Recent plantpath_ucd items

KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants.

Wed, 17 Jun 2026 00:00:00 +0000

Fast-neutron mutagenesis creates diverse genome-wide mutations, providing a powerful tool for crop functional genomics. Here, we present an expanded genomic and phenotypic analysis of 3268 fast-neutron (FN)-induced mutant rice lines (Oryza sativa L. cv. Kitaake). All FN lines were whole-genome sequenced, and mutations were identified by alignment in the Nipponbare and KitaakeX reference genomes. We cataloged over 428,000 mutations affecting 78.49% of Nipponbare genes and 70.38% of KitaakeX genes. In silico expression analysis indicates that 575 non-mutated Nipponbare genes are highly expressed and likely essential for viability. Each mutant carries, on average, 68.5 mutations in the Nipponbare alignments or 63.2 mutations for KitaakeX alignments, distributed randomly across all 12 chromosomes with no evident hotspots. FN lines have approximately 8.5% fewer mutations when using the KitaakeX alignment, underscoring the unique contributions of each reference genome and the importance...

Temporal dynamics of Grapevine red blotch virus accumulation in grapevine leaves is influenced by fruit maturity stages.

Tue, 26 May 2026 00:00:00 +0000

Grapevine red blotch disease (GRBD) poses a serious threat to viticulture in the United States. Grapevine red blotch virus (GRBV), a member species of Grablovirus vitis (family Geminiviridae), the causal agent of GRBD, disrupts grapevine physiology and metabolism, thereby interfering with the natural processes of fruit ripening. To date, there is limited knowledge about how grape maturity stages influence the timing of changes in viral load and disease progression. This study elucidates the effect of fruit maturity stages on GRBV accumulation in Vitis vinifera L. cv. Merlot grapevines in a Central Coast vineyard in California. Petioles from six basal leaves at random from previously GRBV-infected vines were collected at pre-véraison, véraison, post-véraison, and harvest stages, across two years (2021 and 2022). The viral copy number was quantified using digital PCR. The study identified significant differences (p < 0.05) in GRBV copy number across different maturity stages...

Laboratory Protocols for Candidatus Liberibacter asiaticus Transmission Biology and Management Research

Fri, 8 May 2026 00:00:00 +0000

Candidatus Liberibacter asiaticus (CLas), the causal agent of Huanglongbing, is transmitted by the Asian citrus psyllid (Diaphorina citri) in a persistent, propagative manner. Reproducible transmission studies require not only controlled inoculation assays but also standardized propagation of citrus host plants, maintenance of D. citri colonies, and reliable pathogen detection. This study presents a comprehensive set of coordinated protocols that collectively support controlled CLas transmission experimentation. The workflow includes propagation of Citrus macrophylla for colony and assay use; generation and maintenance of CLas-infected citrus and D. citri colonies; synchronization of D. citri populations to enable CLas acquisition; and a controlled single-D. citri transmission assay with defined inoculation access periods, and a Dellaporta-based nucleic acid extraction method compatible with citrus and psyllid tissues. Quantitative PCR detection is integrated throughout to verify...

STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies

Wed, 6 May 2026 00:00:00 +0000

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate...

Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling

Fri, 17 Apr 2026 00:00:00 +0000

Rice paddies significantly contribute to atmospheric methane (CH4). Here, we show that two independent rice genotypes overexpressing genes for PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) reduce cumulative CH4 emissions by 38% (PSY1) and 58% (PSY2) over 70 days of growth compared with controls. Genome-resolved metatranscriptomic data from PSY rhizosphere soils reveal lower ratios of gene activities for (mostly hydrogenotrophic) CH4 production versus consumption, decreased activity of H2-producing genes, and increased activity of bacterial H2 oxidation pathways. Metabolic modeling using metagenomic and metabolomic data predicts elevated H2 oxidation and suppressed H2 production in the PSY rhizosphere. Assembled genomes of rhizosphere H2-oxidizing bacteria are enriched in genes utilizing gluconeogenic acids compared with H2-producing counterparts, and their activities are likely stimulated by elevated levels of gluconeogenic acids, primarily amino acids, in PSY root exudates....

Lifestyle-associated variation in type IV secretion systems between phytopathogenic and environmental Ralstonia.

Fri, 17 Apr 2026 00:00:00 +0000

Type IV secretion systems (T4SSs) are versatile machines with variable functions including DNA uptake and release, protein translocation, and DNA conjugation. However, the diversity, distribution, and functional roles of the T4SS in the Ralstonia genus remain poorly understood. The Ralstonia solanacearum species complex (RSSC) comprises three species of plant-pathogenic bacteria that cause bacterial wilt disease. The Ralstonia genus also includes non-RSSC species that are primarily environmental bacteria and rare opportunistic human pathogens. This study compared the diversity and phylogenetic distribution of T4SSs in the RSSC phytopathogens vs. non-RSSC environmentals. Phylogenetic analysis of VirB4 sequences and synteny analysis revealed 16 distinct T4SS clusters in Ralstonia, with 10 clusters found in RSSC phytopathogen genomes, 12 in non-RSSC environmental genomes, and 6 clusters in both groups. Collectively, these gene clusters were more prevalent...

A protocol for chemical competence in phytopathogenic Ralstonia.

Fri, 3 Apr 2026 00:00:00 +0000

Here, we present a protocol for the transformation of Ralstonia solanacearum species complex (RSSC) strains by calcium chloride-induced chemical competence. We include a step-by-step protocol with media and solution recipes, quantitative results of the protocols efficacy for four of five tested RSSC strains, and an explanation of the logic underlying the protocol development. The protocol involves sequentially treating overnight cultures with a cold calcium chloride solution and a cold calcium chloride/magnesium chloride/glycerol solution, transforming through alternating heat shocks and ice incubations, and recovering cells via an outgrowth in rich medium.

Teaching in Emergencies: Building Resilient Practices as Language-Learning Teachers

Wed, 25 Feb 2026 00:00:00 +0000

Teaching in Emergencies: Building Resilient Practices as Language-Learning Teachers

Deep change in low-resource classrooms: Data-driven teacher professional development for educators from Burma using a choice-based approach

Wed, 11 Feb 2026 00:00:00 +0000

Deep change in low-resource classrooms: Data-driven teacher professional development for educators from Burma using a choice-based approach

Trapping Failure Leads to Discovery of Potent Semiochemical Repellent for the Walnut Twig Beetle

Wed, 11 Feb 2026 00:00:00 +0000

The walnut twig beetle, Pityophthorus juglandis Blackman, and its associated fungal pathogen that causes thousand cankers disease, currently threaten the viability of walnut trees across much of North America. During a 2011 assessment of seasonal flight patterns of P. juglandis with yellow sticky traps baited with the male-produced aggregation pheromone component, 3-methyl-2-buten-1-ol, dramatically reduced catches were recorded when Tree Tanglefoot adhesive was used to coat the traps. In summer 2011, two trap adhesives were tested for potential repellency against P. juglandis in a field trapping bioassay. SuperQ extracts of volatiles from the most repellent adhesive were analyzed by gas chromatography-mass spectrometry, and limonene and α-pinene were identified as predominant components. In field-based, trapping experiments both enantiomers of limonene at a release rate of ~700 mg/d conferred 91-99% reduction in trap catches of P. juglandis to pheromone-baited traps. (+)- and...

Walnut twig beetle landing rates differ between host and nonhost hardwood trees under the influence of aggregation pheromone in a northern California riparian forest

Wed, 11 Feb 2026 00:00:00 +0000

Abstract Host selection behaviour of the walnut twig beetle (WTB) among hardwood trees was investigated in a riparian forest in northern California by monitoring the landing rate of the beetle with sticky traps on branches baited with 3‐methyl‐2‐buten‐1‐ol, the male‐produced aggregation pheromone. The assay was conducted over 7 days (22 May to 29 May 2017) and compared landing rates on branches of six nonhost species paired with northern California black walnut, Juglans hindsii (the host). A total of 2242/1192 WTB were collected on branches of host/nonhost pairs, and more WTB landed on J. hindsii than on nonhosts in 42 of 58 instances. Female landing rate generally exceeded male landing rate, which underscores the influence of the male‐produced synthetic pheromone in this system. Landing rates of WTB males, females, and the combined sexes on boxelder, Acer negundo , and valley oak, Quercus lobata , did not differ significantly from the landing rates on J. hindsii...

The EPS-I exopolysaccharide transforms Ralstonia wilt pathogen biofilms into viscoelastic fluids for rapid dissemination in planta.

Sat, 31 Jan 2026 00:00:00 +0000

Ralstonia solanacearum species complex (RSSC) pathogens cause destructive plant wilt diseases of a wide variety of crops, leading to significant agricultural losses worldwide. These bacteria rapidly spread through the water-transporting xylem where they grow prolifically and produce abundant biofilm that clogs xylem vessels. To understand RSSC biofilm behavior in planta, we examined their complex fluid mechanics. Rheological analyses revealed that unlike all previously analyzed microbial biofilms, RSSC biofilms are shear-thinning, viscoelastic fluids at physiologically relevant shear forces. To determine which factors confer these unique mechanics, we analyzed biofilms of bacterial mutants with altered biofilm components. Genetic analysis demonstrated that development of the viscous-dominant biofilms required production of EPS-I, an amphiphilic exopolysaccharide that is a major virulence factor for all RSSC pathogens. We show that EPS-I confers biofilm mobility, which allows...

Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations

Tue, 27 Jan 2026 00:00:00 +0000

Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but struggle to assemble complicated genome regions (e.g. repeats) compared to long-read sequence assemblies. Accurate metagenome assembly is especially challenging in diverse environments, such as soil, and long-read sequencing has been shown to improve assembly. Here, we use metagenomic data with paired long-read and short-read sequences to identify specific factors that impact genome assembly and assess their relative importance in a natural soil community. Our analysis suggests that low coverage and high sequence diversity are the two main factors leading to misassemblies in short-read data, and many of these "missed" regions tend to be variable parts of the genome, such as integrated viruses or defense system islands. Taken together, our results demonstrate that short-read metagenomes can possibly underestimate the diversity of these genome...

Unlocking expanded flagellin perception through rational receptor engineering

Wed, 5 Nov 2025 00:00:00 +0000

The surface-localized receptor kinase FLS2 detects the flg22 epitope from bacterial flagella. FLS2 is conserved across land plants, but bacterial pathogens exhibit polymorphic flg22 epitopes. Most FLS2 homologues possess narrow perception ranges, but four with expanded perception have been identified. Using diversity analyses, AlphaFold modelling and amino acid properties, key residues enabling expanded recognition were mapped to FLS2’s concave surface, interacting with the co-receptor and polymorphic flg22 residues. Synthetic biology enabled engineering of expanded recognition from QvFLS2 (Quercus variabilis) into a homologue with canonical perception. A similar approach enabled transfer of Agrobacterium perception from FLS2XL (Vitis riparia) into VrFLS2. Evolutionary analyses across three plant orders showed residues under positive selection aligning with those binding the co-receptor and flg22’s C terminus, suggesting more alleles with expanded perception exist. Our experimental...

Direct evidence for the semipersistent transmission of Cucurbit chlorotic yellows virus by a whitefly vector

Wed, 8 Oct 2025 00:00:00 +0000

Cucurbit chlorotic yellows virus (CCYV) (genus Crinivirus, family Closteroviridae) is an emerging plant virus, and is now spreading and causing severe economic losses to cucurbit crops in many Asian countries. CCYV is believed to be transmitted specifically by the sweetpotato whitefly, Bemisia tabaci, in a semipersistent manner. In the present study, we provide direct evidence for the semipersistent transmission of CCYV by Mediterranean (MED) cryptic species of B. tabaci complex. We investigated CCYV transmission characteristics, and immunofluorescently labeled and localized the virus retention site within the vector by laser confocal microscopy. Whiteflies required ≥1 h of acquisition access period (AAP) to successfully acquire CCYV, and the proportion of RT-PCR positive whitefly individuals reached to 100% at 48 h of AAP. CCYV virons could be retained within vectors as long as 12 d, but the proportion of RT-PCR positive whiteflies dropped to 55% by 3 d. Groups of thirty whiteflies...

Carrot mottle virus ORF4 movement protein targets plasmodesmata by interacting with the host cell SUMOylation system

Wed, 8 Oct 2025 00:00:00 +0000

Plant virus movement proteins (MPs) facilitate virus spread in their plant hosts, and some of them are known to target plasmodesmata (PD). However, how the MPs target PD is still largely unknown. Carrot mottle virus (CMoV) encodes the ORF3 and ORF4 proteins, which are involved in CMoV movement. In this study, we used CMoV as a model to study the PD targeting of a plant virus MP. We showed that the CMoV ORF4 protein, but not the ORF3 protein, modified PD and led to the virus movement. We found that the CMoV ORF4 protein interacts with the host cell small ubiquitin-like modifier (SUMO) 1, 2 and the SUMO-conjugating enzyme SCE1, resulting in the ORF4 protein SUMOylation. Downregulation of mRNAs for NbSCE1 and NbSUMO impaired CMoV infection. The SUMO-interacting motifs (SIMs) LVIVF, VIWV, and a lysine residue at position 78 (K78) are required for the ORF4 protein SUMOylation. The mutation of these motifs prevented the protein to efficiently target PD, and further slowed or completely...

RNA Interference Mechanisms and Applications in Plant Pathology

Wed, 8 Oct 2025 00:00:00 +0000

The origin of RNA interference (RNAi), the cell sentinel system widely shared among eukaryotes that recognizes RNAs and specifically degrades or prevents their translation in cells, is suggested to predate the last eukaryote common ancestor ( 138 ). Of particular relevance to plant pathology is that in plants, but also in some fungi, insects, and lower eukaryotes, RNAi is a primary and effective antiviral defense, and recent studies have revealed that small RNAs (sRNAs) involved in RNAi play important roles in other plant diseases, including those caused by cellular plant pathogens. Because of this, and because RNAi can be manipulated to interfere with the expression of endogenous genes in an intra- or interspecific manner, RNAi has been used as a tool in studies of gene function but also for plant protection. Here, we review the discovery of RNAi, canonical mechanisms, experimental and translational applications, and new RNA-based technologies of importance to plant pathology.

Insect-specific viruses: from discovery to potential translational applications

Wed, 8 Oct 2025 00:00:00 +0000

Over the past decade the scientific community has experienced a new age of virus discovery in arthropods in general, and in insects in particular. Next generation sequencing and advanced bioinformatics tools have provided new insights about insect viromes and viral evolution. In this review, we discuss some high-throughput sequencing technologies used to discover viruses in insects and the challenges raised in data interpretations. Additionally, the discovery of these novel viruses that are considered as insect-specific viruses (ISVs) has gained increasing attention in their potential use as biological agents. As example, we show how the ISV Nhumirim virus was used to reduce West Nile virus transmission when co-infecting the mosquito vector. We also discuss new translational opportunities of using ISVs to limit insect vector competence by using them to interfere with pathogen acquisition, to directly target the insect vector or to confer pathogen resistance by the insect vector.

Characterization and Epidemiology of Outbreaks of Impatiens necrotic spot virus on Lettuce in Coastal California.

Wed, 8 Oct 2025 00:00:00 +0000

California is the leading producer of lettuce (Lactuca sativa) for the United States and grows 77% of the country's supply. Prior to 2006, coastal California lettuce was only periodically and incidentally infected by a single tospoviruses species: Tomato spotted wilt virus (TSWV). However, beginning in 2006 and continuing through 2012, severe outbreaks of disease caused by Impatiens necrotic spot virus (INSV) have affected the coastal lettuce crop, though TSWV was also present. In contrast, TSWV was the only tospovirus associated with disease outbreaks in Central Valley lettuce during this period. Disease surveys conducted over two seasons (2008 and 2009) in 10 commercial fields (acreage of 6 to 20 ha) indicated that INSV was the only tospovirus associated with economically damaging disease outbreaks in lettuce in the coastal region, with incidences of 0.5 to 27% (mean = 5.7%). Molecular characterization of INSV isolates associated with these disease outbreaks revealed little...

Emerging strategies for RNA interference (RNAi) applications in insects

Wed, 8 Oct 2025 00:00:00 +0000

RNA interference (RNAi) in insects is a gene regulatory process that also plays a vital role in the maintenance and in the regulation of host defenses against invading viruses. Small RNAs determine the specificity of the RNAi through precise recognition of their targets. These small RNAs in insects comprise small interfering RNAs (siRNAs), micro RNAs (miRNAs) and Piwi interacting RNAs (piRNAs) of various lengths. In this review, we have explored different forms of the RNAi inducers that are presently in use, and their applications for an effective and efficient fundamental and practical RNAi research with insects. Further, we reviewed trends in next generation sequencing (NGS) technologies and their importance for insect RNAi, including the identification of novel insect targets as well as insect viruses. Here we also describe a rapidly emerging trend of using plant viruses to deliver the RNAi inducer molecules into insects for an efficient RNAi response.

RNA interference approaches for plant disease control

Wed, 8 Oct 2025 00:00:00 +0000

Plant diseases caused by a variety of pathogens can have severe effects on crop plants and even plants in natural ecosystems. Despite many effective conventional approaches to control plant diseases, new, efficacious, environmentally sound and cost-effective approaches are needed, particularly with our increasing human population and the effects on crop production and plant health caused by climate change. RNA interference (RNAi) is a gene regulation and antiviral response mechanism in eukaryotes; transgenic and non transgenic plant-based RNAi approaches have shown great effectiveness and potential to target specific plant pathogens and help control plant diseases, especially when no alternatives are available. Here we discuss ways in which RNAi has been used against different plant pathogens, and some new potential applications for plant disease control.

Candidatus Liberibacter asiaticus exploits cytoskeletal system of psyllid vector for circulative propagative infection