Plants

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33 pages, 2768 KB

Open AccessArticle

DC-FusionGNN: A Dual-Channel Framework Integrating Global Self-Attention and Local Topology Learning for Identifying Key Resistance Genes Against Fusarium graminearum Infection in Maize

by YinFei Dai, Mengjiao Qiao, Jie Fan, ShiHao Lu, EnShuang Zhao, YuHeng Zhu, Hanbo Liu and Hao Zhang

Plants 2026, 15(10), 1540; https://doi.org/10.3390/plants15101540 - 18 May 2026

Abstract

Fusarium graminearum infection of maize induces complex transcriptional reprogramming, yet existing differential-expression and local graph convolutional approaches struggle to capture long-range and multi-scale regulatory dependencies. We propose DC-FusionGNN, a dual-channel fusion graph neural network for key resistance-gene identification. Based on the transcriptome dataset [...] Read more.

Fusarium graminearum infection of maize induces complex transcriptional reprogramming, yet existing differential-expression and local graph convolutional approaches struggle to capture long-range and multi-scale regulatory dependencies. We propose DC-FusionGNN, a dual-channel fusion graph neural network for key resistance-gene identification. Based on the transcriptome dataset GSE174508, we first construct a comprehensive gene interaction network by integrating a WGCNA co-expression network with a STRING-based interaction network. The left channel combines structure-aware propagation with a Transformer-based global self-attention mechanism to model long-range cross-module dependencies, while the right channel couples GraphSAGE with a GCN to capture local topology and neighborhood heterogeneity. Embeddings from the two channels are concatenated to form a unified gene representation, trained via self-supervised link prediction. Compared with baseline graph neural networks, DC-FusionGNN achieves competitive and overall improved performance across multiple metrics, and robustness and independent cross-species (rice, GSE39635) experiments further confirm its stability and generalization ability. GO and KEGG enrichment analyses show that the top-ranked candidate genes are significantly enriched in plant defense responses, hormone signaling, and secondary metabolism, supporting the biological relevance of the model’s predictions. Full article

(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)

20 pages, 2029 KB

Open AccessArticle

Understanding the Role of Durum Wheat Thioredoxin h-Type TdTrxh2 in Biotic Stress Tolerance

by Hanen Kamoun, Sahar Keskes, Hanen Dhouib, Sana Tounsi, Olfa Jrad, Faiçal Brini and Kaouthar Feki

Plants 2026, 15(4), 521; https://doi.org/10.3390/plants15040521 - 7 Feb 2026

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Abstract

The thioredoxin h-type (Trxh) proteins play a crucial role as convergence points within plants’ responses to abiotic and biotic stresses. Previously, we demonstrated that the protein TdTrxh2 of durum wheat (Triticum durum Desf.) has a chaperone function and it promotes tolerance [...] Read more.

The thioredoxin h-type (Trxh) proteins play a crucial role as convergence points within plants’ responses to abiotic and biotic stresses. Previously, we demonstrated that the protein TdTrxh2 of durum wheat (Triticum durum Desf.) has a chaperone function and it promotes tolerance to abiotic stress. The aim of this study was to evaluate the antimicrobial effect of TdTrxh2 and its role in the response of durum wheat to Fusarium graminearum attack. First, we demonstrated the involvement of TdTrxh2 in the response of durum wheat to this fungus via the analysis of its expression profile under this fungus attack. In fact, the outcomes showed that the induction of TdTrxh2 expression is spatiotemporal in leaves and roots of durum wheat under F. graminearum infection. Interestingly, this induction was accompanied by H₂O₂ accumulation under short- and long-term stress in roots and leaves, respectively. Besides, the cis elements related to the two phytohormones ET and MeJA, and those implicated in defense and wound stress, were identified in the TdTrxh2 promoter’s sequence. Second, the purified TdTrxh2 protein possessed antimicrobial effects against a diverse range of bacteria and fungi in vitro. Finally, the expression of TdTrxh2 in transgenic Arabidopsis plants enhanced their tolerance to F. graminearum attack through the activation of the two H₂O₂-scavenging enzymes, CAT and POD, and via the induction of a subset of SA- and ABA-related genes. Moreover, the exogenous SA and ABA applications improved the growth of the transgenic lines compared to the non-transformed plants. Taken together, the results highlighted that TdTrxh2 generates tolerance of durum wheat’s response to F. graminearum attack, via the regulation of H₂O₂ homeostasis and the induction of hormone-associated genes. Thus, the TdTrxh2 gene could be considered as an interesting candidate gene to improve wheat tolerance to F. graminearum attack. Full article

(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)

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19 pages, 8946 KB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the WOX Family Reveals Potential Roles in Stem Development of Euphorbia hirta

by Qianyi Lyu, Shutong Chen, Xin Wang, Yuan Yuan, Hongrui Zhang, Wanqi Liang, Han Cheng and Zhi Deng

Plants 2026, 15(3), 509; https://doi.org/10.3390/plants15030509 - 6 Feb 2026

Viewed by 637

Abstract

The homeobox transcription factor (TF) superfamily includes the WUSCHEL-RELATED HOMEOBOX (WOX) family, which plays a critical role in adaptive plant growth. Specifically, WOX regulates stem growth in plants, with stems serving as the structural framework for laticifers in Euphorbia hirta. However, the [...] Read more.

The homeobox transcription factor (TF) superfamily includes the WUSCHEL-RELATED HOMEOBOX (WOX) family, which plays a critical role in adaptive plant growth. Specifically, WOX regulates stem growth in plants, with stems serving as the structural framework for laticifers in Euphorbia hirta. However, the number of WOX gene family members in the E. hirta genome has not been reported. In this study, we identified 14 EhWOX genes in E. hirta and characterized their physicochemical properties, chromosomal locations, phylogenetic relationships, conserved motifs, gene structures, promoter cis elements, gene ontology (GO) enrichment, tissue-specific expression patterns, and subcellular localization. Chromosomal mapping indicated their distribution across nine chromosomes. Phylogenetic analysis classified these genes into three evolutionary clades. Promoter cis-element analysis identified abundant light-responsive, hormone-responsive, and stress-responsive elements. GO enrichment suggested their broad involvement in diverse biological processes. Additionally, RNA-seq revealed high expression levels of EhWOX4-6 and EhWOX14 in stems. Furthermore, RT-qPCR confirmed tissue-specific expression in stems. Moreover, experimental evidence confirmed the subcellular localization and autoactivation capability of some WOX proteins that may be involved in stem development. Overall, this study provides a comprehensive characterization of the candidate EhWOX genes and provides a foundational resource for future functional investigations into their possible roles in stem and laticifer biology. Full article

(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)

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14 pages, 26943 KB

Open AccessArticle

The Influence of Transgenic Insect-Resistance and Herbicide-Tolerance Soybean KM2208-23 on the Rhizosphere Micro-Biome

by Xue Song, Xinyao Xia, Shuke Yang, Chaofeng Hao, Hongwei Sun, Fan Li, Xiaohui Xu, Hongxia Zhang and Xingbo Lu

Plants 2026, 15(2), 329; https://doi.org/10.3390/plants15020329 - 21 Jan 2026

Viewed by 481

Abstract

The consequences of stacking multiple insect-resistance and herbicide-tolerance genes, particularly across the entire plant life cycle, remain inadequately understood. This study investigated the impact of stacked-trait transgenic soybeans on rhizosphere microbial communities across five growth stages (pre-sowing, V3, R3, R5, R8). Using 16S [...] Read more.

The consequences of stacking multiple insect-resistance and herbicide-tolerance genes, particularly across the entire plant life cycle, remain inadequately understood. This study investigated the impact of stacked-trait transgenic soybeans on rhizosphere microbial communities across five growth stages (pre-sowing, V3, R3, R5, R8). Using 16S rRNA and ITS sequencing, we compared the rhizosphere microbiome of the transgenic modified soybean (GMO) with its non-transgenic control check (CK). Results showed transient but significant shifts in soil properties (e.g., available nitrogen) and microbial beta diversity during the V3 stages. However, plant developmental stage was the predominant factor shaping microbial succession, with its effect outweighing that of the transgene. No persistent changes in microbial alpha diversity were observed. We conclude that the influence of this stacked-trait soybean on the rhizosphere is growth-stage-specific and represents a minor, recoverable perturbation rather than a sustained ecological impact. These findings contribute to the ecological safety assessment of multi-gene transgenic crops. Full article

(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)

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13 pages, 1194 KB

Open AccessCommunication

Progress in Flax Genome Assembly from Nanopore Sequencing Data

by Elena N. Pushkova, Alexander A. Arkhipov, Nadezhda L. Bolsheva, Tatiana A. Rozhmina, Alexander A. Zhuchenko, Elena V. Borkhert, Nikolai M. Barsukov, Gavriil A. Oleshnya, Alina V. Milovanova, Olesya D. Moskalenko, Fedor D. Kostromskoy, Elizaveta A. Ivankina, Ekaterina M. Dvorianinova, Daiana A. Krupskaya, Nataliya V. Melnikova and Alexey A. Dmitriev

Plants 2026, 15(1), 151; https://doi.org/10.3390/plants15010151 - 4 Jan 2026

Viewed by 1015

Abstract

In recent years, the quality of genome assemblies has notably improved, primarily due to advances in third-generation sequencing technologies and bioinformatics tools. In the present study, we obtained genome assemblies for two flax (Linum usitatissimum L.) varieties, K-3018 and Svyatogor, using Oxford [...] Read more.

In recent years, the quality of genome assemblies has notably improved, primarily due to advances in third-generation sequencing technologies and bioinformatics tools. In the present study, we obtained genome assemblies for two flax (Linum usitatissimum L.) varieties, K-3018 and Svyatogor, using Oxford Nanopore Technologies (ONT) simplex R10.4.1 data and the Hifiasm algorithm optimized for ONT reads. The K-3018 genome assembly was 491.1 Mb and consisted of thirteen full-length chromosomes and two one-gap chromosomes. The Svyatogor genome assembly was 497.8 Mb and consisted of twelve full-length chromosomes and three one-gap chromosomes. All chromosomes had telomeric repeats at their ends for both varieties. Hi-C contact maps and Illumina genomic data supported the accuracy of the obtained assemblies. The K-3018 and Svyatogor genome assemblies surpassed the quality of the best currently available flax genome assembly of variety T397, which serves as a reference for L. usitatissimum in the NCBI Genome database. Comparative analysis revealed that the flax genomes are generally quite similar at the chromosome level, with only a few large-scale differences. Thus, two near-T2T (telomere-to-telomere) flax genomes were assembled from the ONT simplex R10.4.1 reads using Hifiasm ONT without involving Pacific Biosciences (PacBio) HiFi or ultra-long ONT reads as well as optical maps. High-quality flax genomes are essential for improving the efficiency of genetic research, evaluating genetic diversity at the whole-genome level, and developing breeding and genome editing approaches of this valuable multipurpose crop. Full article

(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)

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17 pages, 8876 KB

Open AccessArticle

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

Cited by 1 | Viewed by 894

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

Open AccessArticle

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

Cited by 1 | Viewed by 1836

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

Open AccessArticle

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 1263

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

Open AccessArticle

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

Cited by 3 | Viewed by 1571

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

Open AccessArticle

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 1291

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

Open AccessReview

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

Cited by 2 | Viewed by 3079

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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24 pages, 4341 KB

Open AccessEssay

Deep Learning-Based Identification of Pathogenicity Genes in Phytophthora infestans Using Time-Series Transcriptomics

by Yinfei Dai, Shihao Lu, Jie Fan, Mengjiao Qiao, Yuheng Zhu, Enshuang Zhao and Hao Zhang

Plants 2026, 15(2), 178; https://doi.org/10.3390/plants15020178 - 6 Jan 2026

Viewed by 599

Abstract

Potato (Solanum tuberosum L.) is the world’s fourth most important food crop, and despite China producing nearly one quarter of the global yield, its potato production is severely constrained by late blight. Identifying genes associated with pathogenicity is essential for breeding resistant [...] Read more.

Potato (Solanum tuberosum L.) is the world’s fourth most important food crop, and despite China producing nearly one quarter of the global yield, its potato production is severely constrained by late blight. Identifying genes associated with pathogenicity is essential for breeding resistant cultivars and strengthening plant protection strategies. Traditional approaches based on differential expression and statistical modeling often fail to capture temporal dynamics or provide interpretable insights. Here, we introduce an LSTM–Transformer hybrid model designed for data-driven discovery of pathogenicity-related genes from gene expression time-series. The analysis was performed on a time-series expression dataset comprising 32,917 genes across 18 samples (three infection time points × six biological replicates per condition). In this study, we identified 200 high-confidence pathogenicity-related genes from potato infection time-series data. These genes are enriched in 15 biologically meaningful pathways, including plant immunity signaling, reactive oxygen species regulation, secondary metabolic processes, and stress-responsive transcriptional programs. Several newly uncovered candidates participate in defense hormone pathways and cell wall modification, suggesting previously unrecognized roles in late blight susceptibility and resistance. By revealing functional groups and regulatory signatures that characterize pathogenicity, this work provides valuable molecular targets for developing late blight-resistant cultivars. The framework integrates a biologically informed temporal–attention architecture, a gene time-series-specific data partitioning strategy, and an interpretable deep analysis module. A final methodological contribution is the use of a temporal attention-based analytical framework that enables reliable gene prioritization from time-series expression data. Full article

(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)

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