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Plants
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Applications of Bioinformatics in Plant Science
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Applications of Bioinformatics in Plant Science

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 January 2026 | Viewed by 3569

Special Issue Editors

Dr. Hua Zhong

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Guest Editor
Population Sciences in the Pacific Program, University of Hawaiʻi at Mānoa, Honolulu, HI 96813, USA
Interests: population genetics; genomics; bioinformatics; post-GWAS
Special Issues, Collections and Topics in MDPI journals
Dr. Junfei Ma

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Guest Editor Assistant
Department of Plant Pathology, University of Florida, Gainesville, FL 32608, USA
Interests: plant; RNA structure; viroid; plant defense

Special Issue Information

Dear Colleagues,

The rapid advancement of high-throughput technologies has generated large-scale datasets that offer unprecedented insights into plant biology. Bioinformatics plays a pivotal role in deciphering this complex information, enabling researchers to explore plant genomics, transcriptomics, proteomics, metabolomics, and epigenomics with enhanced precision. This Special Issue aims to highlight the cutting-edge applications of bioinformatics in plant science, including genome assembly, functional annotation, gene regulatory network analysis, trait mapping, and evolutionary studies. We welcome submissions that utilize novel computational approaches, databases, algorithms, and integrative analyses to solve key questions in plant biology. Studies involving model plants, crops, and non-model species are equally encouraged. By bridging computational innovation and plant research, this Issue seeks to foster collaboration and inspire future advancements in the field.

Dr. Hua Zhong
Guest Editor

Dr. Junfei Ma
Guest Editor Assistant

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

  • plant bioinformatics
  • genomics
  • transcriptomics
  • functional annotation
  • computational biology
  • gene networks
  • genome-wide association studies (GWAS)
  • evolutionary genomics
  • plant systems biology
  • omics data integration

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Published Papers (6 papers)

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Research

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17 pages, 8876 KB  
Article
Genome-Wide Characterization of SNAC Gene Family in Ten Cotton Species and Function Analysis of GhSNAC3D Under Cold Stress
by Jiliang Fan, Lu Meng, Faren Zhu, Jiahuan Niu, Ganggang Zhang, Junwei Wang, Zhonghui Li, Fei Wang and Hongbin Li
Plants 2025, 14(18), 2894; https://doi.org/10.3390/plants14182894 - 18 Sep 2025
Viewed by 237
Abstract
The SNAC (Stress-responsive NAC) subfamily, a key branch of the conserved NAC transcription factor family, plays a central role in regulating plant stress response. However, systematic characterization of the SNAC family in cotton (Gossypium spp.) remains unclear. Employing a genome-wide screening approach, [...] Read more.
The SNAC (Stress-responsive NAC) subfamily, a key branch of the conserved NAC transcription factor family, plays a central role in regulating plant stress response. However, systematic characterization of the SNAC family in cotton (Gossypium spp.) remains unclear. Employing a genome-wide screening approach, this study characterized 75 distinct SNAC transcription factor genes across ten Gossypium species, with tetraploid cottons harboring twice as many as their diploid progenitors. Phylogenetic analysis categorized the genes into three subgroups, with members of the same subgroup exhibiting conserved motif compositions and gene structures. Chromosomal localization revealed a conserved distribution pattern of SNAC genes between the Dt and At subgenomes in tetraploid cotton. Genomic collinearity analysis suggested that the primary driver of SNAC family expansion was segmental duplication. Promoter analysis predicted 2974 cis-regulatory elements, including cold- and hormone-responsive motifs, indicating their potential involvement in stress regulation. These GhSNAC genes indicated significant induced expressions under stress conditions, and GhSNAC3D exhibited the most significant up-regulated expression under low temperature stress. Genetic function studies displayed that VIGS-mediated GhSNAC3D-silencing significantly reduced the cold tolerance in cotton. This study systematically analyzed the genomic characteristics of the cotton SNAC family and functionally validated the molecular mechanism of GhSNAC3D-mediated cryogenic response, which lays a foundation for subsequent research on cold resistance in cotton and stress-resistant breeding. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)
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19 pages, 7094 KB  
Article
Group 1 LEA Proteins in Durum Wheat: Evolution, Expression, and Roles in Abiotic Stress Tolerance
by Najeh Soltani, Ikram Zaidi, Mohamed Najib Saidi and Faiçal Brini
Plants 2025, 14(18), 2817; https://doi.org/10.3390/plants14182817 - 9 Sep 2025
Viewed by 403
Abstract
Group 1 LEA proteins are involved in embryo water dynamics during the maturation stage of seed development and contribute to desiccation stress protection in vegetative and embryonic tissues. Nevertheless, their roles in durum wheat remain largely unexplored. This study represents the first comprehensive [...] Read more.
Group 1 LEA proteins are involved in embryo water dynamics during the maturation stage of seed development and contribute to desiccation stress protection in vegetative and embryonic tissues. Nevertheless, their roles in durum wheat remain largely unexplored. This study represents the first comprehensive survey of group 1 LEA proteins and their encoding genes in Triticum turgidum ssp. Durum (durum wheat). Eight group 1 LEA (TtEM1 to TtEM8) genes were identified in the durum wheat genome, which were named according to their chromosomal location. Analyses of the physiochemical characteristics and subcellular location revealed that all TtEM proteins exhibited a highly disordered structure (more than 90% of tendency of disorder) and were located in the nucleus. Evolutionary analysis between the durum wheat family and all other known group 1 LEA proteins from Arabidopsis thaliana, rice (Oryza sativa), barley (Hordeum vulgare), and barrel medic (Medicago truncatula) showed four phylogenetic groups; each group shares the same conserved motifs and gene structure. Interestingly, almost TtEM genes harbor cis-elements related to hormone regulation, stress response, and growth regulation, indicating their function in stress tolerance and developmental control. Subsequently, Expression analysis of two homoeologous genes, TtEM1 and TtEM4, demonstrated that the two genes exhibited distinct expression profiles across different tissues and in response to various stress treatments, suggesting that these genes may be involved in regulating growth, development, and stress adaptation in durum wheat. TtEM1 and TtEM4 purified proteins act as molecular chaperones and protect LDH activity against desiccation, cold, and heat treatments. Moreover, TtEM1 and TtEM4 genes were proved to enhance heat, cold, oxidative, and drought tolerance in yeast. These results clearly described the characteristics and the evolutionary dynamics of the EM gene family in wheat, and unveiled their role in wheat development and response to abiotic stress. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)
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20 pages, 14306 KB  
Article
Genome-Wide Identification and Expression Analysis of the Melon B-BOX (BBX) Gene Family in Response to Abiotic and Biotic Stresses
by Yu Zhang, Yin Li, Yan Wang, Congsheng Yan, Dekun Yang, Yujie Xing and Xiaomin Lu
Plants 2025, 14(17), 2715; https://doi.org/10.3390/plants14172715 - 1 Sep 2025
Viewed by 503
Abstract
The BBX gene family functions as a key transcription factor implicated in plant growth, development, and stress responses. However, research on this gene family in melon remains absent. In the present study, we identified 19 BBX family genes within the melon genome, distributed [...] Read more.
The BBX gene family functions as a key transcription factor implicated in plant growth, development, and stress responses. However, research on this gene family in melon remains absent. In the present study, we identified 19 BBX family genes within the melon genome, distributed across chromosomes 1, 2, 3, 4, 5, 7, 8, 10, 11, and 12. Phylogenetic analysis categorized these genes into five distinct subfamilies, with notable similarities observed in gene structure and conserved motifs among members of the same subfamily. Synteny analysis revealed seven syntenic relationships among melon BBX genes, 17 between melon and Arabidopsis, and one between melon and rice. Reanalysis of transcriptome data indicated that certain BBX genes exhibit high expression levels across various tissues and developmental stages of fruits, while others display tissue specificity. Under both abiotic and biotic stress conditions, genes such as CmBBX3, CmBBX5, CmBBX2, CmBBX18, CmBBX15, and CmBBX11 demonstrated significant differential expression, highlighting their critical roles in melon growth and development. Additionally, RT-qPCR analysis was conducted to examine the expression levels of melon BBX genes at different time points under salt stress, further validating the transcriptome data. This study provides a theoretical foundation for future molecular breeding efforts in melon. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)
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25 pages, 7432 KB  
Article
Integration of mRNA and miRNA Analysis Reveals the Regulation of Salt Stress Response in Rapeseed (Brassica napus L.)
by Yaqian Liu, Danni Li, Yutong Qiao, Niannian Fan, Ruolin Gong, Hua Zhong, Yunfei Zhang, Linfen Lei, Jihong Hu and Jungang Dong
Plants 2025, 14(15), 2418; https://doi.org/10.3390/plants14152418 - 4 Aug 2025
Viewed by 548
Abstract
Soil salinization is a major constraint to global crop productivity, highlighting the need to identify salt tolerance genes and their molecular mechanisms. Here, we integrated mRNA and miRNA profile analyses to investigate the molecular basis of salt tolerance of an elite Brassica napus [...] Read more.
Soil salinization is a major constraint to global crop productivity, highlighting the need to identify salt tolerance genes and their molecular mechanisms. Here, we integrated mRNA and miRNA profile analyses to investigate the molecular basis of salt tolerance of an elite Brassica napus cultivar S268. Time-course RNA-seq analysis revealed dynamic transcriptional reprogramming under 215 mM NaCl stress, with 212 core genes significantly enriched in organic acid degradation and glyoxylate/dicarboxylate metabolism pathways. Combined with weighted gene co-expression network analysis (WGCNA) and RT-qPCR validation, five candidate genes (WRKY6, WRKY70, NHX1, AVP1, and NAC072) were identified as the regulators of salt tolerance in rapeseed. Haplotype analysis based on association mapping showed that NAC072, ABI5, and NHX1 exhibited two major haplotypes that were significantly associated with salt tolerance variation under salt stress in rapeseed. Integrated miRNA-mRNA analysis and RT-qPCR identified three regulatory miRNA-mRNA pairs (bna-miR160a/BnaA03.BAG1, novel-miR-126/BnaA08.TPS9, and novel-miR-70/BnaA07.AHA1) that might be involved in S268 salt tolerance. These results provide novel insights into the post-transcriptional regulation of salt tolerance in B. napus, offering potential targets for genetic improvement. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)
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16 pages, 4634 KB  
Article
Dynamic Coordination of Alternative Splicing and Subgenome Expression Bias Underlies Rusty Root Symptom Response in Panax ginseng
by Jing Zhao, Juzuo Li, Xiujuan Lei, Peng Di, Hongwei Xun, Zhibin Zhang, Jian Zhang, Xiangru Meng and Yingping Wang
Plants 2025, 14(14), 2120; https://doi.org/10.3390/plants14142120 - 9 Jul 2025
Viewed by 466
Abstract
Ginseng rusty root symptoms (GRSs) compromise the yield and quality of Panax ginseng. While transcriptomic analyses have demonstrated extensive remodeling of stress signaling networks, the post-transcriptional defense circuitry remains obscure. We profiled alternative splicing (AS) in three phloem tissues, the healthy phloem [...] Read more.
Ginseng rusty root symptoms (GRSs) compromise the yield and quality of Panax ginseng. While transcriptomic analyses have demonstrated extensive remodeling of stress signaling networks, the post-transcriptional defense circuitry remains obscure. We profiled alternative splicing (AS) in three phloem tissues, the healthy phloem (AG), the non-reddened phloem neighboring lesions (BG), and the reddened lesion core (CG), to delineate AS reprogramming during GRS progression. The frequency of AS was sharply elevated in CG, with intron retention predominating. Extensive gains and losses of splice events indicate large-scale rewiring of the splice network. Overlapping differentially alternative spliced genes (DAGs) identified in both CG vs AG and CG vs BG contrasts were significantly enriched for RNA–spliceosome assembly and stress–response pathways, revealing a conserved post-transcriptional response associated with lesion formation. Integrative analysis of differentially expressed genes uncovered 671 loci under dual regulation; functional classification categorized these genes in receptor-like kinase signaling and chromatin-remodeling modules, underscoring the synergy between AS and transcriptional control. Moreover, the B subgenome disproportionately contributed stress-responsive transcripts in diseased tissue, suggesting an adaptive, subgenome-biased strategy. These findings demonstrate that dynamic AS remodeling and subgenome expression bias jointly orchestrate ginseng defense against GRS and provide a framework for breeding disease-resilient crops. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)
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Review

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36 pages, 3621 KB  
Review
Harnessing Molecular Phylogeny and Chemometrics for Taxonomic Validation of Korean Aromatic Plants: Integrating Genomics with Practical Applications
by Adnan Amin and Seonjoo Park
Plants 2025, 14(15), 2364; https://doi.org/10.3390/plants14152364 - 1 Aug 2025
Viewed by 899
Abstract
Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a [...] Read more.
Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a comprehensive overview of the chemotaxonomic traits, biological activities, phylogenetic relationships and potential applications of Korean aromatic plants, highlighting their significance in more accurate identification. Chemotaxonomic investigations employing techniques such as gas chromatography mass spectrometry, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy have enabled the identification of essential oils and specialized metabolites that serve as valuable taxonomic and diagnostic markers. These chemical traits play essential roles in species delimitation and in clarifying interspecific variation. The biological activities of selected taxa are reviewed, with emphasis on antimicrobial, antioxidant, anti-inflammatory, and cytotoxic effects, supported by bioassay-guided fractionation and compound isolation. In parallel, recent advances in phylogenetic reconstruction employing DNA barcoding, internal transcribed spacer regions, and chloroplast genes such as rbcL and matK are examined for their role in clarifying taxonomic uncertainties and inferring evolutionary lineages. Overall, the search period was from year 2001 to 2025 and total of 268 records were included in the study. By integrating phytochemical profiling, pharmacological evidence, and molecular systematics, this review highlights the multifaceted significance of Korean endemic aromatic plants. The conclusion highlights the importance of multidisciplinary approaches including metabolomics and phylogenomics in advancing our understanding of species diversity, evolutionary adaptation, and potential applications. Future research directions are proposed to support conservation efforts. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)
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