OmicsCanvas integrates diverse epigenomic and transcriptomic data into a unified framework, enabling users to visualize complex multi-omics patterns, generate publication-ready figures, and uncover regulatory relationshi...OmicsCanvas integrates diverse epigenomic and transcriptomic data into a unified framework, enabling users to visualize complex multi-omics patterns, generate publication-ready figures, and uncover regulatory relationships. This tool makes multi-omics analysis accessible to biologists without bioinformatics expertise.
Zhou H, Xu Z, Zeng F
… +9 more, Sang H, Liu Z, Sun M, Fu Q, Zhao K, Tan D, Bao M, Jin S, Liu X
J Integr Plant Biol
· 2026 Jul · PMID 41968463
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Rhododendron, a globally important group of alpine flowering plants, provides an exceptional system for investigating ecological adaptation and stress resistance owing to its high-altitude specialization. Using 18 Rhodod...Rhododendron, a globally important group of alpine flowering plants, provides an exceptional system for investigating ecological adaptation and stress resistance owing to its high-altitude specialization. Using 18 Rhododendron species, a graph-based pangenome was constructed that captures 72,089 nonredundant structural variants. The findings support the integration of subgenus Azaleastrum into subgenus Tsutsusi, with their comparatively smaller genome sizes likely resulting from the contraction of multiple gene families during lineage differentiation. Gene families specific to high-altitude Rhododendron species were significantly enriched in pathways associated with stress resistance. High-altitude-specific long terminal repeat retrotransposons operate through similar regulatory mechanisms, predominantly influencing stress-responsive genes and promoting adaptive evolution. Through an integrated analysis of population genetics (389 re-sequenced samples with a mean coverage of 50.2×), transcriptomics, and real-time quantitative polymerase chain reaction, conserved genes and gene families linked to alpine adaptation in Rhododendron were identified. These include genes implicated in cold-stress responses and ultraviolet (UV) tolerance, such as CML18, CPK1, DREB1E, LPAT2, GPC1, and UVR8. Structural variant profiles within several of these genes offer insights into divergent adaptive mechanisms between high- and low-altitude Rhododendron species. The rapid induction of cold-sensing genes and CBF/DREB1-centered cold-stress signaling pathways indicates an evolutionary adaptation of alpine Rhododendron species to low-temperature habitats. Furthermore, transgenic analyses indicate that cold-resistance genes, such as GPC1 derived from high-altitude Rhododendron, markedly improve cold tolerance in Arabidopsis thaliana and tobacco. Collectively, this study advances insights into high-altitude adaptation in ornamental plants and underscores the value of super-pangenome resources for evolutionary and functional genomics research.
From seed dormancy to pathogen attacks and senescence, many events in a plant's life are critically controlled by low-molecular-weight signaling molecules, called plant hormones. These master regulators include abscisic...From seed dormancy to pathogen attacks and senescence, many events in a plant's life are critically controlled by low-molecular-weight signaling molecules, called plant hormones. These master regulators include abscisic acid, auxins, brassinosteroids, cytokinins, ethylene, gibberellins, jasmonates, salicylates, and strigolactones. Years of research have unveiled multiple aspects of their biosynthesis, transport, signaling, functions, and interactions. With this knowledge, complex molecular networks have been established and refined over time in an attempt to explain how plant hormones collectively mediate physiological processes, under a wide range of contexts and at various developmental stages. In this context, we aim to shed light on the global molecular framework of plant hormonal signaling. To do so, we first step back and offer a deconvolution of plant hormonal pathways, by addressing their biosynthesis, transport, and signaling. We then explore how hormonal pathways interfere with each other at a molecular level, mostly through transcriptional regulation and protein-protein interactions. We further discuss directions to fine-tune our fundamental understanding of plant hormonal control, and finally, we highlight how this knowledge can be translated into applied prospects to tackle unprecedented agricultural challenges.
Exo-Cas12i2 v1, a fusion of the 5' exonucleases T5E and PapE, facilitates editing of TA-rich regions and mediates deletions of large genomic fragments. Exo-Cas12i2 v1-driven MITE manipulation enables precise regulation o...Exo-Cas12i2 v1, a fusion of the 5' exonucleases T5E and PapE, facilitates editing of TA-rich regions and mediates deletions of large genomic fragments. Exo-Cas12i2 v1-driven MITE manipulation enables precise regulation of genes involved in gibberellin-mediated cell elongation and root ethylene responses to generate favorable agronomic traits.
Newly differentiated leaves of albino ornamental kale turn white as exposed to low temperatures, producing a distinctive and commercially desirable unique color pattern. Here, we show that this low-temperature-induced al...Newly differentiated leaves of albino ornamental kale turn white as exposed to low temperatures, producing a distinctive and commercially desirable unique color pattern. Here, we show that this low-temperature-induced albinism is caused by a mutation in the kale F-box gene BoWl. Using yeast two-hybrid, pull-down, co-immunoprecipitation, and luciferase complementation assays, we demonstrate that BoWl interacts with the transcription factor BoARF1 to form a functional complex. Complementary yeast one-hybrid, electrophoretic mobility shift, chromatin immunoprecipitation, and luciferase assays reveal that this complex activates BoGLK1, a regulator of chloroplast development and chlorophyll synthesis. In the albino line, a mutation in BoWl results in abnormal chloroplast structure and disrupts chlorophyll synthesis. We further identify BoCBF1/BoPHL2 as a low-temperature responsive regulatory module that transcriptionally activates BoWl expression. Together, these findings define a molecular pathway linking cold perception to transcriptional regulation associated with leaf whitening in ornamental kale, providing new insight into how low temperature influences genetically controlled leaf color variation.
Cytosine base editors (CBEs) and adenine base editors (ABEs) are powerful tools for precise genome editing in plants. Conventionally, such base editors are built upon the CRISPR-Cas9 systems where Cas9 nickases are used....Cytosine base editors (CBEs) and adenine base editors (ABEs) are powerful tools for precise genome editing in plants. Conventionally, such base editors are built upon the CRISPR-Cas9 systems where Cas9 nickases are used. To expand the base editing scope and minimize off-target effects, base editors derived from the CRISPR-Cas12a systems are desired. However, the use of deactivated Cas12a (dCas12a) in such base editors constrains the editing activity, preventing the wide use of Cas12a base editors for plant research and trait development. In this study, we demonstrate the use of an ABE based on the efficient LbCas12a-RRV variant to introduce herbicide-resistant mutations in OsACCase in rice. To improve Cas12a CBEs and ABEs, we inserted introns into the coding sequence of dLbCas12a-RRV. This intron-containing Cas12a-CBE shows substantial improvement in editing efficiency in rice, compared to the non-intron counterparts. By contrast, the improvement of ABE with the intron-containing dLbCas12a-RRV is very limited, partly due to the already high baseline editing efficiency of the intron-less dLbCas12a-RRV ABE. Testing of these base editors in poplar shows elevated C-to-T base editing by dLbCas12a-RRV-intron-CBE. For A-to-G editing, ABEs built upon dLbCas12a-RV and dLbCas12a-RRV variants showed significant improvement over ABEs derived from wild-type LbCas12a and the ttLbCas12a variant. The addition of introns to dLbCas12a-RRV does not further improve the base editing efficiency. With whole genome sequencing in rice, we evaluated genome editing specificities with these improved Cas12a base editors. Our analyses show that both intron-containing Cas12a CBE and ABE barely introduce guide RNA-dependent off-target mutations. However, they can generate guide RNA-independent off-target mutations, which are likely attributed to the high enzymatic activities of the deaminases. Collectively, our study demonstrates the successful use of a Cas12a base editor for trait development and reports improved Cas12a CBEs and ABEs for precise base editing in plants.
Crocins, the main active ingredients in Crocus sativus, have anti-inflammatory, antioxidant, hypolipidemic, hypoglycemic, and antitumor properties. Due to the harsh growing conditions and the limited yield of C. sativus,...Crocins, the main active ingredients in Crocus sativus, have anti-inflammatory, antioxidant, hypolipidemic, hypoglycemic, and antitumor properties. Due to the harsh growing conditions and the limited yield of C. sativus, sustainable alternative methods for crocin production need to be explored. In this study, a new rice germplasm resource, "crocin rice", was developed by expressing eight genes of the crocin synthesis pathway in rice endosperm. The content of crocins in rice seeds was up to 9.25 μg/g dry weight, and it was also rich in a variety of carotenoids, including α-carotene, lutein, and violaxanthin. The expression of exogenous genes did not affect normal growth or the major nutritional structure of rice. Feeding experiments on mice showed that crocin rice could effectively reduce lipopolysaccharide-induced liver injury. With the adjuvant therapeutic benefits, crocin rice could be used to improve human nutrition and health. In addition, rice callus also showed the ability to synthesize crocins, which could serve as a potential substitute for C. sativus to alleviate resource shortage.
The transcription factor WRINKLED1a coordinates nitrogen-responsive root and shoot growth in rice, improving nitrogen-use efficiency and yield stability.The transcription factor WRINKLED1a coordinates nitrogen-responsive root and shoot growth in rice, improving nitrogen-use efficiency and yield stability.
This Commentary summarizes the original work by Liao et al. on the role of NITROGEN LIMITATION ADAPTATION (NLA) in cold tolerance, places it within the broader context of climate change and nutrient constraints, and disc...This Commentary summarizes the original work by Liao et al. on the role of NITROGEN LIMITATION ADAPTATION (NLA) in cold tolerance, places it within the broader context of climate change and nutrient constraints, and discusses the engineered NLA allele and its implications for overcoming the trade-off between cold tolerance and phosphorus use efficiency.
Plant pathogens use a diverse arsenal of effectors to suppress host immunity, though the precise mechanisms of their action are often not fully understood. In this study, we characterize FolCP1b, a cerato-platanin (CP) e...Plant pathogens use a diverse arsenal of effectors to suppress host immunity, though the precise mechanisms of their action are often not fully understood. In this study, we characterize FolCP1b, a cerato-platanin (CP) effector secreted by Fusarium oxysporum f. sp. lycopersici (Fol), as a key intracellular virulence factor that disrupts host defenses and protects other Fol effectors. FolCP1b interacts with the host apoplastic subtilase SlSBT1 within the plant cytoplasm, leading to its intracellular retention and preventing its secretion to the apoplast. As a result, SlSBT1-mediated degradation of key Fol effectors, such as FolEP1 and FolEP2, is impaired, thereby promoting Fol infection. Unlike canonical protease inhibitors, FolCP1b operates by altering host protein subcellular localization rather than inhibiting enzymatic activity. Our findings unveil a novel "effector hijacking" mechanism, through which one intracellular effector safeguards apoplastic effectors from host proteolytic degradation, thereby enhancing fungal pathogenicity.
Genetic variation underlying phenotypic diversity between wild and domesticated species has been extensively studied, the contribution of higher-order chromatin architecture to these processes remains less explored. Adva...Genetic variation underlying phenotypic diversity between wild and domesticated species has been extensively studied, the contribution of higher-order chromatin architecture to these processes remains less explored. Advances in Hi-C and related genomic technologies have revealed that plant genomes exhibit complex three-dimensional (3D) genome organization, hierarchically structured into A/B compartments, and topologically associated domains (TADs). TADs represent self-interacting genomic regions that can constrain or regulate without directly determining transcriptional outcomes. Alterations to TAD organization or boundary have been associated with changes in chromatin interactions and gene regulatory potential in specific developmental or environmental contexts. In plants, emerging evidence indicates that TAD structure can be genetically and environmentally modulated, despite the absence of canonical architectural proteins such as CTCF. Both environmental stress and genetic perturbations have been shown to remodel chromatin organization, with context-dependent changes in gene expression. Such plasticity in chromatin dynamics that contribute to adaptive responses raises a potential link between 3D genomic structure and cryptic genetic variations (CGVs). CGVs remain phenotypically silent under normal conditions but can be revealed under environmental or genetic perturbations, representing an additional layer of regulatory potential in plant genomes. Here, we propose that stress-induced chromatin organization, including changes in TAD organization and chromatin compartmentalization, may influence accessibility and expression of CGVs in a context-dependent manner. While a direct mechanistic link between TADs and CGVs remains largely unexplored. Here, we reviewed recent findings from model plants and major crops to highlight how variation in 3D genome organization can contribute to transcriptional plasticity, stress responses, and lineage-specific regulatory evolution. By integrating 3D genomics, chromatin accessibility, and multi-omics data, we outline a conceptual framework for generating hypotheses and open questions on how TAD-associated chromatin dynamics and CGVs together may shape transcriptional plasticity, stress responses, and long-term adaptive evolution in plants with implications for future crop improvement strategies.
ATP binding is an essential event in diverse biological processes including plant immunity. The ATP-binding domains in plant kinases share similar structural properties, providing a potential common target for pathogens....ATP binding is an essential event in diverse biological processes including plant immunity. The ATP-binding domains in plant kinases share similar structural properties, providing a potential common target for pathogens. However, effectors targeting the ATP-binding domains to modulate kinase activity have not been identified. In this study, we identified a conserved effector containing an Egh16-like domain (Cee1) in Fusarium graminearum. As an in planta induced gene, CEE1 plays a stage-specific role in infectious growth within wheat rachis. Upon translocation into plant cells, Cee1 interacts with the ATP-binding domain of TaMPK3 via its Egh16-like domain. This interaction interferes with the ATP binding and impairs the kinase activity of TaMPK3, leading to reduced phosphorylation levels of TaWRKY33 and subsequent inactivation of downstream resistance responses. F. graminearum harbors three paralogs of Cee1, each containing two adjacent motifs responsible for specific interaction with ATP-binding pockets, all crucial for pathogenesis. The quadruple mutant lacking these four CEE genes shows drastically reduced pathogenicity, and CEE genes have been identified as silencing targets for improving wheat FHB resistance. Taken together, Cee1 and its paralogs act as core effectors in F. graminearum by targeting the ATP-binding domains of plant kinases, demonstrating the representative mode of action of the Egh16-like domain in fungal-plant interactions.
Crop yield is largely determined by the size of harvestable organs and understanding the mechanisms that govern organ size is therefore crucial for improving crop productivity. CYP78As are a plant-specific subfamily of c...Crop yield is largely determined by the size of harvestable organs and understanding the mechanisms that govern organ size is therefore crucial for improving crop productivity. CYP78As are a plant-specific subfamily of cytochrome P450 enzymes that have been identified as organ size regulators and are expressed in various plant organs. We previously identified BnaA09.CYP78A9, whose expression is markedly upregulated in long-silique cultivars by a CACTA-like transposable element (CTE) insertion in the regulatory region, acts as a pleiotropic regulator of yield-related traits in long-silique rapeseed varieties. Here, we show that BnaA09.CYP78A9 is expressed predominantly in the siliques and seeds of rapeseed cultivar ZS11. cyp78a9-CRISPR knockout mutants exhibited reductions in silique length, seed size, and seed number per silique. Enzyme assays revealed that BnaA09.CYP78A9 converts lauric acid (LA) to 12-hydroxylauric acid (12-HOLA), and endogenous metabolite quantification revealed that 12-HOLA levels were 5.01-fold greater in long-silique materials versus short-silique materials. Application of exogenous 12-HOLA significantly increased silique/pod elongation and seed weight, enhancing yield per plant by 32.77% in Arabidopsis and yield per unit area by 7.51%-30.82% in rapeseed and 30.14% in soybean compared with controls, respectively. 12-HOLA application also stimulated fruit expansion in horticultural crops, increasing fresh fruit weight by 20.64%-22.96% in cucumber and 11.92%-24.13% in tomato. Transcriptome analyses revealed that 12-HOLA treatment upregulated the expression of genes involved in auxin biosynthesis, transport, and signaling. 12-HOLA treatment not only rapidly activated numerous transcription factors but also significantly promoted carbon metabolism within rapeseed siliques. Our study provides strong evidence that 12-HOLA produced by BnaA09.CYP78A9 activates the auxin pathway, promotes cell elongation, and increases fruit size and seed weight. These findings highlight the potential use of 12-HOLA as a natural plant growth regulator and CYP78A9 as a target for gene editing and molecular breeding.
Canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) is a severe bacterial infection threatening global kiwifruit production. Psa causes lignin degradation, cell wall rupture, leaf wilting, and canker forma...Canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) is a severe bacterial infection threatening global kiwifruit production. Psa causes lignin degradation, cell wall rupture, leaf wilting, and canker formation on branches and trunks, often leading to plant death. The plant cell wall serves as a structural barrier against pathogens, with its thickness, composition, and cell density influencing disease resistance. Comparative studies between resistant germplasms Actinidia eriantha "Maohuaxiong" (A. eriantha 'MHX') and Actinidia latifolia "Kuoye" (A. latifolia 'KY') and susceptible cultivars Actinidia chinensis "Hongyang" (A. chinensis 'HY') and "Donghong" (DH) indicate that the resistant lines developed smaller lesions and slower disease progression after Psa infection, compared with susceptible cultivars. Histological and biochemical analyses revealed that "MHX" and "KY" had denser mesophyll cells and higher lignin deposition. Transcriptomic analysis and transient overexpression screening identified AcLFYL1 as a positive regulator of Psa resistance. AcLFYL1 overexpression increased cell density, lignin content, and disease resistance, while RNAi silencing produced the opposite phenotypes. Yeast one-hybrid, dual-luciferase reporter, and ChIP-qPCR assays confirmed that AcLFYL1 directly activates AcCSE, a key gene in lignin biosynthesis. Consistent with this, overexpression of AcCSE similarly increased cell density and lignin content and improved Psa resistance, whereas knockdown of AcCSE in both wild-type (WT) and AcLFYL1 overexpression lines significantly reduced lignin accumulation and compromised disease resistance. These findings demonstrate that AcLFYL1 enhances resistance by promoting lignin biosynthesis and increasing mesophyll cell density through direct regulation of AcCSE, offering valuable genetic targets for breeding Psa-resistant kiwifruit varieties.
This Commentary highlights a recent study discovering Systemic Stomatal Immunity, a rapid, targeted immune program, filling a research gap by showing local challenge triggers distal stomatal closure within hours.This Commentary highlights a recent study discovering Systemic Stomatal Immunity, a rapid, targeted immune program, filling a research gap by showing local challenge triggers distal stomatal closure within hours.
Wang Y, Fan Z, Wang Y
… +4 more, Vainstein A, Qiu Y, Sun Y, Ma H
J Integr Plant Biol
· 2026 Jul · PMID 41872729
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Rapid softening of fig (Ficus carica L.) fruit during ripening leads to extremely short shelf life; the regulatory mechanisms underlying this process remain largely unknown. Fig softening during ripening is largely attri...Rapid softening of fig (Ficus carica L.) fruit during ripening leads to extremely short shelf life; the regulatory mechanisms underlying this process remain largely unknown. Fig softening during ripening is largely attributed to pectin degradation, and we identified FcPG12 as the crucial polygalacturonase gene involved in the process. We then identified a NAM (ATAF1/2-CUC2) transcription factor, termed FcNOR and sharing 53.09% amino acid identity with Solanum lycopersicum NOR, which binds directly to the promoter of FcPG12 to activate its transcription. The activity of FcNOR increased robustly following FcMAPK4 phosphorylation of Ser-78 and Ser-343, which are essential for FcNOR DNA binding and transcriptional activity, respectively. Ethylene also enhanced FcMAPK4 kinase activity and promoted FcNOR phosphorylation, leading to the latter's elevated activity. APETALA2/Ethylene Response Factor 5 (FcERF5) functioned as a transcriptional activator of FcPG12 expression, which was synergistically enhanced by interaction between FcNOR and FcERF5. Moreover, FcNOR binds to the promoter of FcERF5, increasing the latter's transcription and forming a FcNOR-FcERF5 positive-feedback loop. Collectively, integration of ethylene signaling with MAPK-mediated phosphorylation by the FcMAPK4-FcNOR-FcERF5 regulatory module, leading to transcriptional regulation of FcPG12 expression to drive pectin degradation, reveals new insights into the mechanism of fruit softening.
Zhang R, Ren Y, Zhao Y
… +5 more, Zheng H, Luo Y, Liu Y, Wang L, Zhang L
J Integr Plant Biol
· 2026 Apr · PMID 41866783
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Since its discovery in 1922, vitamin E research has evolved from the search for a mysterious "reproductive factor" to the exploration of a diverse family of bioactive molecules central to plant physiology and human healt...Since its discovery in 1922, vitamin E research has evolved from the search for a mysterious "reproductive factor" to the exploration of a diverse family of bioactive molecules central to plant physiology and human health. This review traces a century of progress, highlighting advances in our understanding of vitamin E's chemical composition, antioxidant and non-antioxidant functions, biosynthetic pathways, and intricate regulatory networks in plants. Recent breakthroughs, such as the discovery of the seed-specific esterase, VTE7, revealed a direct phytol-recycling route linking chlorophyll degradation to tocopherol synthesis. This discovery has opened new possibilities for metabolic engineering. To overcome the persistent bottlenecks of low natural abundance and costly extraction, we also examine two production strategies: chemical synthesis and biotechnological synthesis. While chemical routes remain dominant, they yield racemic mixtures with reduced bioactivity. Emerging synthetic biology approaches, including microbial platforms capable of producing natural vitamin E configurations from key precursors, such as farnesene, mark a new paradigm for green and efficient manufacturing. Looking ahead, future directions include the intelligent evolution of catalytic enzymes, elucidation of transmembrane precursor transport, and exploration of rare homologs such as tocomonoenols. Together, these innovations promise to redefine the molecular and industrial landscape of vitamin E research for the next century.
Wu M, Cai M, Zhai R
… +5 more, Ye J, Zhu G, Yu F, Ye S, Zhang X
J Integr Plant Biol
· 2026 Jul · PMID 41858072
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Pentatricopeptide repeat (PPR) proteins constitute a large superfamily of nuclear-encoded proteins characterized by tandem helical repeats. They function as critical coordinators of nucleus-organelle communication by mod...Pentatricopeptide repeat (PPR) proteins constitute a large superfamily of nuclear-encoded proteins characterized by tandem helical repeats. They function as critical coordinators of nucleus-organelle communication by modulating RNA metabolism within chloroplasts and mitochondria. This review summarizes recent advances in understanding the functional mechanisms of PPR proteins in major cereal and oilseed crops, with a focus on their roles in regulating seedling growth, stress responses, seed development, and cytoplasmic male sterility (CMS) restoration. We highlight how chloroplast-localized PPR proteins mediate RNA metabolism to ensure proper chloroplast biogenesis and seedling photosynthesis, while mitochondrial-targeted PPR proteins are crucial for RNA processing events that support respiration, embryo and endosperm development, and fertility restoration in CMS systems. We also describe how certain PPR proteins mediate biotic and abiotic stress responses through their functions in cold, drought, salt, and disease resistance, with specific members localized in chloroplasts or mitochondria. Finally, we outline unresolved questions regarding PPR protein complex assembly and environmental modulation, and highlight the emerging potential of engineered designer PPR (dPPR) proteins as programmable tools for precise RNA targeting and manipulation in organelles.
Bu Y, Qiu Z, Sun W
… +8 more, Han Y, Liu Y, Yang J, Song M, Li Z, Liu S, Zhang Y, Ma C
J Integr Plant Biol
· 2026 Jul · PMID 41858069
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Transcriptome deep sequencing (RNA-seq) data analysis is often affected by reference bias introduced by the use of a single linear reference (SLR) genome. Graph-based pangenomes can mitigate this bias by integrating the...Transcriptome deep sequencing (RNA-seq) data analysis is often affected by reference bias introduced by the use of a single linear reference (SLR) genome. Graph-based pangenomes can mitigate this bias by integrating the SLR genome with complex genetic variations within a species; however, their application remains limited owing to a lack of dedicated analytical tools. Here, we present PanGraphRNA, an integrated bioinformatics platform for RNA-seq data analysis using a graph pangenome as reference. Built on the Galaxy web-based framework, PanGraphRNA provides functional modules for constructing, evaluating, and applying graph pangenomes across different population scales, thus enabling accessibility, traceability, and reproducibility throughout the analysis. Applied to both real and simulated RNA-seq data sets from Arabidopsis (Arabidopsis thaliana), PanGraphRNA outperformed the SLR approach, achieving higher read alignment accuracy and more precise gene expression quantification. PanGraphRNA enabled the identification of drought stress-induced genes and flowering time-related quantitative trait loci that were previously missed with the conventional SLR approach. Furthermore, we successfully applied PanGraphRNA to process RNA-seq data sets from rice (Oryza sativa) and maize (Zea mays). By providing standardized, containerized workflows, PanGraphRNA will facilitate transcriptomic research in key plant species, including Arabidopsis, rice, and maize.