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 396

Special Issue Editors


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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

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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

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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 (1 paper)

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Research

16 pages, 4634 KiB  
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
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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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