Author: slquinlan

Front Plant Sci. 2026 Feb 10;16:1628122. doi: 10.3389/fpls.2025.1628122. eCollection 2025.

ABSTRACT

INTRODUCTION: Onion (Allium cepa L.) is a globally important crop severely affected by Pantoea ananatis, the causal agent of onion center rot (OCR). The pathogen’s virulence is driven by the chromosomally located HiVir cluster, which produces the phytotoxin pantaphos. Despite its economic significance, resistant Allium genotypes against P. ananatis have not been identified.

METHODS: We screened 982 Allium genotypes under field conditions to evaluate resistance against pantaphos-producing P. ananatis and conducted in vivo transcriptome sequencing of resistant vs. susceptible genotypes under controlled growth-chamber conditions.

RESULTS: Only one genotype, DPLD 19-39, exhibited consistent resistant phenotype, displaying reduced foliar necrosis and bulb rot. Transcriptomic analyses revealed differential regulation of key defense-associated pathways, including cell wall reinforcement, oxidative stress regulation, and programmed cell death.

DISCUSSION: These findings provide the first evidence of a resistant A. cepa genotype against pantaphos-producing P. ananatis. The identified molecular responses highlight potential targets for developing onion cultivars with durable resistance to onion center rot.

PMID:41742960 | PMC:PMC12929489 | DOI:10.3389/fpls.2025.1628122

Trends Genet. 2026 Feb 24:S0168-9525(26)00002-8. doi: 10.1016/j.tig.2026.01.002. Online ahead of print.

ABSTRACT

The sunflower genus, Helianthus, not only includes two crops (cultivated sunflower and Jerusalem artichoke) but also comprises approximately 50 diverse wild species that have served both as a model for foundational studies of adaptation and speciation and as a source of alleles for crop improvement. Extensive genomic resources, including genome assemblies, association populations, and a comprehensive expression atlas, have facilitated both evolutionary and agronomic studies. Despite these advances, sunflower remains recalcitrant to genetic transformation, which impedes functional analyses. The development of tools for functional genetics and genomics, including a graph-based pangenome, improved transformation methods, and doubled haploid technology, is needed to accelerate sunflower improvement and enhance its utility as an evolutionary model.

PMID:41741285 | DOI:10.1016/j.tig.2026.01.002

Sci Rep. 2026 Feb 23. doi: 10.1038/s41598-026-40828-5. Online ahead of print.

ABSTRACT

High-throughput sequencing (HTS) has expanded our perspective on the distribution and diversity of plant viruses. Furthermore, improvements in HTS and decreasing sample costs have enabled the discovery of novel plant viruses in field-collected samples. This study examined the putative virome of cotton samples collected from fields across the southern United States. Leaf samples were collected, and total RNA was extracted. Library preparation was performed from pooled samples within locations before sequencing on an Illumina platform. Sequenced libraries were mapped to the cotton reference genome, and the resulting sequences were de novo assembled. A metatranscriptomics analysis revealed complete genome contigs of cotton leafroll dwarf virus in all tested samples. Additionally, 29 putative families of RNA and DNA plant viruses co-infecting cotton were found. Seven families of RNA viruses were more prevalent across all locations. These families included Botourmiaviridae, Hypoviridae, Mitoviridae, Narnaviridae, Partitiviridae, Solemoviridae, and Totiviridae. The information obtained in this investigation will help develop a broader perspective on cotton virus diversity and whether co-infections of viruses can influence (negatively or positively) plant physiology, product quality, and yield.

PMID:41730992 | DOI:10.1038/s41598-026-40828-5

J Biol Chem. 2026 Feb 20:111305. doi: 10.1016/j.jbc.2026.111305. Online ahead of print.

ABSTRACT

Plant cell walls are glycan-rich extracellular matrices that fundamentally impact essential cellular processes, such as growth, adhesion, and cell shape acquisition. Understanding plant cell wall glycans requires the identification and characterization of the biosynthetic enzymes that produce these polymers. Most successful in vitro protein expression studies of plant cell wall glycosyltranferases have relied on insect, fungal/yeast, or human cell expression systems, while prokaryotic expression systems have been generally unsuccessful. Here we show that Arabidopsis FRIABLE1 (FRB1)/Rhamnogalacturonan-I Rhamnosyltransferase 8 (RRT8) can be produced in E. coli RosettaGami2 cells as N-terminal maltose binding protein fusion proteins containing C-terminal 6X-His-tags. We also report the catalytic constants of FRB1/RRT8 with apparent K_M and K_cat values of 226 μM and 33 min^-1 for UDP-Rhamnose and 117 μM and 28.7 min^-1 for RG-I, respectively. We examine the catalytic activities of mutated FRB1/RRT8 proteins based on an AlphaFold3-generated FRB1/RRT8 protein structural model with a virtually docked UDP-Rha donor. Enzymatic characterization of the mutated and wild type FRB1/RRT8 protein confirmed that mutation of predicted catalytic site amino acid residues resulted in 20-fold reduction in RRT activity. FRB1 also robustly polymerizes RG-I in combination with RG-I Galacturonosyltransferase 1 (RGGAT1). These results show how a robust E. coli expression system combined with AI tools can be used to increase understanding of plant cell wall glycosyltransferase structure and function.

PMID:41724380 | DOI:10.1016/j.jbc.2026.111305

Front Plant Sci. 2026 Jan 30;16:1724403. doi: 10.3389/fpls.2025.1724403. eCollection 2025.

ABSTRACT

Whiteflies, particularly Bemisia tabaci-a rapidly evolving cryptic species complex comprising more than 40 biotypes including the invasive MEAM1 and MED-and Trialeurodes vaporariorum, remain among the most destructive pests of global vegetable production. Their adaptability, wide host range, and efficient virus transmission drive recurrent epidemics in crops such as tomato, pepper, eggplant, cucurbits, and snapbean. Over six decades, breeding for whitefly resistance has progressed from phenotypic selection to the identification of resistance mechanisms such as antibiosis, antixenosis, and tolerance, and to the exploitation of diverse sources from wild relatives and landraces. Recent advances in QTL mapping, pangenomics, multi-omics integration, genomic selection, and CRISPR-based modification of metabolic and structural defense traits have transformed the landscape of resistance breeding. Emerging AI-enabled tools-including machine-learning models for automated whitefly phenotype detection, hyperspectral stress diagnostics, and predictive modelling of resistance loci-are accelerating the dissection and deployment of complex traits. Importantly, durable whitefly resistance enhances climate resilience by reducing dependence on insecticides, stabilizing yields under abiotic-biotic stress combinations, and mitigating climate-driven surges in whitefly populations and virus epidemics. By integrating classical genetics, modern biotechnology, multi-omics, and AI-driven decision frameworks, breeding programs can more rapidly develop robust, climate-resilient vegetable cultivars capable of withstanding evolving whitefly threats.

PMID:41695528 | PMC:PMC12901495 | DOI:10.3389/fpls.2025.1724403

Genome Biol. 2026 Feb 14. doi: 10.1186/s13059-026-03993-4. Online ahead of print.

ABSTRACT

BACKGROUND: Highly repetitive tandem repeat arrays, known as satellite DNAs, are enriched in low-recombination regions such as centromeres. Satellite arrays often contain complex internal structures called higher-order repeats (HORs), which may have functional significance. Maize is unusual in that its satellites occur in two distinct genomic contexts: centromeres, which interact with kinetochore proteins, and knobs, which undergo meiotic drive in the presence of Abnormal chromosome 10. Whether maize centromeres or knobs contain HOR patterns, and how such patterns relate to function, remains unclear.

RESULTS: Here, we generate 13 repeat-sensitive genome assemblies of maize and its recent ancestor, teosinte. We develop a new graph-based pipeline, HiReNET, to classify HORs and demonstrate its utility in both Arabidopsis and maize. We find that HORs are ubiquitous in maize satellites but are typically low-frequency with small patterns, unlike the large, continuous HOR blocks characteristic of human centromeres. Approximately 38% of centromeric CentC monomers occur in HORs; however, no specific HOR class dominates any functional centromere as marked by centromeric histone H3. Arabidopsis centromeres have a similar HOR landscape. In contrast, maize knobs exhibit a more structured HOR distribution. Large knobs contain megabase-scale similarity blocks with repeated HOR patterns. These repeat units likely promote unequal crossing over, enabling rapid knob expansion, and may harbor motifs recognized by trans-acting factors involved in meiotic drive.

CONCLUSIONS: HORs occur in all major maize satellite arrays. Specific HORs are not associated with centromere function, but knobs contain conserved HOR patterns within similarity blocks that may facilitate meiotic drive.

PMID:41691274 | DOI:10.1186/s13059-026-03993-4

Phytopathology. 2026 Feb 13. doi: 10.1094/PHYTO-10-25-0349-R. Online ahead of print.

ABSTRACT

Understanding how biotic and abiotic factors influence vector-borne pathogen spread is essential for effective management. Cotton leafroll dwarf virus (CLRDV), transmitted by the cotton aphid, Aphis gossypii Glover, can cause yield loss in cotton, Gossypium hirsutum L. CLRDV has a variable incidence across the Cotton Belt, but factors underlying this variation are unknown. Field surveys of commercial cotton fields conducted in Alabama and Georgia from 2021-2022, allowed collection of data on A. gossypii, natural enemies, CLRDV weed hosts, CLRDV incidence, landscape composition, temperature, and precipitation. A structural causal modeling analysis using a directed acyclic graph framework was used to test the significance of these factors on CLRDV incidence in cotton while controlling for potentially confounding effects. Aphis gossypii abundance, prevalence of cotton in the landscape, and temperature had significant and positive effects on CLRDV incidence, whereas other variables were not significant. Temperature had a significant and positive effect on A. gossypii abundance, which likely contributed to the overall effect of temperature on CLRDV incidence. Cotton is a host for both the vector and virus, which may increase the abundance of both. Novel findings from this study identify factors associated with regions at high-risk for CLRDV. Future work can leverage these findings to better predict the spatial and temporal variability in disease incidence.

PMID:41687252 | DOI:10.1094/PHYTO-10-25-0349-R

Bio Protoc. 2026 Feb 5;16(3):e5579. doi: 10.21769/BioProtoc.5579. eCollection 2026 Feb 5.

ABSTRACT

The plant cell wall is a dynamic and complex extracellular matrix that not only provides structural integrity and determines cell shape but also mediates intercellular communication. Among its major components, pectins play essential roles in cell adhesion, wall porosity, hydration, and flexibility. Rhamnogalacturonan-I (RG-I), a structurally diverse pectic polysaccharide, remains one of the least understood components of the plant cell wall. Its backbone is substituted with arabinan, galactan, and arabinogalactan side chains that vary in length, branching, and composition across tissues, species, and developmental stages. In addition, RG-I can undergo modifications such as backbone acetylation, further contributing to its structural complexity and functional diversity. To advance understanding of RG-I, we present a detailed method for isolating RG-I from the model plant Arabidopsis thaliana. Leveraging Arabidopsis as a model system provides major advantages owing to its well-characterized genome and powerful molecular toolkit, enabling deeper investigation into the roles of RG-I in plant development and responses to environmental stress. Our method consists of two major steps: an initial chemical extraction using oxalate, followed by endo-polygalacturonase (EPG) digestion to fragment the pectic domains. An advantage of this approach is that it produces a dry material that can be stored at room temperature without special handling and does not introduce chemicals that may interfere with downstream analyses. The purified RG-I can be used for detailed compositional and structural analyses, as well as for functional studies of enzymes involved in pectin biosynthesis, modification, and degradation. Although this protocol was developed for isolating RG-I from Arabidopsis rosette leaves, it is also applicable to other Arabidopsis organs and other plant species. Key features • This protocol provides a detailed description of RG-I isolation from Arabidopsis rosette leaves. • The isolated RG-I can be used for compositional and structural analyses and serves as a substrate for functional studies of enzymes. • This protocol is also applicable for isolating RG-I from other Arabidopsis organs and from different plant species.

PMID:41675992 | PMC:PMC12887878 | DOI:10.21769/BioProtoc.5579

Microb Genom. 2026 Feb;12(2). doi: 10.1099/mgen.0.001624.

ABSTRACT

Pantoea allii, one of four Pantoea species known to cause onion centre rot, is infrequently isolated from onion compared to its closely related onion-pathogenic species in the same genus. To better understand the genomic diversity and genetic determinants of pathogenicity in this species, we analysed a collection of 38 P. allii strains isolated from 2 primary ecological niches, plants and rainwater, across North and South American and African continents using comparative genomics and phylogenetic approaches. Core-genome phylogeny, average nucleotide identity and gene presence-absence analyses revealed three genetically distinct lineages. All strains harboured conserved biosynthetic gene clusters (BGCs) for quorum sensing, carotenoid production, siderophores and thiopeptides. In contrast, two phosphonate BGCs, key determinants of onion pathogenicity, exhibited lineage-specific distributions. Onion-associated strains from lineages 1 and 2 carried the Halophos BGC responsible for onion tissue necrosis and also encoded the alt gene cluster that confers tolerance to thiosulfinates. Lineage 3 strains, isolated from both onion and rainwater, either lacked a phosphonate BGC entirely or possessed the HiVir phosphonate BGC. In addition, lineage 3 strains lacked the alt cluster altogether. The localization of these virulence genes in the genome varied, with Halophos integrated in the chromosome, HiVir encoded on the conserved Large Pantoea Plasmid, and alt located on small, variable plasmids (plasmid B). The type IV secretion system (T4SS) and type VI secretion system (T6SS) showed variable genomic architectures, with plasmid-borne T4SSs and two chromosomal T6SS loci differing in conservation and gene content. Additionally, conserved Pantailocin phage islands were detected in most genomes. Overall, this study reveals that while core metabolic and competitive traits are conserved across P. allii, virulence-associated loci display lineage-specific distribution, reflecting ecological differentiation and evolutionary plasticity within the species.

PMID:41637125 | DOI:10.1099/mgen.0.001624

Proc Natl Acad Sci U S A. 2026 Feb 10;123(6):e2520476123. doi: 10.1073/pnas.2520476123. Epub 2026 Feb 3.

ABSTRACT

Proteins secreted from a mouth stylet of sedentary plant-parasitic root-knot nematodes self-polymerize to form a unique feeding tube structure within host cells modified into giant feeding cells by the nematode. Feeding tubes have essential functions as they complex with the host endomembrane system for nutrient uptake to sustain parasitism. Despite their significance, they remain one of the least understood aspects of nematode parasitism of plants. Their small size and location within giant-cells deeply embedded within galls encasing adult females has prohibited studies to isolate and discern their molecular composition. Here, we developed a protocol for the isolation and semipurification of root-knot nematode feeding tubes from giant-cell cytoplasm of several host plant species to provide a unique view of these structures at the light and scanning electron microscopy level revealing previously undescribed features of their structure. Our methods allowed for the isolation and solubilization of sufficient quantities of enriched feeding tubes enabling a comparative proteome analysis across host species that identified proteins with an increased likelihood to function in feeding tube formation. A comparison across root-knot nematode species further narrowed candidates to a conserved class of secretory proteins that specifically localized within secretory granules of the dorsal gland of adult females and in feeding tubes formed within host cell cytoplasm to unequivocally demonstrate these proteins as core components of feeding tubes. Our finding gives scientists a look into the protein composition of feeding tubes opening the door to a better understanding of their structure and function in nematode parasitism.

PMID:41632840 | DOI:10.1073/pnas.2520476123