Race 1 isolates of Fusarium oxysporum f. sp. lycopersici (FOL) are characterized by the presence of AVR1 in their genomes. The product of this gene, Avr1, triggers resistance in tomato cultivars carrying resistance gene I . In FOL race 2 and race 3 isolates, AVR1 is absent, and hence they are virulent on tomato cultivars carrying I . In this study, we analyzed an approximately 100-kb genomic fragment containing the AVR1 locus of FOL race 1 isolate 004 (FOL004) and compared it to the sequenced genome of FOL race 2 isolate 4287 (FOL4287). A genomic fragment of 31 kb containing AVR1 was found to be missing in FOL4287. Further analysis suggests that race 2 evolved from race 1 by deletion of this 31-kb fragment due to a recombination event between two transposable elements bordering the fragment. A worldwide collection of 71 FOL isolates representing races 1, 2, and 3, all known vegetative compatibility groups (VCGs), and five continents was subjected to PCR analysis of the AVR1 locus, including the two bordering transposable elements. Based on phylogenetic analysis using the EF1-α gene, five evolutionary lineages for FOL that correlate well with VCGs were identified. More importantly, we show that FOL races evolved in a stepwise manner within each VCG by the loss of function of avirulence genes in a number of alternative ways. IMPORTANCE Plant-pathogenic microorganisms frequently mutate to overcome disease resistance genes that have been introduced in crops. For the fungus Fusarium oxysporum f. sp. lycopersici , the causal agent of Fusarium wilt in tomato, we have identified the nature of the mutations that have led to the overcoming of the I and I-2 resistance genes in all five known clonal lineages, which include a newly discovered lineage. Five different deletion events, at least several of which are caused by recombination between transposable elements, have led to loss of AVR1 and overcoming of I . Two new events affecting AVR2 that led to overcoming of I-2 have been identified. We propose a reconstruction of the evolution of races in FOL, in which the same mutations in AVR2 and AVR3 have occurred in different lineages and the FOL pathogenicity chromosome has been transferred to new lineages several times.

Core Ideas: We presents the first chloroplast genome from the genus Trichopus . Comparative analysis revealed that the IR regions are more conserved than the SC regions. Highly divergent sequence hot spots were identified, which could be used as molecular markers. Phylogenetic analysis gave insight into the evolutionary history of Trichopus zeylanicus . In this study, we determined the complete sequence of the chloroplast genome of an important, rare, and endangered medicinal plant, Trichopus zeylanicus . The analysis of the genome showed that the complete chloroplast genome of Trichopus zeylanicus is 153,497 bp in size, and has a quadripartite structure with a large single copy of 81,091 bp and a small single copy of 17,512 bp separated by inverted repeats of 27,447 bp. Sequence analysis revealed that the chloroplast genome encodes 112 unique genes, including 78 protein‐coding genes, 30 tRNA genes, and four rRNA genes. We also identified 95 simple sequence repeats and 54 long repeats including 34 forward repeats, seven inverted repeats, nine palindromes, three reverse repeats, and one complementary repeat within the chloroplast genome of Trichopus zeylanicus . Whole chloroplast genome comparison with those of other Dioscoreales indicated that the inverted regions are more conserved than large single copy and small single copy regions. In the phylogenetic trees based on complete chloroplast genome and 78 shared chloroplast protein‐coding genes in 15 monocot species, including 14 Dioscoreales , Trichopus zeylanicus formed a distinct clade. In summary, the first chloroplast genome from the genus Trichopus reported in this study gave a better insight into the phylogenetic relationships of different genera within the order Dioscoreales . Moreover, the present data will be a valuable chloroplast genomic resource for population genetics.

Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occur widely in plants and animals, and have thus far been relatively little investigated in fungi. Here, we comprehensively survey Helitrons in several completely sequenced genomes representing the F. oxysporum species complex (FOSC). We thoroughly characterize 5 different Helitron subgroups and determine their impact on genome evolution and assembly in this species complex. FOSC Helitrons resemble members of the Helitron2 variant that includes Helentrons and DINEs. The fact that some Helitrons appeared to be still active in FOSC provided the opportunity to determine whether Helitrons occur as a circular intermediate in FOSC. We present experimental evidence suggesting that at least one Helitron subgroup occurs with joined ends, suggesting a circular intermediate. We extend our analyses to other Pezizomycotina and find that most fungal Helitrons we identified group phylogenetically with Helitron2 and probably have similar characteristics. FOSC genomes harbour non-canonical Helitrons that are characterized by asymmetric terminal inverted repeats, show hallmarks of recent activity and likely transpose via a circular intermediate. Bioinformatic analyses indicate that they are representative of a large reservoir of fungal Helitrons that thus far has not been characterized.

Arogyapacha, the local name of Trichopus zeylanicus, is a rare, indigenous medicinal plant of India. This plant is famous for its traditional use as an instant energy stimulant. So far, no genomic resource is available for this important plant and hence its metabolic pathways are poorly understood. Here, we report on a high-quality draft assembly of approximately 713.4 Mb genome of T. zeylanicus, first draft genome from the family Trichopodaceae. The assembly was generated in a hybrid approach using Illumina short-reads and Pacbio longer-reads. The total assembly comprised of 22601 scaffolds with an N50 value of 433.3 Kb. We predicted 34452 protein coding genes in T. zeylanicus genome and found that a significant portion of these predicted genes were associated with various secondary metabolite biosynthetic pathways. Comparative genome analysis revealed extensive gene collinearity between T. zeylanicus and its closely related plant species. The present genome and annotation data provide an essential resource to speed-up the research on secondary metabolism, breeding and molecular evolution of T. zeylanicus.

Fusarium wilt of cabbage (Brassica oleracea var. capitata), caused by Fusarium oxysporum f. sp. conglutinans (Foc), poses a significant threat to global cabbage production. Although resistance screening and the initial cloning of resistance genes in cabbage have been previously reported, the specific molecular mechanisms underlying cabbage resistance to Foc remain largely unknown. To elucidate the underlying mechanisms, we performed RNA sequencing analysis on a near-isogenic resistant line YR01_20 and a susceptible NIL line S01_20 by comparing both Foc-inoculated and mock-inoculated conditions. A total of 508.6 million sequencing raw reads (76.8 Gb data volume) were generated across all samples. Bioinformatics analysis of differentially expressed genes (DEGs) between S01_20 and YR01_20 revealed significant enrichment in plant hormone signaling and mitogen-activated protein kinase (MAPK) pathways. Notably, BolC06g030650.2J, encoding the plant defensin protein PDF1.2, was significantly upregulated in both pathways. Real-time quantitative PCR (RT-qPCR) analysis confirmed that PDF1.2 was significantly upregulated in the resistant line at 12 h post-inoculation and remained elevated for up to 144 h. Furthermore, transgenic cabbage overexpressing PDF1.2 exhibited significantly enhanced resistance to Foc. Taken together, these findings advance our understanding of the molecular mechanisms governing cabbage resistance to Fusarium wilt and identify PDF1.2 as a genetic target for breeding Foc-resistant cabbage cultivars through molecular approaches.

Cucumber mosaic virus (CMV) is a destructive viral pathogen of vegetables, fruits, grains, and ornamentals across the globe. This study investigated the comparative antiviral efficacy of chitosan–salicylic acid nanocomposite (Ch/SA NC) and salicylic acid (SA) against CMV in cucumber plants. Transmission electron microscopy (TEM) analyses revealed that Ch/SA NCs can aggregate on the viral coat protein surface, suggesting direct nanoparticle–virus interaction. Greenhouse trials showed that Ch/SA NC, particularly at 90 ppm applied 24 h before CMV inoculation, was the most effective treatment in reducing disease severity and viral load. SA at the same concentration also conferred significant protection when used prophylactically. An RT-PCR analysis confirmed suppression or complete silencing of CMV coat protein gene expression, especially Ch/SA NC-treated plants. Both treatments significantly enhanced the physiological condition of infected plants, including restoration of chlorophyll a, chlorophyll b, and carotenoids, and elevated levels of total phenolics, flavonoids carbohydrates, and proteins. In addition, they boosted the key antioxidant enzymes activities (POX, PPO, SOD) and improved vegetative growth indicators such as plant height, fruit fresh weight, and number of fruits per plant. These results indicate that Ch/SA NC and SA not only inhibit CMV replication but also stimulate host defense responses, improving overall plant health. The strong antiviral effect is likely due to the dual action of Ch/SA NC: direct virus binding and induction of systemic acquired resistance (SAR). Given their efficacy and eco-friendly nature, especially the Ch/SA NC, these treatments offer a promising strategy for integrated viral disease management. Future studies should investigate long-term environmental safety, molecular mechanisms, and field-level applicability.