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TALEs, TALENs, and TALE Base Editors: From Plant Pathology to Biotechnology.

TALEs (transcription activator-like effectors) are an excellent example of how studying pathogen-host interactions can lead to significant biotechnology inventions. TALEs are bacterial effectors that are translocated into plant cells via a bacterial type III secretion system. Once inside the host cell, they are imported into the nucleus to bind specific promoters and induce expression of target genes, thereby supporting the bacterial infection. TALEs are found throughout many, but not all, Xanthomonas pathovars, which can be severe pathogens of different crops. The key feature of TALEs is their modular DNA-binding domain, which allows a simple evolutionary adaptation to novel DNA sequences as well as simple cloning of designer TALEs with desired DNA-binding specificity. Accordingly, TALE nucleases started the genome-editing revolution, and TALE base editors are the latest tools to efficiently edit chloroplast and mitochondrial genomes. We review recent advances in Xanthomonas genomics, synthesize current knowledge about naturally occurring TALEs, and highlight current roles of TALEs in genome editing and synthetic biology.

Xanthomonas

Shining Light on Late Blight.

In this retrospective on my journey in science, I shine light on the ins and outs of the late blight pathogen Phytophthora infestans. While studying plant pathology, I became fascinated by the molecular mechanisms that govern the development of cells and organisms and ended up unraveling intimate plant-microbe interactions. I have been fortunate to work in an inspiring environment and with committed coworkers. I am proud of what we achieved as a team. By digging into the biology of Phytophthora and exploring genomes and pathogenicity mechanisms, we uncovered a treasure trove of novelties and peculiarities that offer ample opportunities for designing pathogen-informed control strategies.

Plant Diseases

Temporal proteomic analysis reveals a three-phase adaptation strategy in Phytophthora cinnamomi during salinity stress.

Phytophthora cinnamomi, a highly invasive hemibiotrophic oomycete, threatens global agriculture, forestry, and native ecosystems. Although drought and temperature effects on P. cinnamomi-host interactions are well studied, current knowledge of abiotic stress responses in P. cinnamomi remains largely centered on infection and phytopathology, with limited molecular insight into the pathogen's direct response to salinity independent of its host. To address this gap, we combined growth assays, time-resolved proteomics, and network analysis to define how P. cinnamomi responds and adapts to salinity exposure. Growth assays showed that NaCl-modified agar enhanced mycelial expansion in a concentration-dependent manner, with 100 mM NaCl significantly increasing growth at 48, 72, and 96 h compared with controls, while 50 mM NaCl remained comparable to control conditions. Temporal proteomic analysis of 100 mM NaCl treatment at 0, 1, 6, 12, and 24 h post treatment revealed dynamic shifts in protein abundance. Early induction of ROS (Reactive Oxygen Species)-detoxifying enzymes, including glutathione S-transferases and peroxidases, was consistent with ROS-specific staining assays. Network analysis identified modules enriched for redox regulation, ATP generation, ion transport, and translational control, highlighting multi-layered adaptation to elevated NaCl levels. Notably, clusters of conserved hypothetical proteins were strongly upregulated, indicating unexplored stress tolerance components in Phytophthora species. Here, we propose that P. cinnamomi rapidly activates a three-phase strategy involving metabolism readjustments, redox defenses, and cellular structure alterations under salinity conditions. With increasing soil salinization due to climate change, our study provides first mechanistic insights into P. cinnamomi's adaptive plasticity and ecological resilience to abiotic stress. SIGNIFICANCE: This study represents the first temporal proteomic analysis of salinity stress adaptation in Phytophthora cinnamomi, revealing a sophisticated three-phase adaptation strategy. This research fundamentally advances our understanding of how this globally destructive plant pathogen, P. cinnamomi, maintains environmental resilience. Our findings reveal proteome remodelling as a mechanistic framework for understanding stress tolerance in oomycetes, a group of microorganisms responsible for some of the world's most destructive agricultural and forest diseases. Our results show proteins involved in emergency damage control through metabolic recalibration to sustained adaptation. These findings have relevance for predicting pathogen behavior under climate change scenarios, where increasing soil salinity threatens agricultural productivity while simultaneously enhancing pathogen survival and virulence. Understanding how P. cinnamomi responds to prolonged salinity exposure may inform targeted biocontrol strategies and improve predictive models of disease pressure in salt-affected agricultural regions. The temporal analysis framework we present offers a broadly applicable approach for understanding microbial stress adaptation, with implications extending beyond plant pathology to environmental microbiology and biotechnology applications where stress tolerance is paramount.

Phytophthora

A gene with a thousand alleles: The hyper-variable effectors of plant-parasitic nematodes.

Pathogens are engaged in a fierce evolutionary arms race with their host. The genes at the forefront of the engagement between kingdoms are often part of diverse and highly mutable gene families. Even in this context, we discovered unprecedented variation in the hyper-variable (HYP) effectors of plant-parasitic nematodes. HYP effectors are single-gene loci that potentially harbor thousands of alleles. Alleles vary in the organization, as well as the number, of motifs within a central hyper-variable domain (HVD). We dramatically expand the HYP repertoire of two plant-parasitic nematodes and define distinct species-specific "rules" underlying the apparently flawless genetic rearrangements. Finally, by analyzing the HYPs in 68 individual nematodes, we unexpectedly found that despite the huge number of alleles, most individuals are germline homozygous. These data support a mechanism of programmed genetic variation, termed HVD editing, where alterations are locus specific, strictly governed by rules, and theoretically produce thousands of variants without errors.

Animals

Genome-Wide Identification of the PAL Gene Family in Idesia polycarpa and Transcriptomic Responses to Botryosphaeria dothidea Infection.

Idesia polycarpa is a woody oil tree threatened by stem canker caused by Botryosphaeria dothidea, yet the organization and infection-responsive behavior of its phenylalanine ammonia-lyase (PAL) gene family remain poorly understood. Here, we identified five IpPAL genes and characterized their phylogenetic relationships, conserved features, duplication patterns, promoter cis-elements, and infection-associated expression profiles. Segmental and tandem duplication contributed to IpPAL family evolution, and all duplicated pairs showed Ka/Ks ratios below 1, consistent with purifying selection. RNA sequencing (RNA-seq) of contrasting Chengdu and Zhangjiajie provenances revealed distinct temporal responses. In Chengdu, IpPAL2-IpPAL4 were significantly upregulated at 24 h after inoculation, whereas all five genes were upregulated at 96 h. In Zhangjiajie, all five IpPAL genes were significantly upregulated at 24 h, while IpPAL2-IpPAL5 remained upregulated at 96 h. No IpPAL gene met the differential-expression criteria between provenances under mock conditions or at 24 h; at 96 h, IpPAL1 and IpPAL3 were lower and IpPAL5 was higher in Zhangjiajie than in Chengdu. Scanning electron microscopy (SEM) provided complementary qualitative evidence of provenance-associated tissue responses. These findings demonstrate time- and gene-specific IpPAL responses to B. dothidea and identify candidate genes for further functional analysis.

Ascomycota

Ramu stunt virus genome reveals previously unreported segments and nucleocapsid domain duplication in Mechlorovirus.

Ramu stunt virus (RmSV), a member of the genus Mechlorovirus within the family Phenuiviridae, was previously described as a six-segmented RNA virus infecting sugarcane. In this study, we re-examined type material and additional isolates using high-throughput sequencing and RT-PCR validation, revealing that RmSV possesses a nine-segmented genome, making it the largest reported in the Phenuiviridae. This expanded architecture includes duplicated RNA segments (RNA 2a and RNA 2b) encoding nucleocapsid-like proteins and two novel segments (RNA 7 and RNA 8). Comparative analysis showed that RNA 2a and 2b share about 84% amino acid identity, while RNA 5 encodes a third nucleocapsid homolog, indicating unprecedented domain redundancy. Structural modeling confirmed that all three nucleocapsid proteins maintain a conserved fold despite low sequence identity, with electrostatic mapping suggesting differential RNA-binding potential. Additionally, RNA 6 encodes a hypothetical protein structurally similar to the rice stripe virus disease-specific S-protein, implicating a role in symptom development. Transcript abundance analysis revealed RNA 6 as the most highly expressed segment across isolates. These findings revise the genomic composition of RmSV, highlight mechanisms of genome plasticity and adaptive evolution in plant-infecting bunyaviruses, and underscore practical implications for diagnostic assay design, resistance breeding, and biosecurity surveillance.

Genome, Viral

A Leucine-Rich Repeat Receptor-Like Protein Associated with a QTL for Septoria Stem Canker in Populus trichocarpa × Populus deltoides Hybrid Poplar.

The fungal plant pathogen Sphaerulina musiva (Ascomycota) causes Septoria stem canker, the most economically damaging disease of Populus plantations in North America, yet the genetic determinants of host resistance remain uncharacterized in hybrid poplar. Using an inoculation experiment with the 52-124 pseudo-backcross family of Populus trichocarpa × Populus deltoides (TD × D) hybrid poplar, a single significant QTL was identified on Chromosome 16 (LOD = 4.93) associated with both stem canker count and disease severity score. Transcriptomic analysis of two resistant and two susceptible genotypes across a 72-hour infection time course identified a single differentially expressed gene within the QTL candidate gene window: Podel.16G125900, a putative leucine-rich repeat receptor-like protein (LRR-RLP) with homology to receptor-like protein 33 in Arabidopsis thaliana. Podel.16G125900 is located 3001 bp (0.019 cM) upstream of the QTL peak and showed a strong infection-induced upregulation in susceptible genotype 852 (log2 fold-change = 20.47) and higher baseline expression in resistant genotypes relative to susceptible genotypes across all infection time points, consistent with a resistance mechanism in which expression level contributes to the degree of resistance conferred. Two P. trichocarpa homologs were not differentially expressed and differ substantially in sequence content, suggesting the resistance function is specific to the resistant P. deltoides lineage. These findings identify Podel.16G125900 as a strong candidate gene underlying quantitative resistance mechanisms modulating Septoria stem canker resistance in the 52-124 family of TD × D hybrid poplar and provide a target for future functional validation and marker-assisted resistance breeding.

Disease Resistance

Tree Killer, Qu'est-ce Que C'est? Insights From Forest Pathogen Genomes.

Forests are central to planetary health but are increasingly challenged by emerging diseases driven by climate change, global trade, and anthropogenic disturbance. Despite the apparent resilience of long-lived, genetically diverse tree hosts, forest ecosystems have repeatedly experienced landscape-level pathogen-driven transformations. Advances in genomics, transcriptomics, and functional biology have transformed our understanding of how fungal and oomycete pathogens interact with their hosts across a continuum of lifestyles, from saprotrophy and necrotrophy to biotrophy. Here, we synthesize insights from comparative and population genomics and functional studies across diverse forest pathosystems to examine the traits that characterize successful tree pathogens. We highlight how lifestyle plasticity, adaptations to woody tissues, vector-mediated transmission, and biotrophic stealth enable pathogens to colonize perennial hosts and persist over long temporal scales. We further examine how genome plasticity, hybridization, and horizontal gene transfer generate adaptive potential that often outpaces host evolutionary responses under current environmental change. Finally, we discuss emerging genomic tools, including biosurveillance, machine learning-based classification, and genome editing, that are beginning to link genotype to phenotype and inform assessments of disease risk. By integrating genomic, ecological, and evolutionary perspectives, this review outlines general principles governing forest pathogen success and identifies priorities for future research aimed at improving understanding, early detection, and management of forest diseases in a changing world.

Trees

First detection of African swine fever in a swine farm in Taiwan.

INTRODUCTION: African swine fever (ASF) is a highly contagious, high-consequence transboundary animal disease that poses a critical threat to global swine production and agricultural economics. Since its emergence in China in 2018, ASF has spread to over 20 Asia-Pacific countries, causing significant economic disruption. While Taiwan previously detected ASF virus several times in dead pigs drifting offshore, or in illegal pork-related products brought by international tourists and inspected at airport and seaport border controls, no local domestic swine farm had tested positive before this October 2025 ASF event. However, maintaining this disease-free status requires constant vigilance against evolving regional biosecurity threats. METHODS: The first ASF detection in a domestic swine herd in Taichung City, Taiwan, reported on October 22, 2025, was triggered by abnormal alerts of the monitoring system in the rendering plant; the index farm captured a cumulative herd mortality rate of 35.2% that exceeded the predefined threshold (3% mortality daily in the nursery to finish pigs). Five finisher pigs were submitted for diagnostic evaluation, which subsequently confirmed ASFV infection via real-time PCR, pathological examination, immunohistochemistry, virus isolation, and whole-genome sequencing. RESULTS: Affected pigs showed clinical signs including wheezing, sudden death, nasal bleeding, uncoagulated blood in the nostrils, and mild hemorrhage on the skin surface of the neck, abdomen, and buttocks. Histopathological examination revealed severe multisystemic hemorrhagic lesions. Based on assay results of the P72, P54, P30, and CD2v genes, and whole-genome sequence, phylogenetic analysis confirmed that the isolate (ASFV/TWN/2025) is a genotype I/II recombinant strain, most similar to prevailing strains isolated in China and Vietnam, sharing 99.95%-99.97% and 99.92%-99.97% nucleotide similarity of whole genome sequence, respectively. DISCUSSION: Upon confirmation of the ASF case, authorities immediately implemented a nationwide swine movement standstill for 15 days to mitigate transmission risk. To date, no secondary cases have been detected. This article details the early monitoring and rapid diagnosis process of the first case of ASF infection in a farm in Taiwan, and highlights the information from this case to provide lessons for disease diagnosis and prevention in ASF-free areas.

African swine fever

The Anti-Osteoporosis Effects of Panax japonicus via Downregulation of Inflammatory Factors: A Network Pharmacology and Ovariectomized Rat Model Study.

OBJECTIVE: Osteoporosis is a major and growing public health problem characterized by decreased bone mineral density and destroyed bone microarchitecture. Panax japonicus has been clinically used in the treatment of bone diseases, especially osteoporosis. However, there is a lack of study on the mechanism of osteoporosis treatment with Panax japonicus. MATERIALS AND METHODS: A network pharmacology approach was employed to identify the targets of osteoporosis and Panax japonicus. Cytoscape 3.7.2 and DAVID were used to visualize the pharmacological mechanism of Panax japonicus in treating osteoporosis by building up compound-target and protein-protein interaction (PPI) networks and conducting Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. An ovariectomized SD rat osteoporosis model was used to assess the potential therapeutic effect of Panax japonicus in vivo. The biomechanical properties, pathological changes, inflammatory cytokines, bone density, and bone microstructural parameters in rat bone tissue were carefully measured. The biochemical markers of bone metabolism in serum were detected by Enzyme-Linked Immunosorbent Assay (ELISA). RESULTS AND DISCUSSION: Fifty-two active components and sixty-five target genes of Panax japonicus involved in the treatment of osteoporosis were identified. The PPI network revealed IL-6, TNF, NR3C1, IL-1β, CASP3, ESR1, PGR, and AR to be involved in the treatment of osteoporosis with Panax japonicus. Chikusetsusaponin IVa and Radix ginsenoside-Ro were the main saponins found in Panax japonicus. Panax japonicus was found to exert potent preventive effects on osteoporosis by maintaining biomechanical properties, increasing bone mineral density, and protecting the trabecular microstructure in an ovariectomized rat osteoporosis model. Panax japonicus hindered the initiation of osteoporosis induced by ovariectomy by regulating bone metabolism and downregulating the expression of IL-6 and TNF-α. CONCLUSION: Panax japonicus was found to contain 52 compounds and 65 targets in the treatment of osteoporosis. The administration of Panax japonicus could mitigate osteoporosis in rats induced by ovariectomy, and one of the mechanisms was associated with downregulating the expression of inflammatory factors.

Animals