Author: slquinlan

Phytopathology. 2026 Jun 17. doi: 10.1094/PHYTO-04-26-0136-SC. Online ahead of print.

ABSTRACT

Pantoea ananatis is a widely distributed bacterium and is one of the causal agents of onion center rot, a disease responsible for significant global yield losses. While the environmental isolate P. ananatis SK-1, recovered from the Shirakawa River, Japan, is known to induce tissue necrosis in onion, the genetic basis of its pathogenicity remained uncharacterized. In this study, we generated a high-quality hybrid genome assembly of SK-1 using Oxford Nanopore and Illumina sequencing, yielding a 5.0 Mb genome across three contigs with 100% completeness as determined by CheckM. Genomic analysis identified a highly conserved HiVir (high virulence) cluster, a known pathogenicity gene cluster in onion-pathogenic Pantoea spp. However, the alt (allicin tolerance) cluster, which is responsible for imparting tolerance to thiosulfinates in onion tissue, was absent. Functional assays demonstrated that deletion of pepM, a key gene in the HiVir cluster, abolished necrosis in onion tissues, while complementation restored pathogenesis. In contrast, SK-1 exhibited reduced growth in onion juice, consistent with increased sensitivity to thiosulfinates that supports the lack of alt cluster in the bacterium. These findings indicate that although SK-1 possesses onion-pathogenic potential, it lacked the ability to proliferate in onion tissue, suggesting a limited capacity to rot onion.

PMID:42308459 | DOI:10.1094/PHYTO-04-26-0136-SC

Annu Rev Phytopathol. 2026 Jun 15. doi: 10.1146/annurev-phyto-011325-102141. Online ahead of print.

ABSTRACT

Plant diseases threaten global food security, causing up to 40% crop yield losses and more than $220 billion in annual economic damage. This review synthesizes recent advances in understanding the genomic variations and mutational events underlying plant-pathogen interactions and durable plant disease resistance. Key insights into evolutionary dynamics, genetic variability, and coadaptive strategies reveal the complexity of host-pathogen relationships and the implications for developing durable disease resistance. Integrative approaches combining genome-wide association studies and functional genomics have uncovered the polygenic and epistatic architecture of quantitative resistance. Advances in pan-genomics and high-throughput sequencing have revealed extensive genetic variability in cultivated/elite germplasm and wild relatives. Emerging technologies, including gene editing, multi-omics, and machine learning, enable predictive modeling of resistance traits and support evolution that informs plant breeding strategies. Collectively, these advances provide a robust framework for developing durable resistance and sustainable crop protection in the face of global agricultural challenges.

PMID:42296190 | DOI:10.1146/annurev-phyto-011325-102141

Microbiologyopen. 2026 Jun;15(3):e70325. doi: 10.1002/mbo3.70325.

ABSTRACT

Pseudomonas citronellolis M03 was isolated from the soil of a field, which has been under continuous onion production for approximately 20 years. The soil was naturally infested with onion-pathogenic Burkholderia spp. but over the last 2 years bacterial populations had declined. The genome of the bacterial isolate was sequenced. The average nucleotide identity (ANIm) analysis showed > 97% identity and > 84% alignment coverage with the type strain P. citronellolis DSM50332^T. Digital DNA-DNA hybridization (dDDH) values were 73.6% (formula d4) and 77.8% (formula d0), exceeding the 70% species delineation threshold. The genome comprised of a single 6.73 Mb circular chromosome encoding 5802 coding sequences, including 10 pseudogenes, 428 hypothetical genes, and 81 RNA genes (15 rRNAs, 66 tRNAs). We also identified two NRP-metallophore/NRPS biosynthetic gene clusters showing high similarity to the pyoverdine and enantio-pyochelin clusters of Pseudomonas protegens Pf-5, suggesting the presence of uncharacterized metabolites with potential ecological or biocontrol functions. Phenotypic assays demonstrated strong antagonistic activity of P. citronellolis M03 against Burkholderia cepacia and Burkholderia gladioli in vitro, reducing their populations by > 10-fold and approximately 50%, respectively, after 48 h of co-inoculation. Assessment of onion bulb rot showed significant reductions in both disease incidence and severity when P. citronellolis M03 was co-inoculated with B. cepacia. The ability of P. citronellolis M03 to persist and exert antagonistic effects in complex soil microflora highlights its ecological fitness and adaptability in natural environments. This study provides a valuable genomic resource and experimental evidence for the biocontrol capability of this potentially beneficial bacterium.

PMID:42290189 | DOI:10.1002/mbo3.70325

Carbohydr Polym. 2026 Sep 1;387:125464. doi: 10.1016/j.carbpol.2026.125464. Epub 2026 May 25.

ABSTRACT

Vascular plants require boron to cross-link the rhamnogalacturonan-II (RG-II) domain of pectin to form functional cell walls. Boronic acids, which form reversible esters with cis-diols like borate, have been proposed to influence RG-II cross-linking, though the mechanism remains unclear. We used suspension-cultured rose cells adapted to grow without boron to investigate the effect of boronic acids on RG-II dimerization. When grown with phenylboronic acid (PBA) as the sole boron source, nearly all RG-II was crosslinked, whereas methylboronic acid (MBA) only partially restored cross-linking. In contrast, in vitro assays showed that homogeneous RG-II monomers did not dimerize with alkyl or aryl boronic acids unless supplemented with hydrogen peroxide (H₂O₂), which oxidatively converts boronic acids to boric acid. Real-time NMR spectroscopy and density functional theory calculations provided insight into the reaction mechanism and energetics of oxidation respectively. Together, our data show that exogenous boronic acids are a source of boric acid for plants, and that the deboronation reaction generates aryl or alkyl alcohol byproducts that can undergo further chemical modification in planta. The fate and potential roles of these byproducts in planta remain to be determined.

PMID:42285657 | DOI:10.1016/j.carbpol.2026.125464

Annu Rev Phytopathol. 2026 Jun 12. doi: 10.1146/annurev-phyto-121423-082016. Online ahead of print.

ABSTRACT

This review aims to fill a critical gap-phytosanitation methods for inert surfaces, such as farming equipment, containers, tools, and shoes, to mitigate plant pathogen establishment and expansion. Although a core component to food system security and ecosystem stability, especially for mitigating emerging pathogen impacts, this is one of the least studied disease management tools and often lacks robust science-based practices. We herein synthesize what is known about inert surface phytosanitation practices across diverse microbiological and plant pest systems and highlight opportunities for improving both phytosanitation practices and approaches used for phytosanitation science. Basic frameworks are first established for the types of plant pathogen propagules that are spread on surfaces and dispersal risks posed by key inert surface types. This is followed by a discussion of primary surface phytosanitation methods, including physical, chemical, and heat-based approaches. Case studies of nursery/greenhouse and farm equipment phytosanitation are used to demonstrate both systems-strategies for application of phytosanitation best management practices and methods for developing science-based practices using the hazard analysis for critical control points (HACCP) approach. Opportunities for growth discussed throughout include the use of pathogen-specific analyses and epidemiological modeling to improve phytosanitation science and engineering advancements to make phytosanitation practices more efficient. Taken together, it is hoped that this synthesis can both function as a resource for research/extension practitioners looking to develop and improve phytosanitation practices and provide impetus for innovation.

PMID:42285548 | DOI:10.1146/annurev-phyto-121423-082016

Plants (Basel). 2026 May 27;15(11):1646. doi: 10.3390/plants15111646.

ABSTRACT

Magnolia cavaleriei var. platypetala ‘Tanchun’ is a newly registered flower variety in China, known for its characteristic floral aroma that intensifies toward full bloom. However, the composition of the volatiles of this aromatic flower remains uncharacterized. Here, we compared the volatile organic compound composition of Tanchun through gas chromatography-mass spectrometry and comparative transcriptome sequencing analyses of the stamen (S), pistil (P), and petals (T) during flower development, i.e., the bud (S1), semi-opened (S2), and bloom (S3) stages. We present a first comprehensive profile of 1395 metabolites from Tanchun’s floral organs. Terpenoids (26.2%) constituted the largest chemical group, followed by esters (17.52%), nitrogen compounds (9.83%), hydrocarbons (8.11%), alcohols (7.97%), aldehydes (6.53%), and others. We found that volatile organic compound (VOC) accumulation was both spatiotemporal and stage-specific. The S1 and S2 transition was characterized by scent notes of green, herbal, and waxy aromas, while the S2 and S3 shift exhibited a richer profile of fruity, sweet, and creamy notes, primarily in petals. A comparative VOC and transcriptomic analysis revealed that petals activate pathways for structural expansion and precursor mobilization, stamens enhance lipid and terpenoid metabolism, and pistils maintain a conserved profile. Importantly, the S1 and S2 transition in petals establishes the biochemical foundation by activating acyl-CoA, phenylpropanoid, and terpenoid synthesis pathways, which enables the activation of the butanoate metabolism pathway at S3, leading to the production of ester-rich compounds that define the floral scent. The transition to full bloom involves a shift to energy-efficient volatile biosynthesis, supported by carbohydrate restructuring and phytohormonal regulation. Our results provide the first comprehensive volatilome and transcriptome resource for ‘Tanchun’, revealing a highly efficient, multi-stage strategy for floral fragrance biosynthesis. This work lays a molecular foundation for future horticultural improvement and biotechnological applications in the flavor and fragrance industries.

PMID:42280683 | DOI:10.3390/plants15111646

Am J Bot. 2026 Jun 10:e70214. doi: 10.1002/ajb2.70214. Online ahead of print.

ABSTRACT

PREMISE: Global climate change has altered the eco-evolutionary trajectories of plant species, leading to observed shifts in phenotypes, such as earlier flowering. However, disentangling the contributions of plasticity and adaptation to trait changes remains challenging. The resurrection approach is a powerful method to study genetic and plastic responses by contrasting ancestral and descendant lineages from the same populations under common conditions.

METHODS: We compiled a database of resurrection studies to examine plant evolutionary responses to global change using a meta-analysis (46 studies) and quantitative and qualitative review (61 studies). Studies varied widely in the number of focal populations and intervening years separating generations, yet most involved annual plant species in North America and Europe.

RESULTS: We found evidence for rapid, contemporary evolution in over half of the cases. Moreover, evolution was often adaptive. As hypothesized, annuals showed greater magnitudes of evolutionary change than perennials. Across studies, annual descendants evolved earlier phenology and more resource-acquisitive leaf traits relative to ancestors. Under drought stress, annual and perennial species both evolved earlier phenology. Furthermore, in response to drought, annuals evolved increased plasticity in phenological and physiological traits but reduced plasticity in leaf traits, whereas perennials showed no evidence for evolution in plasticity.

CONCLUSIONS: Our study reveals that rapid evolution is common but not ubiquitous and highlights the key role of drought escape in plant responses to a warming world. Our review also suggests promising avenues for future resurrection research.

PMID:42272039 | DOI:10.1002/ajb2.70214

bioRxiv [Preprint]. 2026 May 15:2026.05.13.724861. doi: 10.64898/2026.05.13.724861.

ABSTRACT

Plants produce specialized metabolites that function in plant defense and as attractants to pollinators and symbionts. One class of specialized metabolites are terpenoids that are synthesized from universal C₅ building blocks via activities including terpene synthases, cytochromes P450, and glycosyl transferases. Some terpenes are highly valued for their use as insect repellants, fragrances, antimicrobial compounds, low calorie sweeteners, flavors, and medicines. Low abundance in target tissues, present in complex mixtures, as well as challenging extraction logistics are barriers to economic sustainable production of these compounds from their native species. While heterologous expression of terpenoid biosynthetic genes is feasible, the potential derivation of the products into conjugates via endogenous cytochromes P450 and glycosyl transferases limits this approach. In this project, we used multiplex gene editing technologies to overcome these challenges by creating novel tomato chassis with altered terpenoid biosynthetic capacity in fruit. Excluding central metabolic genes to minimalize impacts on growth and development, we selected 23 known and potential terpene-related genes expressed specifically in the fruit for gene editing. Fruit production and metabolic profiles of three chassis lines with alterations in the major classes of fruit specialized metabolites indicate loss of these genes is tolerated for fruit production. These combinatorial knockouts also showed modulation of native carbon reallocation toward endogenous sinks beneficial for a biosynthetic chassis. Establishing metabolite-modified fruit chassis demonstrates efficient combinatorial editing of entire branches of plant specialized metabolism, facilitating engineering of heterologous terpenes of industrial interest in tomato fruit.

PMID:42182293 | PMC:PMC13192727 | DOI:10.64898/2026.05.13.724861

Sci Rep. 2026 Jun 7. doi: 10.1038/s41598-026-55629-z. Online ahead of print.

ABSTRACT

Analysis of gene sequences showing signatures of selection can provide insights into the evolution and domestication of an organism and can suggest ways to accelerate crop improvement. Using whole-genome resequencing and RNA-seq-derived SNP data from 69 diverse sorghum accessions, we characterized genetic variation and identified genes showing evidence of potentially important roles in sorghum domestication and adaptation. Sorghum genes showing evidence of recent selection based on fixation index (Fst) include Sb02g037735, a protease inhibitor functioning in seed storage; and Sb02g029450, with a double-stranded RNA binding motif. Ten genes showing evidence of selective sweeps include 4 ion transporters that all are located in likelihood intervals for QTLs related to drought resilience of sorghum. Of 15 genes containing 16 deleterious SNPs fixed for different alleles between domesticated and wild sorghums, significantly low Tajima’s D indicates recent selection in two apoptotic ATPase-containing NB-ARC domain genes, signaling proteins involved in disease resistance and regulation of cell death. A group of 22 genes show evidence of convergent selection in sorghum, maize and rice. Integration of selection signatures, large-effect mutations, gene functional annotations, and positional (QTL) information suggests a small number of strong candidate genes involved in sorghum domestication and adaptation, while also identifying a broader set of plausible candidates. Comparison of genes under selection in sorghum, rice, and maize supports both convergent and divergent selection patterns during cereal evolution and domestication.

PMID:42252316 | DOI:10.1038/s41598-026-55629-z

J Econ Entomol. 2026 Jun 2:toag151. doi: 10.1093/jee/toag151. Online ahead of print.

ABSTRACT

Bemisia tabaci (Gennadius) is an economically damaging invasive pest to global vegetable production. Current management strategies rely heavily on insecticides, but increasing levels of resistance raise sustainability concerns. Therefore, strengthening integrated pest management (IPM) programs requires enhancing biocontrol through improved predator-pest interactions. Despite the well-established relevance of functional response modulation by multiple environmental factors, limited research has explored how plant traits and prey life stages interact to influence the efficiency of generalist predators in vegetable systems. To address this gap, we evaluated the functional responses of 2 adult generalist predators, Hippodamia convergens (Guérin-Méneville) and Geocoris punctipes (Say), against 3 nymphal instars of B. tabaci (second, third, and fourth) on 2 vegetable crops: yellow summer squash (Cucurbita pepo L.) and green beans (Phaseolus vulgaris L.) at 6 prey densities (5, 15, 25, 50, 75, and 100) under laboratory conditions. Results showed that both predators successfully preyed on all nymphal instars. Overall, predation did not differ significantly between host plants but varied among nymphal instars and increased with prey density. Both predators exhibited a Type III (sigmoidal) response to second instars and a Type II (hyperbolic) response to third and fourth instars. Attack rate increased with prey stage, with H. convergens showing the highest attack rate on fourth instars. Our findings highlight the importance of prey life stage in determining predator efficiency and support the potential of H. convergens and G. punctipes as promising biocontrol agents of B. tabaci, contributing to the development of more effective IPM strategies for vegetable production systems.

PMID:42228042 | DOI:10.1093/jee/toag151