and expression pattern of the PgGT25-04 gene in ginseng revealed that its expression is spatiotemporally specific. The interfering vector pBI121-PgGT25-04 containing the PgGT25-04 gene was constructed, and the ginseng adventitious roots were transformed using the Agrobacterium-mediated method to obtain the pBI121-PgGT25-04 positive hairy root monocot line. The saponin contents of positive ginseng hair roots were measured by HPLC, and the changes in PgGT25-04 and key enzyme genes in positive ginseng hair roots were detected via fluorescence quantitative RT-PCR. These results preliminarily identified the role of the PgGT25-04 gene in the secondary metabolism of ginseng in Jilin to provide a theoretical basis for the study of Trihelix transcription factors in Panax ginseng. Full article
(This article belongs to the Special Issue Plant Synthetic Biology and Plant Transcriptome)
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19 pages, 3736 KiB  
Article
Divergent Metabolic Changes in Rhizomes of Lowland and Upland Switchgrass (Panicum virgatum) from Early Season through Dormancy Onset
by Nathan A. Palmer, Gautam Sarath, Michael J. Bowman, Aaron J. Saathoff, Serge J. Edmé, Robert B. Mitchell, Christian M. Tobias, Soundararajan Madhavan, Erin D. Scully and Scott E. Sattler
Plants 2023, 12(8), 1732; https://doi.org/10.3390/plants12081732 - 21 Apr 2023
Viewed by 1202
Abstract
High-biomass-yielding southerly adapted switchgrasses (Panicum virgatum L.) frequently suffer from unpredictable winter hardiness at more northerly sites arising from damage to rhizomes that prevent effective spring regrowth. Previously, changes occurring over the growing season in rhizomes sampled from a cold-adapted tetraploid upland [...] Read more.
High-biomass-yielding southerly adapted switchgrasses (Panicum virgatum L.) frequently suffer from unpredictable winter hardiness at more northerly sites arising from damage to rhizomes that prevent effective spring regrowth. Previously, changes occurring over the growing season in rhizomes sampled from a cold-adapted tetraploid upland cultivar, Summer, demonstrated a role for abscisic acid (ABA), starch accumulation, and transcriptional reprogramming as drivers of dormancy onset and potential keys to rhizome health during winter dormancy. Here, rhizome metabolism of a high-yielding southerly adapted tetraploid switchgrass cultivar, Kanlow—which is a significant source of genetics for yield improvement—was studied over a growing season at a northern site. Metabolite levels and transcript abundances were combined to develop physiological profiles accompanying greening through the onset of dormancy in Kanlow rhizomes. Next, comparisons of the data to rhizome metabolism occurring in the adapted upland cultivar Summer were performed. These data revealed both similarities as well as numerous differences in rhizome metabolism that were indicative of physiological adaptations unique to each cultivar. Similarities included elevated ABA levels and accumulation of starch in rhizomes during dormancy onset. Notable differences were observed in the accumulation of specific metabolites, the expression of genes encoding transcription factors, and several enzymes linked to primary metabolism. Full article
(This article belongs to the Special Issue Plant Synthetic Biology and Plant Transcriptome)
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18 pages, 3115 KiB  
Article
An Evidence Theory and Fuzzy Logic Combined Approach for the Prediction of Potential ARF-Regulated Genes in Quinoa
by Nesrine Sghaier, Jemaa Essemine, Rayda Ben Ayed, Mustapha Gorai, Riadh Ben Marzoug, Ahmed Rebai and Mingnan Qu
Plants 2023, 12(1), 71; https://doi.org/10.3390/plants12010071 - 23 Dec 2022
Cited by 2 | Viewed by 1932
Abstract
Quinoa constitutes among the tolerant plants to the challenging and harmful abiotic environmental factors. Quinoa was selected as among the model crops destined for bio-saline agriculture that could contribute to the staple food security for an ever-growing worldwide population under various climate change [...] Read more.
Quinoa constitutes among the tolerant plants to the challenging and harmful abiotic environmental factors. Quinoa was selected as among the model crops destined for bio-saline agriculture that could contribute to the staple food security for an ever-growing worldwide population under various climate change scenarios. The auxin response factors (ARFs) constitute the main contributors in the plant adaptation to severe environmental conditions. Thus, the determination of the ARF-binding sites represents the major step that could provide promising insights helping in plant breeding programs and improving agronomic traits. Hence, determining the ARF-binding sites is a challenging task, particularly in species with large genome sizes. In this report, we present a data fusion approach based on Dempster–Shafer evidence theory and fuzzy set theory to predict the ARF-binding sites. We then performed an “In-silico” identification of the ARF-binding sites in Chenopodium quinoa. The characterization of some known pathways implicated in the auxin signaling in other higher plants confirms our prediction reliability. Furthermore, several pathways with no or little available information about their functions were identified to play important roles in the adaptation of quinoa to environmental conditions. The predictive auxin response genes associated with the detected ARF-binding sites may certainly help to explore the biological roles of some unknown genes newly identified in quinoa. Full article
(This article belongs to the Special Issue Plant Synthetic Biology and Plant Transcriptome)
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17 pages, 3422 KiB  
Article
Biochemical Analyses of Bioactive Extracts from Plants Native to Lampedusa, Sicily Minor Island
by Roberta Di Lecce, Natacha Mérindol, Mayra Galarza Pérez, Vahid Karimzadegan, Lionel Berthoux, Angela Boari, Christian Zidorn, Maurizio Vurro, Giuseppe Surico, Isabel Desgagné-Penix and Antonio Evidente
Plants 2022, 11(24), 3447; https://doi.org/10.3390/plants11243447 - 9 Dec 2022
Cited by 2 | Viewed by 1980
Abstract
Major threats to the human lifespan include cancer, infectious diseases, diabetes, mental degenerative conditions and also reduced agricultural productivity due to climate changes, together with new and more devastating plant diseases. From all of this, the need arises to find new biopesticides and [...] Read more.
Major threats to the human lifespan include cancer, infectious diseases, diabetes, mental degenerative conditions and also reduced agricultural productivity due to climate changes, together with new and more devastating plant diseases. From all of this, the need arises to find new biopesticides and new medicines. Plants and microorganisms are the most important sources for isolating new metabolites. Lampedusa Island host a rich contingent of endemic species and subspecies. Seven plant species spontaneously growing in Lampedusa, i.e., Atriplex halimus L. (Ap), Daucus lopadusanus Tineo (Dl), Echinops spinosus Fiori (Es) Glaucium flavum Crantz (Gf) Hypericum aegypticum L: (Ha), Periploca angustifolia Labill (Pa), and Prasium majus L. (Pm) were collected, assessed for their metabolite content, and evaluated for potential applications in agriculture and medicine. The HPLC-MS analysis of n-hexane (HE) and CH2Cl2 (MC) extracts and the residual aqueous phases (WR) showed the presence of several metabolites in both organic extracts. Crude HE and MC extracts from Dl and He significantly inhibited butyrylcholinesterase, as did WR from the extraction of Dl and Pa. HE and MC extracts showed a significant toxicity towards hepatocarcinoma Huh7, while Dl, Ha and Er HE extracts were the most potently cytotoxic to ileocecal colorectal adenocarcinoma HCT-8 cell lines. Most extracts showed antiviral activity. At the lowest concentration tested (1.56 μg/mL), Dl, Gf and Ap MC extracts inhibited betacoronavirus HCoV-OC43 infection by> 2 fold, while the n-hexane extract of Pm was the most potent. In addition, at 1.56 μg/mL, potent inhibition (>10 fold) of dengue virus was detected for Dl, Er, and Pm HE extracts, while Pa and Ap MC extracts dampened infections to undetectable levels. Regarding to phytotoxicity, MC extracts from Er, Ap and Pm were more effective in inhibiting tomato rootlet elongation; the same first two extracts also inhibited seed cress germination while its radicle elongation, due to high sensitivity, was affected by all the extracts. Es and Gf MC extracts also inhibited seed germination of Phelipanche ramosa. Thus, we have uncovered that many of these Lampedusa plants displayed promising biopesticide, antiviral, and biological properties. Full article
(This article belongs to the Special Issue Plant Synthetic Biology and Plant Transcriptome)
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