Editorial: Advances in genomics of plant pathogens and host-pathogen interaction

Worldwide phytopathogens are a major threat to agricultural production, causing 20 to 40% losses in crop yield annually (Ye et al. , 2025). All major taxa of pathogens, including fungi, oomycetes, viruses, and bacteria, have the potential to reduce crop plant resistance. To sustain agricultural production, an efficient disease management approach must be adopted. Over the past decade, advances in genomics have significantly transformed our understanding of host-pathogen interactions by enabling high-resolution insights into the genetic and molecular basis of disease (Ahmadikhah et al. , 2025). Genome sequencing of fungi, oomycetes, bacteria, and viruses has become faster and more affordable with the advent of next-generation sequencing. This can help researchers to identify key genes that determine virulence, effector proteins, and pathogenicity. On the other hand, comparative genomics has revealed the evolution of pathogen genomes, including gene gain/loss, horizontal gene transfer, and the role of transposable elements in adaptability (Pandey et al. , 2023). Through transcriptomics and proteomics, plantpathogen interactions have been studied in parallel, particularly how pathogens manipulate host defense mechanisms and how plants activate immune responses such as PAMP-triggered immunity and effector-triggered immunity. Further, the integration of genomics with bioinformatics tools has also facilitated the discovery of resistance (R) genes in plants and the development of molecular markers for breeding disease-resistant crops. In addition, CRISPR-Cas-based genome editing has opened new paths for functional genomics studies, empowering precise validation of gene function in both hosts and pathogens (Chowdhury et al. , 2025). In agriculture, these advances are paving the way for innovative and sustainable disease management strategies. The research topic "Advances in genomics of plant pathogens and host-pathogen interaction" was aimed at next-generation sequencing technologies, comparative and population genomics, and phylogenomics that could shed light on the genomics and how pathogens intermingle with the host plant. Our goal was to provide novel insights into sustainable disease management, particularly related to host resistance and breeding. This topic addresses investigations of the genomes of plant pathogens (fungi, bacteria, and viruses), genes involved in virulence, the microbiome, transcriptome, metagenomics, resistance mechanisms, population genetics, genetic diversity, and next-generation sequencing that provide insights into genomic dynamics and the interactions between pathogens and their host plants based on recent research. The call attracted significant interest, collecting ten accepted articles from 106 authors globally. The potential findings of these articles are discussed below. Wei et al. used average nucleotide identity and digital DNA-DNA hybridization to determine the taxonomic status of Streptomyces scabiei D6, causing potato common scab disease in China. In whole genome analysis, they identified a core set of 74 virulenceassociated genes of this actinobacterium, which were closely related to the pathogenic strain S. scabiei LBUM848, but not with avirulent strain S. lincolnensis NRRL 2936. The key virulence genes evaluated in this study were PROKKA₀6934, PROKKA₀2771, PROKKA₀5140, and PROKKA₀8104. These findings offer both investigational and genomic indications supporting genomic insights into virulence evolution in pathogenic Streptomyces species. In another study, Karan et al. investigated the interaction between Plasmopara viticola and grapevine using genome and transcriptome approaches. They conducted the firsttime whole genome assembly of P. viticola PV01 in India, which provided an assembled genome spanning 84. 09 Mb across 182 contigs, with an N50 of ~971 kb and BUSCO completeness 97%, and encodes 12, 404 predicted protein-coding genes, lineage-specific expansions, and diverse transposable elements. Functional annotation showed a rich repertoire of effectors, including putative virulence-related and secretory proteins likely involved in host infection and immune suppression. They also studied isolate-level diversification across P. viticola isolates using comparative ortholog analysis. In addition, transcriptome analysis of grapevine-infected leaves exhibited strong suppression of chloroplast-and photosynthesis-associated pathways coupled with the induction of various defense-related genes such as WRKY transcription factors, PR proteins, JA/ET-mediated pathways, and calcium signaling components. Thus, a combined genomic and transcriptomic analysis provides insight into the molecular mechanisms underlying the pathogenicity of P. viticola and the modulation of grapevine immunity. (Xanthomonas oryzae pv. oryzicola) in NDCMP49, a Thai rice variety with strong resistance, using transcriptomic analysis. The obtained transcriptomes of NDCMP49 were also compared with DV85 and HCS, a xa5-based resistance and susceptible rice variety at 0-and 9-hours postinoculation. Differentially expressed genes analysis showed a lower transcriptional response in the two resistant genotypes than in the susceptible ones. All varieties showed differential expression of NB-LRR proteins, receptor-like kinases, NAC transcription factors, chitinase, WRKY, and heat shock proteins at the initial stage of infection, indicating a key role for pathogen effector-triggered and pattern-triggered immunity pathways. In addition, this study also identified Xa21-mediated resistance to the pathogen. Genome-wide association study on 249 rice accessions showed that RIR1b had few InDels in the gene's coding region, which segregated accessions according to their resistance response. The identified genes are valuable candidates for their functional characterization and deployment in the rice breeding programs with strong bacterial leaf streak resistance. In transcriptome analysis of alfalfa seedling roots infected with Sclerotium rolfsii, Jia et al. identified 11, 433 and 12, 063 differentially expressed genes at control versus T24 h (24 hpi) and T4 d (4 dpi), respectively. Plant hormone signal transduction pathways unveiled the highest number of differentially expressed genes at 24 hpi, whereas pathways of plantpathogen interaction were dominant at 4 dpi. Key genes in these pathways include F-box Kelch-repeat protein, Pentatricopeptide Repeat protein, and Pathogenesis-Related protein 1. In addition, the phenylpropanoid biosynthesis pathway also played an important role in disease resistance with the involvement of PAL, 4CL, C4H, CHI, and CHS genes. Besides, the transcription factors, e. g. WRKY family was recognized as a key controller of several metabolic pathways linked with disease resistance. These results deliver a comprehensive understanding of the important molecular factors involved in the response of alfalfa to S. rolfsii infection, putting a theoretical basis for future disease resistance research. In a similar line, Feng et al. revealed that millet (Setaria italica) resistance against Pyricularia setariae was due to early activation of MAPK pathways. They reported downregulation of photosynthesis and ribosome-related genes in the resistant variety at the early stage of infection, and rapid upregulation, signifying a strong self-repairing ability. However, in susceptible varieties, these genes were incessantly downregulated, resulting in severe damage to physiological functions. Further studies revealed that this regulatory process was closely related to the MAPK signaling pathway. A key focus of this study was the expression variances of MAPK pathways and downstream transcription factors in resistant and susceptible varieties. By using both theoretical and genetic resources, this pathway will offer a theoretical basis and genetic resources for analysing disease resistance mechanisms in millet. MicroRNAs (miRNAs) play a key role in gene regulation and are gradually being used to envisage molecular networks and disease resistance genes. In India, Kashyap et al. the microbial community dynamics and enzymatic activities in the potato rhizosphere using high-throughput sequencing. Urease activity was higher under S. scabies stress, while lower under P. infestans stress, whereas catalase activity reduced significantly during the full flowering and seedling phases for S. scabies. Likewise, the activities of sucrose, urease, and alkaline phosphatase decreased under S. subterranea and M. nematode stresses. In addition, microbial community composition was considerably correlated with disease incidence, with specific taxa such as Basidiomycota and Planctomycetes displaying negative correlations with S. subterranea incidence, while Ascomycota and Candidatus Dormibacteraeota were positively associated with P. infestans. These results suggest that pathogen-induced alterations in enzymatic activities play a crucial role in microbial interaction and disease dynamics. Thus, disease management strategies in potato production can be improved by understanding the effects of soilborne pathogens on soil enzyme activity and beneficial microbial communities. In China, Zhao et al. identified Thalictrum squarrosum as an alternate host of Puccinia triticina and its infection phenomenon using molecular approaches. It was shown that basidiospores were capable of infecting plants and causing rust symptoms after being artificially inoculated on the alternate host T. squarrosum. Further, ITS-based molecular and phylogenetic analysis revealed that rust on T. squarrosum could be caused by P. triticina, which was originally originated from wheat. This study provides new insights into the sexual cycle of P. triticina in China and offers a systematic basis for learning about its virulence evolution and optimizing mitigation strategies for wheat leaf rust. Likewise, Kumar et al. also studied the genetic basis of resistance to maydis leaf blight caused by Cochliobolus heterostrophus and maturity-related traits in maize. They evaluated six genetic populations, namely P1, P2, F1, BC1P1, BC1P2, and F2 originated from resistant (CML269-1 and P72c1Xbrasil1177-2) and susceptible (HKIPC4B and ESM113) lines under artificial epiphytotic conditions. Disease resistance showed a dominant genetic effect with significant additive and additive interactions. Traits related to maturity displayed dominance genetic effects, with dominance × dominance interactions, signifying the suitability of hybrid breeding. The estimated genes accountable for maydis leaf blight resistance ranged from 0. 002 to 5. 78 per cross. Further, there was a negative correlation between disease response and maturity-related traits, signifying that long-duration accessions are more disease resistant than short-duration accessions. A thorough understanding of gene actions can help in developing resistant cultivars in the breeding program, with the essential duration for many stress-prone regions. Contributions to this research topic emphasize the genomics and transcriptomics analysis of various agricultural plants and pathogens, the impact of microbial communities on disease progress, and the development of disease-resistant cultivars using a molecular breeding approach. The research topic presents all aspects that are relevant to genomics of plant pathogens and host-pathogen interaction, but not all relevant aspects are included with respect to some notorious pathogens like Macrophomina phaseolina. The application of genomics to the development of innovative disease management strategies is another promising frontier. Using genome editing tools such as CRISPR/Cas systems, disease-resistant crops can be engineered by enhancing innate immunity or targeting susceptibility genes. Early disease management and surveillance are also being improved by advances in pathogen diagnostics, including rapid molecular detection techniques. Despite these remarkable achievements, several challenges remain. It is still difficult to characterize genes identified through genomic studies, and interdisciplinary collaboration is required to translate genomic data into field-level applications. Further, it is imperative that genomic databases are continually monitored and updated in light of the rapid evolution of pathogens. Ultimately, genomics has revolutionized plant pathology by providing a comprehensive framework for understanding host-pathogen interactions including disease resistance at the molecular level. To develop resilient agricultural systems capable of withstanding emerging plant diseases, genomics must be integrated with breeding, biotechnology, and ecological approaches.