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25th Anniversary of IJMS: Updates and Advances in Molecular Plant Sciences

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 August 2026 | Viewed by 6227

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Dr. Andrei Smertenko

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Institute of Biological Chemistry, Washington State University, Plant Sciences Building, Room 281, Washington, WA, USA
Interests: drought; heat; organelles; peroxisomes; signaling; cytoskeleton; cytokinesis
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Special Issue Information

Dear Colleagues,

The International Journal of Molecular Sciences proudly marks its 25th anniversary in 2025. Over the past quarter-century, IJMS has published thousands of original research and review articles spanning a wide array of disciplines. Among these, plant molecular science has been a particularly dynamic and rapidly evolving field. To commemorate this milestone, the editorial board is pleased to announce a dedicated Special Issue titled “25th Anniversary of IJMS: Updates and Advances in Molecular Plant Sciences”. We warmly invite contributions that explore any of the following timely and impactful areas:

Epigenetics and Gene Regulation—DNA methylation and stress memory, histone modifications, non-coding RNAs
Signal Transduction and Hormone Pathways—ABA signaling, jasmonate–salicylate crosstalk, peptide signaling
Genome Editing and Synthetic Biology—Base and prime editing, multiplexed CRISPR, synthetic promoters
Protein–Protein Interactions and Post-Translational Modifications—Ubiquitin–proteasome system, phosphorylation networks, SUMOylation
Metabolic Engineering—Terpenoid and phenylpropanoid pathways, C₄ photosynthesis engineering, nitrogen fixation in non-legumes
Cell Wall Biology—Lignin engineering, cellulose synthase complexes, dynamic remodeling of cell walls
Organelle Communication—Retrograde signaling, mitochondrial ROS pathways, plasmodesmata regulation
Single-Cell and Spatial Omics—Single-cell RNA sequencing, spatial transcriptomics, proteomics, metabolomics
Circadian Rhythms and Environmental Sensing—Photoreceptor signaling networks, circadian regulation of nutrient uptake
Molecular Plant Immunity—NLR resistosomes, effector-triggered immunity, exosome-mediated defense
Evolutionary and Comparative Genomics—Pangenome analyses, rediscovery of domestication genes
Nanobiotechnology in Plants—Nanoparticle delivery systems, carbon nanotube-based sensors
Emerging Tools and Techniques—Nanotechnology applications in plant science, synthesis of secondary metabolites for drug development

Dr. Andrei Smertenko
Guest Editor

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

plant science
plant biochemistry
mechanisms
plant development
stress responses
plant physiology
genetics

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Published Papers (8 papers)

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Research

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12 pages, 1952 KB

Open AccessArticle

TP-ARMS: A Cost-Effective PCR-Based Genotyping System for Precision Breeding of Small InDels in Crops

by Yuan Wang, Jiahong Chen and Yi Liu

Int. J. Mol. Sci. 2026, 27(3), 1406; https://doi.org/10.3390/ijms27031406 - 30 Jan 2026

Viewed by 449

Abstract

Accurate genotyping of small insertions and deletions (InDels; <5 bp) remains technically challenging in routine molecular breeding, largely due to the limited resolution of agarose gel electrophoresis and the labor-intensive nature of polyacrylamide-based assays. Here, we present the Tri-Primer Amplification Refractory Mutation System (TP-ARMS), a simple and cost-effective PCR-based strategy that enables high-resolution genotyping of small InDels using standard agarose gels. The TP-ARMS employs a universal reverse primer in combination with two allele-specific forward primers targeting insertion and deletion alleles, respectively. This design allows clear discrimination of homozygous and heterozygous genotypes using a two-tube PCR workflow. The method showed complete concordance with Sanger sequencing in detecting 1–5 bp InDels across multiple crop species, including rice (Oryza sativa) and quinoa (Chenopodium quinoa). In addition, using a TP-ARMS reduced experimental time by approximately 90% compared with PAGE-based approaches and avoided the high equipment and DNA quality requirements of fluorescence-based assays. The practical applicability of the TP-ARMS was demonstrated in breeding populations, including efficient genotyping of a 3-bp InDel in OsNRAMP5 associated with cadmium accumulation and a 6-bp promoter InDel in OsSPL10 underlying natural variation in rice trichome density across 370 accessions. Collectively, the TP-ARMS provides a robust, scalable, and low-cost solution for precise small InDel genotyping, with broad applicability in marker-assisted breeding and functional genetic studies. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Plant Sciences)

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20 pages, 4398 KB

Open AccessArticle

DNA Methylation Fine-Tunes Light- and Hormone-Responsive Growth Plasticity in Arabidopsis Seedlings

by Emanuela Talarico, Eleonora Greco, Adriana Chiappetta, Fabrizio Araniti and Leonardo Bruno

Int. J. Mol. Sci. 2026, 27(2), 1034; https://doi.org/10.3390/ijms27021034 - 20 Jan 2026

Viewed by 606

Abstract

DNA methylation regulates plant growth by modulating gene expression; however, its contribution to hormone responsiveness and photomorphogenesis remains only partially understood. We examined Arabidopsis thaliana DNA methylation mutants met1 and drm1, drm2, and cmt3 (ddc) under defined light regimes and following exogenous treatments with auxin, gibberellin, and the auxin transport inhibitor TIBA. Hypocotyl elongation and cotyledon expansion exhibited strong light dependency across all genotypes, with met1 seedlings developing a consistently reduced cotyledon area and ddc seedlings displaying impaired hypocotyl elongation under specific light qualities. Exogenous auxin inhibited growth in all genotypes, whereas GA₃ promoted elongation in hypocotyls and roots (by approximately 75–80% and 15–35%, respectively, in Col0 and met1), with ddc exhibiting delayed and non-linear dose-dependent sensitivity. Quantitative RT–PCR analysis revealed differential expression of genes involved in auxin transport (PIN1, PIN3, PIN7), auxin signalling (ARF7, IAA3, LAX3), circadian regulation (TOC1, LHY, CCA1), and light signalling (PIFs, HY5, HYH), supporting a link between DNA methylation status and coordinated regulation of hormone-, light-, and clock-controlled transcriptional networks. Together, these findings demonstrate that MET1- and DRM/CMT-dependent methylation pathways integrate epigenetic regulation with environmental and hormonal cues, modulating the intensity, timing, and organ specificity of growth responses, thereby fine-tuning growth plasticity during early Arabidopsis seedling development. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Plant Sciences)

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21 pages, 2750 KB

Open AccessArticle

Characteristics and Phylogenetic Analysis of the Complete Chloroplast Genome of Hibiscus sabdariffa L.

by Junyuan Dong, Qingqing Ji, Xingcai An, Xiahong Luo, Changli Chen, Tingting Liu, Lina Zou, Shaocui Li, Guanghui Du, Jikang Chen and Xia An

Int. J. Mol. Sci. 2025, 26(22), 11001; https://doi.org/10.3390/ijms262211001 - 13 Nov 2025

Viewed by 831

Abstract

Roselle (Hibiscus sabdariffa L.) is a plant rich in bioactive constituents, serving as a unique material for the food and beverage industry and therapeutic applications. Despite its significant utility, few studies have focused on the molecular breeding of the plant. Chloroplasts are organelles in plant cells with independent genetic information, making them ideal for investigating plant phylogeny and genetic evolution. In this study, the roselle breeding material ‘Zhe Xiao Luo 1’ was selected to assemble and analyze the entire chloroplast genome using the Illumina NovaSeq X Plus platform. The phylogenetic relationships between roselle and other species within Malvaceae family, particularly within the genus Hibiscus, were clarified. The results showed that the complete chloroplast genome of roselle was 162,428 bp in length, with nucleotide proportions of 31.14% (A), 18.73% (C), 18.01% (G), 32.12% (T), and 36.74% (GC). It exhibited a typical tetrad structure consisting of four segments: the large single copy (LSC) region (90,327 bp), the small single-copy (SSC) region (19,617 bp), and two inverted repeat sequences (IRa and IRb, each 26,242 bp). A total of 130 genes were identified, including 37 tRNA genes, 8 rRNA genes, and 85 mRNA genes, and no pseudogenes were detected. Phylogenetic analysis using 23 revealed a clear phylogenetic relationship between H. sabdariffa and H. esculentus (okra) among all tested species. Building on previous research, this study further explored the functional annotation of genes in the roselle chloroplast genome, as well as its codon preference, repetitive sequences, simple sequence repeats (SSR), Ka/Ks ratio, nucleotide diversity (pi) analysis, and boundary analysis. The complete gene sequences have been uploaded to the NCBI database (accession number PX363576). This study provides evidence for elucidating the phylogenetic relationships and taxonomic status of H. sabdariffa, laying a theoretical foundation for studies on molecular mechanism resolution and cultivar development. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Plant Sciences)

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18 pages, 4242 KB

Open AccessArticle

Genome-Wide Identification and Biotic Stress Responses of TLP Gene Family in Citrus sinensis

by Xingtao Li, Lizhen Fan, Chang Liu, Xinrui Wang, Xiaoyuan Zhang and Xiaonan Tong

Int. J. Mol. Sci. 2025, 26(20), 10133; https://doi.org/10.3390/ijms262010133 - 18 Oct 2025

Viewed by 769

Abstract

Thaumatin-like proteins (TLPs), a subfamily of pathogenesis-related (PR) proteins, play a vital role in plant defense against pathogens. In this study, 23 CsTLP genes were identified in the Citrus sinensis genome. These genes encode proteins ranging from 203 to 512 amino acids, with molecular weights between 21.88 and 53.75 kDa, classifying them as small molecular weight proteins. The CsTLP genes are unevenly distributed across eight chromosomes, with chromosome 3 containing the highest number (6 genes). Subcellular localization predictions indicate that most CsTLPs are located in the extracellular space. Phylogenetic analysis with Arabidopsis thaliana TLPs classified the CsTLPs into 10 clades, with clade 5 being the largest. Three segmentally duplicated gene pairs were identified, suggesting a mechanism for the expansion of this gene family. Expression profiling revealed tissue-specific patterns, with the highest expression levels observed in roots and leaves. Under biotic stress, qRT-PCR analysis of 12 selected CsTLPs demonstrated pathogen-specific responses: CsTLP9 and CsTLP22 were strongly upregulated during Huanglongbing (HLB, bacterial) infection, by 21.70-fold and 9.47-fold, respectively. Multiple genes, including CsTLP5/13/18/21/23, exhibited over 10-fold upregulation following Citrus Anthracnose (CA, fungal) infection; however, most genes showed only weak responses to Citrus tristeza virus (CTV, viral). These findings underscore the regulatory significance of CsTLPs in pathogen responses and provide an important theoretical foundation for enhancing molecular disease-resistance breeding in Citrus sinensis. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Plant Sciences)

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21 pages, 1887 KB

Open AccessArticle

Effect of Nickel Stress on Nitrogen Metabolism in Cucumber Plants

by Ewa Gajewska and Aleksandra Witusińska

Int. J. Mol. Sci. 2025, 26(19), 9327; https://doi.org/10.3390/ijms26199327 - 24 Sep 2025

Viewed by 811

Abstract

Excessive concentrations of nickel (Ni) are phytotoxic, leading to disturbances in plant cell structure and function. Although some attempts have been made to elucidate the Ni impact on plant metabolism, the effect of this metal on nitrogen assimilation and transformation of nitrogen compounds still remains poorly understood. The objective of our study was to gain a better insight into the Ni influence on nitrogen metabolism in cucumber plants. Nitrogen metabolism-related enzyme activities and selected metabolite contents were assayed using spectrophotometric methods. Additionally, in the leaves, nitrogen assimilation-involved gene expression was analyzed using quantitative real-time PCR. Nickel treatment resulted in a decline in

{NO}_{3}^{-}

content in the leaf and

{NH}_{4}^{+}

content in the root. In the leaf, ferredoxin-dependent glutamate synthase (Fd-GOGAT) activity decreased, while NADH-dependent glutamate synthase (NADH-GOGAT) and glutamate dehydrogenase (GDH) activities increased. The GDH activity showed increases in both its aminating (NADH-GDH) and deaminating (NAD-GDH) functions. The activities of the other enzymes involved in nitrogen assimilation were not influenced by Ni stress. In the root, the activities of most enzymes were downregulated by Ni treatment except for NADH-GDH and NAD-GDH activities which showed increases. While glutamate content remained unaltered after Ni exposure in the leaf, in the root it was slightly lowered. In contrast to the leaf, showing accumulation of non-protein thiols and proline, in the root, these compound contents were markedly decreased. Our study revealed an organ-specific response of cucumber plants to Ni treatment. Accumulation of glutamate derivatives involved in response to heavy metal stress without significant changes in glutamate content may suggest that in the leaf, the induction of NADH-GOGAT and NADH-GDH activities efficiently compensates for the reduced Fd-GOGAT activity. Additionally, the increased NADP-ICDH activity may support glutamate production by providing 2-oxoglutarate for reactions catalyzed by NADH-GOGAT and NADH-GDH. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Plant Sciences)

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18 pages, 6955 KB

Open AccessArticle

Plastid Phylogenomics of Camphora officinarum Nees: Unraveling Genetic Diversity and Geographic Differentiation in East Asian Subtropical Forests

by Chen Hou, Yingchao Jiang, Qian Zhang, Jun Yao, Huiming Lian, Minghuai Wang, Peiwu Xie, Yiqun Chen and Yanling Cai

Int. J. Mol. Sci. 2025, 26(18), 9229; https://doi.org/10.3390/ijms26189229 - 21 Sep 2025

Cited by 1 | Viewed by 916

Abstract

Camphora officinarum Nees constitutes a pivotal tree species within the evergreen broad-leaved forests of East Asia, endowed with significant economic, ornamental, and ecological importance. Nevertheless, previous research has markedly underestimated the genetic diversity of this species, thereby hindering our efforts in conserving resources and enhancing genetic breeding. The current study generated 155 chloroplast genomes from specimens of C. officinarum obtained from six provinces/regions in China. The results reveal the identification of seven distinct clades (I–VII), with Clades II, III, V, and VII exhibiting genome expansions, primarily influenced by lineage-specific elongation of inverted repeats (IRs), whereas Clades I, IV, and VI maintained conserved IR lengths. Despite the structural plasticity, the GC content remained highly conserved. Geographic patterns indicated gene flow between adjacent regions (e.g., Hunan and Hubei with identical IR lengths), but genetic isolation in Fujian. High-polymorphism regions (psba-matK, ycf1, ycf2, and ndhF) were identified as superior phylogenetic markers, enhancing intraspecies-level resolution. Simple sequence repeats (SSRs) varied significantly among clades, dominated by A/T-rich mononucleotide repeats. These repeats, along with divergent repeat types (e.g., absence of reverse repeats in Clades V/VI), serve as robust tools for resource identification and evolutionary trajectory inference. Phylogenetically, samples from Fujian formed a distinct lineage, while samples from other regions, especially Guangdong, were mixed, with this finding probably being a reflection of historical cultivation and anthropogenic translocation. This study offers a framework for the genetic breeding and investigation of the evolutionary history of C. officinarum. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Plant Sciences)

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Review

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14 pages, 1577 KB

Open AccessReview

GDSL Lipases/Esterases: Versatile Regulators of Plant Development and Stress Resilience

by Ke Dong, Rehman Sarwar, Yuanxue Liang, Wei Zhang, Rui Geng, Wenlong Jiang, Xiang Fan and Xiao-Li Tan

Int. J. Mol. Sci. 2026, 27(9), 3872; https://doi.org/10.3390/ijms27093872 - 27 Apr 2026

Viewed by 171

Abstract

GDSL esterase/lipase (GELP) proteins constitute an evolutionarily conserved yet functionally diversified hydrolase family in land plants. They participate in cuticle and secondary cell wall biosynthesis, seed lipid remobilization, reproductive development, and hormone-mediated responses to biotic and abiotic stresses. Despite extensive genome-wide and comparative genomic studies that have categorized large GELPs across numerous crops and model species, only a fraction of members have been functionally characterized in plants, and their catalytic mechanisms and regulatory architectures remain poorly understood. Recent population genomics and cross-species orthogroup analyses in 46 angiosperms have uncovered substantial natural variation within GELP coding sequences and regulatory regions, providing a powerful framework to link allelic diversity to evolutionary trajectories and physiological functions. This review synthesizes current knowledge on GELP evolution, biochemical properties, and roles in development and stress adaptation, and critically evaluates how these insights can be translated into biotechnology and molecular breeding strategies. It highlights emerging resources and concepts from orthogroup-based classification and multi-species datasets that enable systematic discovery of GELP alleles affecting agronomic traits. It further outlines research exploiting GELPs in crop improvement, emphasizing the integration of reverse and forward genetics with multi-omics profiling, biochemical and structural characterization, and gene regulatory network reconstruction. Systematic assessment of the phenotypic impacts of single and combinatorial GELP perturbations on yield, quality, and stress resilience is proposed as a key step toward translating basic insights into breeding and engineering strategies. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Plant Sciences)

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23 pages, 2306 KB

Open AccessReview

Harnessing Plant Microbiomes to Modulate Molecular Signaling and Regulatory Networks in Drought Stress Adaptation

by Shahjadi-Nur-Us Shams, Md Arifur Rahman Khan, Sayed Shahidul Islam, Afsana Jarin, Md. Nahidul Islam, Touhidur Rahman Anik, Mostafa Abdelrahman, Chien Van Ha, Thayne Montague and Lam-Son Phan Tran

Int. J. Mol. Sci. 2026, 27(3), 1139; https://doi.org/10.3390/ijms27031139 - 23 Jan 2026

Viewed by 937

Abstract

Drought stress is a major abiotic factor limiting global crop productivity by disrupting cellular homeostasis, impairing photosynthesis, and restricting metabolic activity. Plant-associated microorganisms, including rhizobacteria, endophytes, and arbuscular mycorrhizal fungi, play key roles in enhancing drought resilience through molecular, biochemical, and physiological mechanisms. These beneficial microbes modulate phytohormone biosynthesis, enhance osmolyte accumulation, increase organic acid exudation, and activate ROS-scavenging antioxidant pathways. Microbe-mediated regulation of aquaporins, heat shock proteins, and root system architecture further improves water-use efficiency, hydraulic conductance, and stress acclimation. Advances in microbial genomics and systems biology have revealed the molecular drivers of plant–microbe synergism, enabling the development of tailored microbial consortia and next-generation bioinoculants. Complementarily, genetic and genome-guided modulation of drought-responsive regulatory hubs including transcription factors (e.g., DREBs, NACs, MYBs, and bZIPs), signal transducers (e.g., MAPKs and CDPKs), and protective proteins enhances adaptive plasticity under water deficit conditions. This review integrates current molecular insights into drought-induced perturbations in plants and highlights the convergence of microbial interventions and genome-guided strategies in reinforcing drought tolerance. Emphasizing mechanistic frameworks, scalable microbial technologies, and molecular breeding approaches, this work underscores their potential to improve crop resilience in increasingly water-limited environments. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Plant Sciences)

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