The core of the story lies in RNA interference, or RNAi, a gene-regulation system shared across much of life. Small interfering RNAs and microRNAs can be loaded into Argonaute proteins to form silencing complexes that seek out and destroy matching messenger RNAs. What has stunned researchers is that these molecules do not respect species barriers. A fungal pathogen can ship its own small RNAs into a plant cell, where they hijack the host’s Argonaute machinery and switch off immunity genes. Conversely, a plant can package its small RNAs into extracellular vesicles and send them into an invading fungus, where they silence the very genes the pathogen needs to cause disease.

The evidence is strikingly specific. The gray mold fungus Botrytis cinerea secretes small RNAs such as Bc-siR3.1 and Bc-siR5 into plant cells, where they co-opt the host AGO1 complex to suppress immunity-related genes. The wheat rust pathogen Puccinia striiformis delivers a microRNA-like RNA called Pst-milR1 that silences PR2, a gene encoding beta-1,3-glucanase involved in degrading fungal cell walls. In the banana-wilting Fusarium oxysporum system, fungal milRNAs target banana transcription factors and receptor-like kinases, dismantling early defense signaling. Rhizoctonia solani deploys a battery of milRNAs against rice, suppressing vacuolar sorting receptors, NB-ARC immune receptors, and F-box proteins to blunt the hypersensitive response. Even Valsa mali, the apple canker pathogen, uses a single milRNA to silence two receptor-like kinases and reduce reactive oxygen accumulation and callose deposition in host tissue.

Crucially, the traffic runs both ways. Plants selectively load small RNAs into extracellular vesicles with the help of RNA-binding proteins including AGO1, the helicases RH11 and RH37, and the annexins ANN1 and ANN2, which sort, stabilize, and transport the cargo. Encapsulation shields the RNA from extracellular nucleases during the journey. In the Brachypodium distachyon and Fusarium graminearum system, researchers identified 258 plant-derived small RNAs that target fungal messenger RNAs and significantly reduce pathogenicity. Wheat roots even send microRNAs into the beneficial fungus Clonostachys rosea, where they fine-tune fungal secondary metabolism rather than triggering defense, showing that RNA exchange also shapes cooperative relationships, not just conflict.

Bacteria play this game too, though the evidence is younger. The rice pathogen Xanthomonas oryzae pv. oryzicola packages a small RNA called Xosr001 into outer membrane vesicles, which deliver it into rice cells to silence OsJMT1, a jasmonate metabolism gene, thereby suppressing stomatal immunity. In the opposite direction, Arabidopsis plants have been shown to silence virulence genes of Pseudomonas syringae, reducing bacterial colonization and impairing stomatal reopening, with the silencing RNAs exported through both vesicle-associated and non-vesicular routes. Plant-derived small RNAs can also suppress gene expression in Ralstonia pseudosolanacearum, the agent of bacterial wilt. Even mutualistic partnerships show RNA crosstalk: Bradyrhizobium japonicum produces tRNA-derived fragments that accumulate in soybean nodules and use the host AGO1 machinery to regulate plant transcripts involved in nodulation.

Viruses occupy a special place in this landscape. Because viral RNA replicates continuously inside host cells, the review’s authors treat plant-virus systems as a closely related but mechanistically distinct model rather than classical cross-kingdom transfer. Still, the dynamics are instructive. Plants process viral double-stranded RNA with Dicer-like enzymes into virus-derived small interfering RNAs that guide sequence-specific degradation of viral genomes. Viruses fight back with silencing suppressor proteins such as the NS3 protein of Rice stripe virus, which binds small RNAs and interferes with microRNA biogenesis. Virus-derived siRNAs from Rice black-streaked dwarf virus directly target host genes in rice and maize, while virally activated siRNAs extend RNA regulation to endogenous plant transcripts during infection, creating layered, bidirectional control networks.

These discoveries have crystallized into three agricultural technologies that share a common RNAi mechanism but differ in delivery. Spray-induced gene silencing, or SIGS, applies double-stranded RNAs directly onto plant surfaces, where they are taken up by tissues and silence invading pathogens. It is non-transgenic, rapid, and flexible, and has been shown to suppress gray mold, Fusarium head blight, stem rot, powdery mildew, and late blight across cereals, vegetables, fruits, and ornamentals. Artificial vesicles and nanocarriers such as layered double-hydroxide nanosheets dramatically extend the persistence of sprayed RNAs, with encapsulated double-stranded RNAs protecting tomato and grape tissues for up to ten days and grape leaves for up to twenty-one days.

Host-induced gene silencing, or HIGS, takes the opposite approach: the plant itself is genetically engineered to continuously produce silencing RNAs directed at pathogen genes. Stable HIGS lines have delivered durable resistance in sugarcane against Pokkah boeng and smut, in rice against Bakanae disease and blast, in potato against late blight, and in apple against ring rot. In one notable strategy, transgenic Arabidopsis expressing short tandem target mimics effectively blocked the immune-suppressing small RNAs of Botrytis cinerea, reducing gray mold infection. HIGS offers long-lasting, tissue-specific protection, but it inherits the regulatory hurdles, biosafety debates, and public concerns that surround genetically modified crops, and it demands years of development time.

The newest and perhaps most intriguing strategy is microbe-induced gene silencing, or MIGS, which recruits beneficial microorganisms as living RNA delivery vehicles. Engineered Trichoderma harzianum strains colonizing the rhizosphere produce small RNAs that silence virulence genes in Verticillium dahliae and Fusarium oxysporum. Even more remarkably, engineered Bacillus subtilis and Pseudomonas putida can package double-stranded RNAs into extracellular vesicles and deliver them across kingdoms to fungal pathogens, suppressing Botrytis and Verticillium infections in Arabidopsis and tomato. Because microbes protect their RNA cargo from environmental degradation and can be produced at relatively low cost, MIGS could overcome the two biggest weaknesses of sprayed RNA: instability and expense.

The field is moving from laboratory proof-of-concept toward commercial reality. RNA-based pesticides are a rapidly growing industry, and China has officially released the first batch of registered RNA pesticide products, targeting Tobacco Mosaic Virus. The review argues that the safest and most effective targets will come from cross-kingdom small RNAs themselves, molecules already filtered through millions of years of co-evolution, whose natural trafficking suggests low off-target risk and environmental compatibility. Pairing these evolutionarily optimized sequences with microbial bio-factories for production and delivery, the authors contend, could dissolve the techno-economic barriers that have slowed RNA biopesticides. Significant questions remain, including how RNAs are packaged and recognized by recipient cells, how stable they are under field conditions, and what ecological effects engineered microbes might have on soil biodiversity. But the direction is clear: the quiet molecular conversation between plants and microbes is becoming a blueprint for agriculture that protects crops with the precision of a key in a lock rather than the blunt force of a chemical spray.

Subject of Research: Cross-kingdom RNA communication between plants and microbes and its application in RNA interference-based crop protection

Article Title: Cross-kingdom RNA in plant–microbe interactions: from molecular interactions to next-generation crop protection

Article References: Cross-kingdom RNA in plant–microbe interactions: from molecular interactions to next-generation crop protection. (n.d.). https://doi.org/10.1007/s44154-026-00337-x

Image Credits: AI Generated

DOI: 10.1007/s44154-026-00337-x

Keywords: cross-kingdom RNA, RNA interference, plant-microbe interactions, spray-induced gene silencing, host-induced gene silencing, microbe-induced gene silencing, small RNAs, extracellular vesicles, RNA pesticides, fungal pathogens, plant immunity, sustainable agriculture

Long noncoding RNAs, typically defined as transcripts longer than two hundred nucleotides that are not translated into proteins, were once dismissed by many researchers as transcriptional noise. Early genome sequencing projects revealed that while only a small fraction of the human genome encodes proteins, the vast majority of it is transcribed into RNA. Skeptics argued that most of these transcripts were accidental byproducts of a cellular machinery that transcribes promiscuously. Over the past two decades, however, careful functional studies have dismantled that view. Individual long noncoding RNAs have been shown to sculpt chromatin, modulate the stability and translation of messenger RNAs, serve as scaffolds for multi-protein complexes, and act as molecular decoys that sequester transcription factors or microRNAs. Their regulatory reach extends across nearly every layer of gene expression, and their expression patterns are often exquisitely specific to particular cell types, developmental stages, and physiological conditions, including infection.

What makes the cross-kingdom framing particularly compelling is that long noncoding RNAs are not a peculiarity of animals. Plants produce them in abundance, and plant pathologists have documented RNA molecules that move from fungal pathogens into plant cells and vice versa. Small RNAs were the first cross-kingdom RNA travelers to be described in detail, with fungal pathogens such as Botrytis cinerea shown to deliver small RNAs into plant cells where they hijack the host’s own RNA interference machinery to suppress immune genes. Long noncoding RNAs now appear to participate in comparable exchanges, functioning both as sources of regulatory small RNAs and as independent effectors in their own right. In agricultural contexts, this discovery has opened an entirely new frontier: if pathogen RNAs silence crop immune genes, then engineered host RNAs might be deployed to silence essential pathogen genes, a strategy sometimes described as host-induced gene silencing.

In mammalian systems, the interplay between long noncoding RNAs and pathogens is equally rich. Upon infection, host cells reprogram their long noncoding RNA landscape on a massive scale. Interferon signaling, the centerpiece of antiviral immunity, induces a constellation of noncoding transcripts whose functions are only beginning to be mapped. Some of these RNAs amplify antiviral responses, acting as positive regulators that stabilize interferon-stimulated messenger RNAs or promote the signaling cascades triggered by pattern-recognition receptors. Others do the opposite, serving as brakes on inflammation that prevent immune damage to host tissues. Pathogens, in turn, have learned to manipulate this layer of regulation. Viruses encode their own noncoding RNAs and also reshape the abundance of host long noncoding RNAs, co-opting regulatory molecules to create a cellular environment favorable to viral replication, persistence, and escape from immune surveillance.

Bacterial pathogens add yet another dimension to the dialogue. Although bacteria do not possess the same RNA processing machinery as eukaryotes, they are masters of RNA regulation, using small RNAs and structured RNA elements to fine-tune gene expression in response to environmental cues. Emerging work suggests that bacterial RNAs can be released into host cells, whether through outer membrane vesicles, secretion systems, or the controlled lysis of bacterial cells, and that these molecules can modulate host signaling pathways. Conversely, host long noncoding RNAs influence the outcome of bacterial infection by regulating the expression of genes involved in innate immunity, inflammasome activation, autophagy, and cell death. Each of these pathways is a battleground, and RNA regulation sits at the heart of the fight.

The mechanistic versatility of long noncoding RNAs helps explain why they are such effective mediators of this dialogue. Unlike proteins, which must be synthesized, folded, and often trafficked through elaborate pathways, RNAs can be produced rapidly and can act through base-pairing interactions that are comparatively simple to predict and, at least in principle, to engineer. A single long noncoding RNA can interact with DNA, other RNAs, and proteins simultaneously, functioning as a hub that integrates multiple regulatory inputs. This multifunctionality means that a pathogen that targets one host long noncoding RNA can, in a single move, perturb an entire regulatory network. It also means that experimental perturbation of these RNAs, through antisense oligonucleotides, small interfering RNAs, or CRISPR-based approaches, can reveal network-level effects that single-gene knockout studies of proteins might miss.

Technological advances have driven much of the recent progress. Long-read sequencing technologies now allow full-length characterization of transcript isoforms, revealing complexity that short-read approaches obscured. Strand-specific and single-cell RNA sequencing methods have made it possible to profile the noncoding transcriptome of individual infected cells, exposing the heterogeneity of host responses within a tissue. Cross-kingdom RNA detection has benefited from computational pipelines designed to distinguish pathogen-derived reads from host transcripts, a nontrivial challenge given the low abundance of microbial RNAs within a sea of host RNA. Functional validation remains the rate-limiting step: assigning a concrete mechanism to a differentially expressed long noncoding RNA requires loss-of-function and gain-of-function experiments, mapping of interaction partners, and careful demonstration that observed effects are not artifacts of off-target perturbation. The field has matured considerably in its rigor, and the commentary in Cell Research reflects that maturation, emphasizing that the most convincing examples of cross-kingdom RNA communication are those in which the transferred RNA is detected in the recipient, its target is identified, and a functional consequence is demonstrated.

The translational implications are substantial. Host long noncoding RNAs that promote antiviral or antibacterial defense could serve as biomarkers that distinguish active infection from convalescence, or as predictors of disease severity. Therapeutically, RNA-based drugs have finally come of age: antisense oligonucleotides and small interfering RNA therapeutics have been approved for a range of conditions, and the mRNA vaccine success of the COVID-19 pandemic demonstrated that RNA delivery technologies can be scaled to global public health needs. Applying these tools to infection biology, whether by enhancing protective host noncoding RNAs or by directly silencing pathogen transcripts, is a logical next step. In agriculture, RNA-based crop protection strategies are already moving from the laboratory to the field, and a deeper understanding of cross-kingdom RNA exchange will inform both the design of such products and the assessment of their ecological effects on the wider microbiome.

Significant questions remain open. The mechanisms by which RNAs cross cellular boundaries, survive extracellular environments, and enter recipient cells are still incompletely understood, and the physiological relevance of some reported transfers continues to be debated. Dosage is a critical issue: RNA communication depends on molecules reaching functional concentrations in recipient cells, and measuring that accurately in vivo is technically demanding. Specificity is another challenge, since long noncoding RNAs often act at low levels through partial complementarity, raising the risk of unintended interactions when RNAs are manipulated therapeutically. Nonetheless, the conceptual shift is clear and consequential. Host and pathogen are no longer best understood as two organisms exchanging only molecular blows at the protein level; they are two transcriptomes in conversation, each reading and misreading the other’s RNA messages. The commentary’s central message, that long noncoding RNAs broaden the host–pathogen dialogue across kingdoms, captures a field in the midst of redefining itself, and it points toward a future in which the language of RNA becomes as central to infection biology as the language of proteins has always been.

Subject of Research: The role of long noncoding RNAs in cross-kingdom host–pathogen communication and infection biology.

Article Title: Long noncoding RNAs cross kingdoms to broaden host–pathogen dialogue

Article References: Halilovic, L., & Jin, H. (2026). Long noncoding RNAs cross kingdoms to broaden host–pathogen dialogue. Cell Research. https://doi.org/10.1038/s41422-026-01289-7

Image Credits: AI Generated

DOI: 10.1038/s41422-026-01289-7

Keywords: long noncoding RNAs, host-pathogen interactions, cross-kingdom RNA, infection biology, antiviral immunity, gene regulation, RNA therapeutics, plant pathology, viral replication, interferon signaling, host-induced gene silencing, Cell Research