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Biology
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Plant Functional Genomics in the Era of Omics Approaches
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Plant Functional Genomics in the Era of Omics Approaches

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 13212

Special Issue Editors

Dr. Mariateresa Volpicella

E-Mail Website
Guest Editor
Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
Interests: plant molecular biology; NGS approaches; metagenomics and functional genomics
Dr. Cinzia Montemurro

E-Mail Website
Guest Editor
Department of Soil, Plants and Food Sciences, Faculty of Agricultural Science, University of Bari “Aldo Moro”, 70126 Bari, Italy
Interests: genotyping by sequencing; olive germplasm; grapevine; genetic diversity; functional genomics; molecular polymorphism
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, omics approaches have offered an extraordinary opportunity to identify and measure a huge number of genes and proteins that play a crucial role in the regulation of several plant cellular processes. The availability of the entire genome from model plants, such as Arabidopsis thaliana and rice, lays the foundations for understanding and assigning functions to unknown genes, using different and multiparallel approaches. Indeed, comparative genome analysis is actually a powerful approach, which is useful in the identification of gene functions associated with plant metabolic processes and development. In this perspective, all the data derived from transcriptomics, proteomics and metabolomics studies allow the investigation of the intricate network of relationships between biomolecules within the plant system.

This Special Issue welcomes the submission of original research and review manuscripts focusing on plant functional genomic studies, including methods and developments that have made contributions to field development.

Dr. Mariateresa Volpicella
Prof. Dr. Cinzia Montemurro
Guest Editors

Manuscript Submission Information

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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

  • plant systems biology
  • gene expression
  • transcriptomics
  • proteomics
  • metabolomics
  • functional genomics

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Published Papers (5 papers)

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Research

18 pages, 4823 KiB  
Article
Comprehensive Analysis of WUSCEL-Related Homeobox Gene Family in Ramie (Boehmeria nivea) Indicates Its Potential Role in Adventitious Root Development
by Aminu Shehu Abubakar, Yongmei Wu, Fengming Chen, Aiguo Zhu, Ping Chen, Kunmei Chen, Xiaojun Qiu, Xiaoyu Huang, Haohan Zhao, Jikang Chen and Gang Gao
Biology 2023, 12(12), 1475; https://doi.org/10.3390/biology12121475 - 28 Nov 2023
Cited by 2 | Viewed by 1589
Abstract
A WUSCHEL-related homeobox (WOX) gene family has been implicated in promoting vegetative organs to embryonic transition and maintaining plant embryonic stem cell identity. Using genome-wide analysis, we identified 17 candidates, WOX genes in ramie (Boehmeria nivea). The genes (BnWOX) showed highly [...] Read more.
A WUSCHEL-related homeobox (WOX) gene family has been implicated in promoting vegetative organs to embryonic transition and maintaining plant embryonic stem cell identity. Using genome-wide analysis, we identified 17 candidates, WOX genes in ramie (Boehmeria nivea). The genes (BnWOX) showed highly conserved homeodomain regions typical of WOX. Based on phylogenetic analysis, they were classified into three distinct groups: modern, intermediate, and ancient clades. The genes displayed 65% and 35% collinearities with their Arabidopsis thaliana and Oryza sativa ortholog, respectively, and exhibited similar motifs, suggesting similar functions. Furthermore, four segmental duplications (BnWOX10/14, BnWOX13A/13B, BnWOX9A/9B, and BnWOX6A/Maker00021031) and a tandem-duplicated pair (BnWOX5/7) among the putative ramie WOX genes were obtained, suggesting that whole-genome duplication (WGD) played a role in WOX gene expansion. Expression profiling analysis of the genes in the bud, leaf, stem, and root of the stem cuttings revealed higher expression levels of BnWOX10 and BnWOX14 in the stem and root and lower in the leaf consistent with the qRT-PCR analysis, suggesting their direct roles in ramie root formation. Analysis of the rooting characteristics and expression in the stem cuttings of sixty-seven different ramie genetic resources showed a possible involvement of BnWOX14 in the adventitious rooting of ramie. Thus, this study provides valuable information on ramie WOX genes and lays the foundation for further research. Full article
(This article belongs to the Special Issue Plant Functional Genomics in the Era of Omics Approaches)
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16 pages, 3891 KiB  
Article
Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand
by Chaiwat Naktang, Supaporn Khanbo, Chutintorn Yundaeng, Sonicha U-thoomporn, Wasitthee Kongkachana, Darunee Jiumjamrassil, Chatree Maknual, Poonsri Wanthongchai, Sithichoke Tangphatsornruang and Wirulda Pootakham
Biology 2023, 12(3), 484; https://doi.org/10.3390/biology12030484 - 21 Mar 2023
Cited by 1 | Viewed by 3014
Abstract
Unique and biodiverse, mangrove ecosystems provide humans with benefits and contribute to coastal protection. Rhizophora mucronata, a member of the Rhizophoraceae family, is prevalent in the mangrove forests of Thailand. R. mucronata’s population structure and genetic diversity have received scant attention. [...] Read more.
Unique and biodiverse, mangrove ecosystems provide humans with benefits and contribute to coastal protection. Rhizophora mucronata, a member of the Rhizophoraceae family, is prevalent in the mangrove forests of Thailand. R. mucronata’s population structure and genetic diversity have received scant attention. Here, we sequenced the entire genome of R. mucronata using 10× Genomics technology and obtained an assembly size of 219 Mb with the N50 length of 542,540 bases. Using 2857 single nucleotide polymorphism (SNP) markers, this study investigated the genetic diversity and population structure of 80 R. mucronata accessions obtained from the mangrove forests in Thailand. The genetic diversity of R. mucronata was moderate (I = 0.573, Ho = 0.619, He = 0.391). Two subpopulations were observed and confirmed from both population structure and principal component analysis (PCA). Analysis of molecular variance (AMOVA) showed that there was more variation within populations than between them. Mean pairwise genetic differentiation (FST = 0.09) showed that there was not much genetic difference between populations. Intriguingly, the predominant clustering pattern in the R. mucronata population did not correspond to the Gulf of Thailand and the Andaman Sea, which are separated by the Malay Peninsula. Several factors could have influenced the R. mucronata genetic pattern, such as hybridization and anthropogenic factors. This research will provide important information for the future conservation and management of R. mucronata in Thailand. Full article
(This article belongs to the Special Issue Plant Functional Genomics in the Era of Omics Approaches)
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17 pages, 8142 KiB  
Article
Comprehensive Identification and Expression Profiling of the VQ Motif-Containing Gene Family in Brassica juncea
by Jie Zheng, Haibo Li, Ziqi Guo, Xiaoman Zhuang, Weifeng Huang, Cui Mao, Huimin Feng, Yang Zhang, Hao Wu and Yong Zhou
Biology 2022, 11(12), 1814; https://doi.org/10.3390/biology11121814 - 14 Dec 2022
Cited by 4 | Viewed by 1947
Abstract
Valine-glutamine (VQ) motif-containing proteins are a class of highly conserved transcriptional regulators in plants and play key roles in plant growth, development, and response to various stresses. However, the VQ family genes in mustard have not yet been comprehensively identified and analyzed. In [...] Read more.
Valine-glutamine (VQ) motif-containing proteins are a class of highly conserved transcriptional regulators in plants and play key roles in plant growth, development, and response to various stresses. However, the VQ family genes in mustard have not yet been comprehensively identified and analyzed. In this study, a total of 120 VQ family genes (BjuVQ1 to BjuVQ120), which were unevenly distributed on 18 chromosomes (AA_Chr01 to BB_Chr08), were characterized in mustard. A phylogenetic tree analysis revealed that the BjuVQ proteins were clustered into nine distinct groups (groups I to IX), and members in the same group shared a highly conserved motif composition. A gene structure analysis suggested that most BjuVQ genes were intronless. A gene duplication analysis revealed that 254 pairs of BjuVQ genes were segmentally duplicated and one pair was tandemly duplicated. Expression profiles obtained from RNA-seq data demonstrated that most BjuVQ genes have different gene expression profiles in different organs, including leaf, stem, root, flower bud, pod, and seed. In addition, over half of the BjuVQ genes were differentially expressed at some time points under low temperature treatment. The qRT-PCR data revealed that BjuVQ23, BjuVQ55, BjuVQ57, BjuVQ67, BjuVQ100, and BjuVQ117 were upregulated in response to cold stress. Taken together, our study provides new insights into the roles of different BjuVQ genes in mustard and their possible roles in growth and development, as well as in response to cold stress. Full article
(This article belongs to the Special Issue Plant Functional Genomics in the Era of Omics Approaches)
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15 pages, 6531 KiB  
Article
Molecular Characterization and Functional Localization of a Novel SUMOylation Gene in Oryza sativa
by Eid I. Ibrahim, Kotb A. Attia, Abdelhalim I. Ghazy, Kimiko Itoh, Fahad N. Almajhdi and Abdullah A. Al-Doss
Biology 2022, 11(1), 53; https://doi.org/10.3390/biology11010053 - 31 Dec 2021
Cited by 4 | Viewed by 2379
Abstract
Small ubiquitin-related modifier (SUMO) regulates the cellular function of diverse proteins through post-translational modifications. The current study defined a new homolog of SUMO genes in the rice genome and named it OsSUMO7. Putative protein analysis of OsSUMO7 detected SUMOylation features, including di-glycine [...] Read more.
Small ubiquitin-related modifier (SUMO) regulates the cellular function of diverse proteins through post-translational modifications. The current study defined a new homolog of SUMO genes in the rice genome and named it OsSUMO7. Putative protein analysis of OsSUMO7 detected SUMOylation features, including di-glycine (GG) and consensus motifs (ΨKXE/D) for the SUMOylation site. Phylogenetic analysis demonstrated the high homology of OsSUMO7 with identified rice SUMO genes, which indicates that the OsSUMO7 gene is an evolutionarily conserved SUMO member. RT-PCR analysis revealed that OsSUMO7 was constitutively expressed in all plant organs. Bioinformatic analysis defined the physicochemical properties and structural model prediction of OsSUMO7 proteins. A red fluorescent protein (DsRed), fused with the OsSUMO7 protein, was expressed and localized mainly in the nucleus and formed nuclear subdomain structures. The fusion proteins of SUMO-conjugating enzymes with the OsSUMO7 protein were co-expressed and co-localized in the nucleus and formed nuclear subdomains. This indicated that the OsSUMO7 precursor is processed, activated, and transported to the nucleus through the SUMOylation system of the plant cell. Full article
(This article belongs to the Special Issue Plant Functional Genomics in the Era of Omics Approaches)
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24 pages, 7536 KiB  
Article
Targeting Penicillium expansum GMC Oxidoreductase with High Affinity Small Molecules for Reducing Patulin Production
by Vincenzo Tragni, Pietro Cotugno, Anna De Grassi, Maria Maddalena Cavalluzzi, Annamaria Mincuzzi, Giovanni Lentini, Simona Marianna Sanzani, Antonio Ippolito and Ciro Leonardo Pierri
Biology 2021, 10(1), 21; https://doi.org/10.3390/biology10010021 - 31 Dec 2020
Cited by 4 | Viewed by 3051
Abstract
Flavine adenine dinucleotide (FAD) dependent glucose methanol choline oxidoreductase (GMC oxidoreductase) is the terminal key enzyme of the patulin biosynthetic pathway. GMC oxidoreductase catalyzes the oxidative ring closure of (E)-ascladiol to patulin. Currently, no protein involved in the patulin biosynthesis in [...] Read more.
Flavine adenine dinucleotide (FAD) dependent glucose methanol choline oxidoreductase (GMC oxidoreductase) is the terminal key enzyme of the patulin biosynthetic pathway. GMC oxidoreductase catalyzes the oxidative ring closure of (E)-ascladiol to patulin. Currently, no protein involved in the patulin biosynthesis in Penicillium expansum has been experimentally characterized or solved by X-ray diffraction. Consequently, nothing is known about P. expansum GMC oxidoreductase substrate-binding site and mode of action. In the present investigation, a 3D comparative model for P. expansum GMC oxidoreductase has been described. Furthermore, a multistep computational approach was used to identify P. expansum GMC oxidoreductase residues involved in the FAD binding and in substrate recognition. Notably, the obtained 3D comparative model of P. expansum GMC oxidoreductase was used for performing a virtual screening of a chemical/drug library, which allowed to predict new GMC oxidoreductase high affinity ligands to be tested in in vitro/in vivo assays. In vitro assays performed in presence of 6-hydroxycoumarin and meticrane, among the highly affinity predicted binders, confirmed a dose-dependent inhibition (17–81%) of patulin production by 6-hydroxycoumarin (10 µM–1 mM concentration range), whereas the approved drug meticrane inhibited patulin production by 43% already at 10 µM. Furthermore, 6-hydroxycoumarin and meticrane caused a 60 and 41% reduction of patulin production, respectively, in vivo on apples at 100 µg/wound. Full article
(This article belongs to the Special Issue Plant Functional Genomics in the Era of Omics Approaches)
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