The CRISPR Journal

Plant genetic transformation technologies are essential for functional genomics and genome engineering in plants. While transient expression systems offer a rapid alternative to stable transformation, existing platforms are often constrained by low efficiency, technical complexity, and limited scalability. Here, we developed AgroGem, an efficient Agrobacterium-mediated transient transformation system utilizing a geminiviral replicon-based T-DNA vector for Arabidopsis and Brassicaceae species. AgroGem significantly outperformed existing transient approaches, including AGROBEST and protoplast-based assays, in CRISPR-mediated editing efficiency. Moreover, AgroGem recapitulated the mutation spectra and chromatin accessibility-dependent editing patterns observed in stable transformation across both Cas9 and Cas12a systems, indicating that it captures genome editing outcomes in native chromatin contexts. Leveraging this capability, we performed high-resolution profiling of CRISPR-induced mutation outcomes across a panel of DNA repair mutants and identified distinct repair signatures, including unexpected roles for KU80 and XRCC4 in regulating non-homologous end joining (NHEJ). AgroGem also supported bimolecular fluorescence complementation assays for protein-protein interaction studies in Arabidopsis and was readily adapted to plate-based formats for high-throughput applications. Together, these results establish AgroGem as a robust, scalable, and versatile platform for genome editing, DNA repair analysis, and functional genetics in plants.

Homing endonuclease genes spread by cleaving homologous chromosomes that lack the endonuclease cassette, after which repair from the endonuclease-containing chromosome converts the cut allele into a copy of the drive allele. This mechanism has provided a conceptual foundation for synthetic gene drive systems, including CRISPR-based drives, that represent promising strategies for the genetic control of insect pests. However gene drive performance depends critically on the repair pathways available in the germline of the target organism. Here, we report a set of transgenic assays originally developed as part of an attempt to establish gene targeting in the malaria mosquito Anopheles gambiae using an in vivo-generated linear targeting molecule. Although the intended FLP-mediated excision step was not achieved in the mosquito germline, analysis of the component strains revealed efficient germline activity of the rare-cutting homing endonuclease I-SceI and a striking bias towards homology-based repair of I-SceI-induced double-strand breaks. Across reporter and donor configurations, cleavage outcomes were dominated by single-strand annealing, microhomology-mediated repair, synthesis-dependent strand annealing and gene conversion-like events, with comparatively limited evidence for classical non-homologous end joining. In reciprocal crosses designed to distinguish gene conversion from gamete loss, I-SceI cleavage also produced inheritance distortion consistent with both conversion of the cleaved allele and reduced recovery of gametes carrying extensively damaged donor alleles. These findings indicate that the An. gambiae germline can strongly favour homology-dependent repair following homing endonuclease cleavage and that cleavage can also generate meiotic drive-like distortion through selective loss of damaged gametes. The results have direct relevance for the design and interpretation of homing endonuclease and CRISPR-based gene drives in malaria mosquitoes, where the balance between homology-directed repair, end joining and gamete viability will determine drive efficiency, resistance formation and transmission bias. Author summaryGene drives depend on a simple but demanding principle: a nuclease cuts one chromosome, and the cell repairs the break using the homologous chromosome as a template, copying the drive element in the process. Before CRISPR, this type of system was explored using naturally occurring homing endonucleases such as I-SceI. We attempted to develop a gene targeting system in Anopheles gambiae based on the Rong and Golic strategy, in which FLP recombinase would excise a donor molecule and I-SceI would linearise it to stimulate recombination. The full knockout technology did not work because FLP-mediated excision was not detected in the mosquito germline. However, the component tests revealed something more broadly important: I-SceI-induced breaks were repaired predominantly through homology-based pathways rather than simple end joining. We also observed inheritance distortion consistent with both gene conversion and loss of damaged gametes. These results help explain why homing-based systems can work in mosquitoes, while also highlighting why repair pathway choice and gamete viability need to be measured directly in any new drive configuration.

Cas9 precision editing is increasingly predictable because guide, donor and target-context effects have been systematically characterized. Extending this framework to other nucleases is essential for installing variants outside convenient Cas9 target space. Cas12a provides a T-rich protospacer-adjacent motif (PAM) alternative, but determinants of efficient donor-templated Cas12a editing remain poorly defined. Here, we systematically dissected Cas12a precision editing in Saccharomyces cerevisiae across nuclease, direct repeat, expression, crRNA, donor, genomic context and time-course variables. Reporter and amplicon-sequencing assays showed that cleavage activity alone did not predict precise editing. Highly active configurations often reduced viability or lost edited alleles over time, whereas attenuated configurations better preserved programmed edits. Enhanced AsCas12a edited rapidly and tolerated shorter crRNAs, resulting in a narrower editing window, while an attenuated FnCas12a configuration edited more slowly but maintained higher viability and better distal-edit recovery. Alternative repair outcomes were rare, target-dependent, and further suppressed by LexA-FHA donor recruitment. To define design parameters at scale, we established a pooled Cas12a platform with 530 barcoded edit cassettes and recovered programmed edits for 70.2% of designs. Successful editing was reduced with TTTG PAMs, a C upstream of the PAM and at distal edit positions. Excluding these features increased the edited fraction to 85.4% and adding high predicted cleavage scores further elevated it to 91.4%. Applied retrospectively, these criteria also identified poorly edited loci in the targeted panels. Together, these data define design principles for Cas12a-mediated precision editing and establish a scalable platform for genome-scale pooled variant engineering and phenotyping in yeast.

Reported CRISPR/SpCas9 editing efficiencies in crops span 0-100%, but no quantitative synthesis has separated taxonomic family from delivery method, ploidy, clustering or publication bias. This meta-analysis estimated pooled per-T0-line editing efficiency across Cucurbitaceae, Brassicaceae, Solanaceae and Poaceae, and tested whether family is an independent moderator after adjustment for delivery and ploidy. A PRISMA 2020 systematic review identified peer-reviewed studies using SpCas9 with extractable per-line T0 edit counts; data were extracted independently by two reviewers, with inter-rater agreement reported. Logit proportions were synthesised with a binomial-normal generalised linear mixed model, and the family-as-moderator hypothesis was tested by a small-sample CR2 cluster-robust F-test on a three-level model with study-level clustering. Publication bias was assessed by Eggers regression and trim-and-fill. Twenty-two studies contributed 172 per-line effect sizes (Cucurbitaceae k=14, Brassicaceae k=20, Solanaceae k=68, Poaceae k=70). Pooled editing efficiency was 61.8% (95% CI 54.5-68.6%) with I{superscript 2}=93.4% ({tau}{superscript 2}=3.21) and a 95% prediction interval of approximately 5-98%. Per-family estimates ranged from 47.8% (Poaceae) to 73.8% (Brassicaceae); the univariate Q test was significant (p=0.0016), but family did not survive cluster-robust adjustment (F=0.73, p=0.63). Intraclass correlation placed 64.4% of variance at the study level, and Solanaceae remained dominated by a single study (58/68 rows). Funnel asymmetry was severe (Egger p<0.0001), and trim-and-fill reduced the bias-adjusted estimate to 45.2% (95% CI 39.0-51.5%). Apparent crop-family differences dissolve once within-study clustering and methodological covariates are accounted for; the bias-adjusted pooled estimate is closer to 45% than to 62%, and reported editing efficiencies reflect study-level factors more than taxonomic family. Key MessageApparent between-family differences in CRISPR/SpCas9 editing efficiency across four crop families reflect within-study clustering and publication bias, not intrinsic biology; family is not an independent moderator after cluster-robust adjustment.

Drosophila suzukii (Matsumura, 1931, Diptera: Drosophilidae) is a globally invasive pest of soft-skinned fruits that is currently controlled largely through the use of broad-spectrum insecticides. Increasing resistance to pesticides and regulatory pressures have motivated the development of genetic control strategies. We previously developed a CRISPR/Cas9-based homing gene drive targeting the coding sequence of the female-specific exon of the sex-determination gene doublesex, achieving highly efficient inheritance (94-99%) in both male and female germlines. A major limitation of homing gene drives is the formation of resistant alleles that evade cleavage yet retain gene function. Multiplexing guide RNAs (gRNAs) could reduce the formation of such functional resistance alleles. Here, we generated and tested homing constructs expressing one, two, or three gRNAs targeting different regions of the female-specific exon of doublesex, including a splice-junction target site. A single gRNA targeting the splice junction supported high inheritance in males but showed reduced efficiency in females. Combining this gRNA with a coding sequence-targeting guide further reduced drive efficiency, particularly in the female germline. Constructs expressing two gRNAs performed similarly whether guides were linked by transfer RNA (tRNA) sequences or expressed from independent promoters. Constructs expressing three gRNAs using tRNA processing showed consistently low drive inheritance in both sexes, likely a consequence of reduced cleavage efficiency due to inefficient gRNA production. Inheritance was significantly higher in male than female germlines for several constructs, indicating that germline context strongly influences drive performance. Our findings highlight that the approach used for multi-gRNA expression, target site choice and sex-specific germline environments can impact gene drive efficiency, and emphasize the need to optimize construct design within the biological context of the target species.

Multidrug-resistant pathogens pose a major threat to One Health. Within the past decade, CRISPR-Cas systems have been explored as sequence-specific antimicrobials. While chromosomal injury has been considered the primary mechanism underlying pathogen killing by CRISPR-Cas antimicrobials, the synergistic role of gene disruption together with chromosomal injuries remains poorly understood. In this study, we characterized a new class of CRISPR-Cas antimicrobials that simultaneously cotarget essential and defensive genes to enhance potency against the clinically relevant pathogen Staphylococcus aureus. High-throughput CRISPR screening identified top-performing guide RNAs for twenty functionally diverse essential and defensive genes across the S. aureus genome. CRISPR-Cas antimicrobials were modularly formulated to target single or multiple gene loci and packaged in phage-like particles for specific delivery. By engineering an S. aureus production host with a chromosomally integrated anti-CRISPR protein, we demonstrated efficient production of CRISPR-Cas antimicrobials targeting any S. aureus chromosomal locus without self-targeting. Characterization of CRISPR-Cas antimicrobials with single guide RNA designs revealed that potency varied according to targeted gene function, achieving up to a 4-log10 reduction in viability and outperforming traditional antibiotics. Multiplexed configurations were consistently more effective than single-targeting designs, with the top-performing design demonstrating a 4.7-log10 reduction in viability. Cotargeting essential and defensive genes revealed synergies that led to improved lethality and attenuated resistance, with enhanced activity in biofilms compared to traditional antibiotics. Genes involved in signaling and stress responses were important defensive targets for developing cotargeting CRISPR-Cas antimicrobials. Overall, this study establishes design principles for synergistic CRISPR-Cas antimicrobials applicable to next-generation precision antimicrobial development. SIGNIFICANCEThe ability to effectively combat multidrug-resistant pathogens is of primary importance to One Health. This study develops a generalizable design principle for formulating potent CRISPR-Cas antimicrobials that exploit synergistic cotargeting strategies for enhanced pathogen killing. In addition to chromosomal injuries, we found that disruption of gene function plays a crucial role in determining the lethality of CRISPR-Cas antimicrobials, providing a generalizable framework for effective CRISPR-Cas antimicrobial design. The development of a CRISPR-Cas antimicrobial production host with stable, chromosomally integrated anti-CRISPR genes greatly expands the modularity, adaptability, and efficiency of formulating CRISPR-Cas antimicrobials and enables deeper insights into the molecular mechanisms involved in eliminating multidrug-resistant pathogens.

Precision phage therapeutics provide a promising strategy to combat multidrug-resistant pathogens, including Staphylococcus aureus. Efficient, specific packaging of genetic cargoes remains challenging. Using modular design principles, we report a minimal phagemid packaging signal consisting of the phage terminase small subunit under its native promoter that significantly outperforms conventional packaging signals. The utility of this synthetic terS operon was demonstrated through production of highly concentrated and genetically pure CRISPR-Cas antimicrobials. To circumvent CRISPR-mediated self-targeting during antimicrobial generation, a terS-deficient strain was engineered to express the anti-CRISPR protein AcrIIA4, enabling titers above 1010 transducing units per milliliter (TRU/mL) with over 94% purity. With a high-copy origin of replication module, CRISPR-Cas phage-like particle titers could approach 1012 TRU/mL. We discovered that pure CRISPR-Cas antimicrobials are potent and can be amplified in hosts possessing prophages. Taken altogether, this study defines the minimal and optimal genetic requirements for efficient, specific creation of phage-based technologies. Technological ReadinessThe described system for engineering phage-like particles has reached a technological readiness level (TRL) of 4-5 based on the provided laboratory validation and strong literature support from other engineered phage therapies applied to in vivo models. Previous systems have demonstrated high-purity phage-like particle preparation, but always at the cost of severely reduced productivity. Therefore, our demarcation of a specific, efficient, and minimal system for packaging nucleic acid cargoes into phage vectors is a critical step toward real-world use. Despite this, low levels of contaminating host/phage DNA remain a key barrier to phage-based therapies. Protein and strain engineering efforts can help mitigate terminase nonspecificity, but care must be taken to not compromise productivity. More generally, widespread adoption will require deeper understanding of host-pathogen-phage interactions, development of scalable GMP manufacturing processes, and harmonized regulatory guidance that recognizes the dynamic nature of phage-derived technologies.

CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) are two workhorse technologies for loss-of-function studies, yet direct comparisons between the two are scant relative to their widespread adoption. Here, we establish benchmarking libraries for Cas9-based CRISPRko and CRISPRi screens using Perturb-seq as the read-out. For both modalities, we observe consistent transcriptional signatures among cells with the same genes perturbed, strong evidence of on-target signal. We also examine tradeoffs between modalities: while CRISPRi guides demonstrate heightened rates of off-target activity, we also observe artifacts stemming from the cellular response to double-stranded breaks with the use of CRISPRko. The libraries and analyses presented here will be a useful benchmarking and de-risking resource for any group preparing for a large-scale Perturb-seq screen.

Precise knock-in of fluorescent reporters is a powerful tool for studying the dynamic cellular and molecular processes of embryogenesis. However, conventional CRISPR-Cas9 knock-in of large inserts, such as full-length fluorescent proteins, is inefficient. This has limited its application in many emerging model systems, including sea urchins. Here, we overcome this barrier using a transgenic Lytechinus pictus line that constitutively and ubiquitously expresses a large fragment of mNeonGreen (mNG3K1-10). In this line, fluorescence is only reconstituted when CRISPR-mediated knock-in delivers mNG211, the 11th beta strand of the fluorescent protein, to complement the constitutively expressed fragment. Because this strategy requires integrating only the short 11th-strand, together with short homology arms (~130 nt total), by homology directed repair, it circumvents the size constraints that limit conventional full-length reporter knock-ins using CRISPR. Using this approach, we achieved integration efficiencies of 14-22%, roughly an order of magnitude higher than those obtained with full-length fluorescent protein knock-ins. This provides a streamlined, scalable method for endogenous protein visualization in echinoderm embryos and a valuable resource for studying gene function, morphogenesis, and toxicant response in this classic developmental model.

Targeted knock-in technologies have enabled precise insertion of reporters, affinity tags, degrons, and other functional payloads into endogenous genomic loci. Over the past decade, a diverse collection of genome engineering strategies has emerged, including approaches based on homology-directed repair (HDR), microhomology-mediated end joining (MMEJ), homology-mediated end joining (HMEJ), and related methodologies. While these advances have greatly expanded the capabilities of endogenous genome engineering, they have also increased the complexity of donor design, assembly, and validation. Here, we describe FORGE-KI (Functional Oncology Research Genetic Engineering - Knock in), a pathway-matched design workflow for endogenous knock-in engineering that aligns the assembly strategy with the underlying repair mechanism. For large-cargo insertions, we use a modular five-component framework that separates gene-specific targeting arms from reusable functional modules, allowing rapid assembly of HDR donor constructs targeting AHR, IRF1, and FOSL1 from a shared reagent collection. For MMEJ/PITCh applications, where short targeting elements permit rapid fabrication, we developed a streamlined one-step pipeline in which the entire donor and selection payload is synthesized as a single continuous fragment for direct cloning, compressing the design-to-reagent cycle time. This MMEJ workflow is paired with a dual-promoter nuclease vector (pForge-KI-MMEJ-Cas9-DualGuide) that drives the PITCh-release and locus-specific guides from distinct promoters, a design intended to reduce the repeated-promoter instability associated with some dual-guide vectors. We also established a standardized workflow for donor assembly, generation of knock-in cell populations, molecular validation, and selectable-cassette removal, and we demonstrate it by generating a functional, selection-marker-free, cytokine-inducible IRF1 HDR reporter line and an inducible IRF1 PITCh/MMEJ reporter pool with confirmed junction enrichment. In parallel, we developed forgeKI, an R package that automates C-terminal reporter knock-in design across both HDR and PITCh/MMEJ repair pathways, including guide selection, target-biology validation, targeting-arm design, domestication, donor-assembly planning, and generation of synthesis-ready constructs. Together, the reagents and software provide a practical system for endogenous knock-in engineering that supports multiple payloads, selection strategies, and repair pathways within a shared donor organization. Rather than replacing existing knock-in technologies, this framework provides a modular foundation for incorporating, extending, and automating the published knock-in methods.

The kynurenine pathway metabolizes tryptophan into 3-hydroxykynurenine (3-HK), a precursor for ommochrome eye pigments synthesized via the cardinal (cd) gene in mosquitoes. While cd disruption was presumed neutral, we observed fitness costs in Anopheles stephensi knock-in but not knock-out cd mutants. Here we investigated this anomaly further by assessing survival, fecundity, and midgut integrity across multiple cd mutant lines. Heterozygous knock-in lines, expressing a fluorescent marker and guide RNA for CRISPR/Cas9, exhibited reduced survival post-blood feeding, larva-to-adult survival deficits, and midgut barrier dysfunction, whereas knock-outs showed no such costs. Oral supplementation with xanthurenic acid partially rescued knock-in mortality, implicating oxidative stress linked to 3-HK metabolism. Expression analyses suggest transgene insertion effects, rather than cd disruption, underlie these fitness costs. These findings highlight the importance of evaluating insertional effects in gene drive target selection and support cd as a viable target for genetic control strategies in An. stephensi.

RNA interference (RNAi) is a widely exploited reverse-genetics tool with potential uses for disease control. Successful RNAi has been reported in trematode-vectoring snails, but the composition of RNAi effector-encoding gene complements, a key driver for RNAi efficiency, remain unstudied in these species. Using bioinformatics and comparative genomics, we searched for orthologues of 115 RNAi effector sequences in genomes or transcriptomes of four snail vectors: Biomphalaria glabrata, B. pfeifferi, Bulinus truncatus, and Lymnaea staginalis. Gene expression patterns of selected RNAi effectors were then examined across developmental stages and tissues of the model B. glabrata snail. At least 74 RNAi-related proteins were conserved across all four species, including core components known to be essential for gene silencing. Classical systemic RNAi-deficient (SID) genes that facilitate systemic RNAi in other systems were absent, suggesting that alternative pathways may compensate for dsRNA uptake and transport. Core effectors of secondary RNAi amplification and heritable RNAi were not detected. Expressions of Dicer-1, Argonaute-2, and the exonuclease Eri-1 did not vary significantly with snail size. A putative RNAi-inhibiting Staufen orthologue showed elevated expression in the ovotestis, while another putative cholesterol-interacting gene was overexpressed in the trunk tissue and may partly contribute to RNAi import. Altogether, our results present the most comprehensive overview of RNAi pathway effectors in major intermediate snail hosts for trematodes. The findings underscore the likely broad potential for RNAi use in trematode intermediate hosts as an experimental tool and potential control method.

Genetic manipulation of bacteriophages is essential for interrogating phage biology and advancing antimicrobial therapies. However, current genome editing approaches can be inefficient, require multiple steps, or drastically reduce phage titers. Here, we show that targeted DNA nicking enables template-mediated editing of phage genomes in one step without reducing phage titers. Using T7 phage, we show that Cas9-mediated nicking achieved up to 100% recombination across multiple loci, including substitutions and deletions of up to 200 bp and insertions of up to 500 bp, all while preserving phage titers. Editing in T7 was RecA-independent and extended to other phages. Leveraging high titers, we engineered a T7 library of over 440,000 tail-fiber mutants, with isolated mutants restoring infection of two LPS-deficient Escherichia coli hosts by shifting recognition to core LPS components. Overall, DNA nicking is a simple and distinct editing strategy that can advance phage genome engineering, genetic interrogation, and antimicrobial development.

Cas12a2 CRISPR nucleases, including SuCas12a2, have been shown to have extensive collateral activity towards RNA, ssDNA, and dsDNA. This collateral activity results in targeted cell elimination and has applications across biotechnology, agriculture, and human health. We explored the natural genetic diversity of Cas12a2 nucleases and characterized nine novel orthologs in a DNA damage kinetic assay in E. coli. Three new Cas12a2 orthologs (RsCas12a2, SdCas12a2, and HmCas12a2) were shown to have high collateral activity towards DNA. These nucleases are highly divergent from SuCas12a2, have conserved core RuvC catalytic residues, and have sequence diversity in the previously reported aromatic clamp residues required for nucleic acid positioning in the active site. We defined PFS preferences and mismatch tolerance for each high-activity Cas12a2 nuclease, expanding the available Cas12a2 toolbox, and discovered functional differences with obvious impacts on downstream applications.

In recent years, aptamers have transitioned from mere laboratory tools to highly potent molecular recognition agents capable of overcoming the strict limitations of conventional antibiotic therapies. We have developed AptBacterialDB, a manually curated, large, comprehensive database of experimentally validated antibacterial aptamers spanning 1996 to 2026. The database contains a total of 2131 aptamers targeting approx 75 different bacterial classes, and 124 aptamer targets with 95 entries found in UTexas databases, 97 in AptaDB, and 28 in Aptabase. It contains 1555 unique aptamer sequences, 189 unique modifications, 40 different selection approaches, and 44 different affinity methods. It integrates detailed annotations of about 20 fields, including sequence information, nucleic acid type, binding affinity, modifications, experimental and functional details. The secondary structure of the aptamers was predicted using ViennaRNA Package 2.0, demonstrating that they adopt mostly stable conformations, with a structured stem region. MySQL was implemented for database development, and a knowledge graph was integrated using ArcadeDB/openCypher for graphical visualization of aptamer-target-organisation relationships. Facilities such as different search modes, browsing, similarity search, REST API access, and entries linked to the existing database for a broader view of the aptamers have been provided. AptBacterialDB (https://webs.iiitd.edu.in/raghava/aptbacterialdb/) provides a user-friendly centralized platform to accelerate antibacterial aptamer research, therapeutic development, biosensor design, and computational modelling efforts.

Whole-genome sequencing identifies focal DNA amplifications with base-pair resolution but cannot determine whether amplified sequences reside on extrachromosomal DNA (ecDNA, also known as double minutes) or within chromosomally integrated homogeneously staining regions (HSRs). DNA fluorescence in situ hybridization (DNA-FISH) metaphase spreads remain the gold standard for distinguishing these amplification states at single-cell resolution. Here, we present a detailed protocol for DNA-FISH metaphase spreads using human cancer cell lines, encompassing cell culture, metaphase arrest, hypotonic treatment, fixation, chromosome spreading, fluorescent probe hybridization, and fluorescence imaging. The protocol incorporates intermediate quality-control steps to verify successful chromosome dispersion and optimize metaphase spread quality, making the workflow accessible to laboratories without specialized cytogenetics expertise. Results demonstrate clear visualization of ecDNA and HSR amplification states using locus-specific probes and illustrate common technical artifacts that can affect interpretation. This protocol provides a robust and reproducible approach for studying the structural organization of oncogene amplification in cancer cells.

Viroids are plant infectious agents that threaten agricultural production. Current viroid detection methods rely on RT-PCR-based assays, which require specialized laboratory equipment and can sometimes produce false-negative results or non-specific amplification due to the high sequence conservation among closely related viroid species. CRISPR-based diagnostics, particularly Cas12-based systems for DNA detection (DETECTR) and Cas13a-based systems (SHERLOCK) for RNA detection, have emerged as powerful tools for nucleic acid diagnostics. However, most existing workflows still rely on target amplification and, in the case of Cas13a systems, require additional in vitro transcription steps, limiting their simplicity and direct applicability for plant diagnostics. Here, we developed a direct amplification-free Cas13a-based detection platform for viroids using potato spindle tuber viroid (PSTVd) as a model. We optimized CRISPR RNA (crRNA) design, identified inhibitory effects of plant total RNA on readout signal, and employed simplified viroid RNA enrichment workflows enabling robust detection in plant samples. The system further supported both PSTVd-specific and broad-spectrum pospiviroid (genus Pospiviroid) detection and was successfully extended to avocado sunblotch viroid (family Avsunviroidae), demonstrating its adaptability across distinct viroid families. Together, these results establish a practical and modular Cas13a-based platform, not only for viroid diagnostics, but also for broader applications in RNA-derived plant pathogen detection. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/736049v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1d04170org.highwire.dtl.DTLVardef@1783aa3org.highwire.dtl.DTLVardef@51baa7org.highwire.dtl.DTLVardef@1b542b9_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance statementA simplified RNA enrichment workflow combined with CRISPR-Cas13a enables direct, amplification-free detection of plant viroids. The assay supports early and reliable diagnosis across different tomato varieties and provides a practical strategy for improving molecular detection of plant pathogens.

To facilitate the translation of NF1 exon 17 skipping as a mutation-specific therapy for Neurofibromatosis type 1 into in vivo testing, we have continued to develop more efficient antisense oligonucleotides (ASOs), humanized mouse models, and explored multiple delivery platforms including an adeno-associated virus (AAV)-U7-SnRNA vector approach. We evaluated both biodistribution and exon skipping efficacy of a U7-SnRNA targeting NF1 exon 17 with an SFFV-driven cassette containing T2A-linked Luciferase (Luc) and eGFP packaged in AAV-9, AAV-F and AAV-B1 capsids. We show that AAV-F is superior to AAV-9 and AAV-B1 for mouse brain delivery based on DNA transduction, GFP expression, and luciferase activity, but AAV-B1 delivers 2-4 fold more to sciatic nerve (SCN). In terms of exon skipping, AAV-F appears to induce the most skipping in liver and optic nerve (ON), while AAV-B1 mediates highest skipping in the liver, SCN, and ON. The identification of AAV serotypes that allow efficient transduction and delivery of transgenes to the mouse CNS and PNS is impactful for preclinical research in murine models of other diseases. Furthermore, this is both the first report of NF1 exon skipping efficacy in vivo and the first successful application of an U7-SnRNA for the restoration of functional neurofibromin for NF1.

Zebrafish combines the power of genetics and unparalleled in vivo imaging for investigating the dynamics of vertebrate hematopoietic development. Across species, the transcription factor Runx1 is essential for definitive hematopoiesis. We generated a zebrafish runx1-2A-creERT2 CRISPR knock-in for tamoxifen-regulated Cre recombinase Runx1 lineage tracing and characterized its activity using the ubi:Switch recombinase-dependent fluorescence reporter, microscopic live imaging and flow cytometry. Tamoxifen treatment beginning at gastrula stage labeled all expected Runx1 lineages in the early embryo, including neuroectodermal olfactory placode and Rohan-Beard neurons, primitive hematopoietic blood cells, and nascent hematopoietic stem and progenitor cells (HSPCs) in the dorsal aorta. Runx1 HSPCs colonized the larval caudal hematopoietic tissue and thymus from three to five days of development. Timed tamoxifen induction of Cre activity allowed separation of Runx1 primitive hematopoiesis from definitive HSPC emergence and larval stem cell niche colonization. Flow cytometry of kidney marrow and peripheral blood from adults treated with tamoxifen at gastrula stage revealed Runx1 embryonic hematopoietic cells contributed to adult hematopoietic precursors, myeloid, lymphoid, and peripheral blood lineages. Labeling of all blood lineages was also effective by tamoxifen treatment of 5-month-old adults. The zebrafish runx1-2A-creERT2 line provides a powerful tool for precise spatial and temporal analysis of Runx1 progenitor mechanisms in developmental and adult hematopoiesis. Key PointsO_LIzebrafish endogenous runx1-2A-creERT2 provides inducible Cre recombinase genetic analysis in all runx1 neuromesodermal and blood lineages C_LIO_LIzebrafish runx1-2A-creERT2 line enables in vivo spatial and temporal analysis of embryonic and adult hematopoiesis C_LI

In vitro regeneration of Citrus plants is a widely used method, however, induction of adventitious roots from regenerated shoots remains a major bottleneck, limiting the recovery of healthy plants for commercial production and genomic research for crop improvement. We established an in vitro regeneration system producing profuse, healthy roots for sweet orange (Citrus sinensis cv. Benyenda) by optimising combinations and concentrations of auxins. Prior to optimising the rooting media (RTMs), we obtained a shoot regeneration rate of 90.6% from sweet orange epicotyl explants using a cytokinin, 6-benzylaminopurine (BAP). Across twelve auxin-supplemented RTMs containing different concentrations of indole-3-butyric acid (IBA) and/or 1-naphthaleneacetic acid (NAA), rooting percentages ranged from 8 - 87.5%. The combination of IBA 1.0 mg L-1 and NAA 0.1 mg L-1 promoted the best overall performance, 75 {+/-} 7.2% rooting percentage with healthy, callus-free roots ([&ge;]5 cm in length), whereas other RTMs with other auxin combinations induced callus and limited root elongation. The best-performing SRM and RTM were subsequently used for selection and recovery of transgenic sweet orange lines carrying an empty CRISPR/Cas9 construct, resulting in an 4.8% transformation efficiency. Both transgenic and non-transgenic rooted plantlets were successfully acclimatised under glasshouse conditions with a survival rate of 90%. This enhanced regeneration system overcomes rooting bottleneck and improves plant survival,enabling faster recovery of transgenic citrus lines within four months. It supports accelerated development for commercial applications and advances in citrus genetic improvement.