Tobamovirus fructirugosum (ToBRFV) and Crinivirus tomatichlorosis (ToCV) are emerging viral threats to tomato production worldwide, with expanding global distribution. Both viruses exhibit distinct biological characteristics and transmission mechanisms that influence their spread. This study aimed to reconstruct the complete genomes of ToBRFV and ToCV from infected tomato plants and wastewater samples in Argentina to explore their global evolutionary dynamics. Additionally, it compared the genetic diversity of ToBRFV in plant tissue and sewage samples. Using metagenomic analysis, the complete genome sequences of two ToBRFV isolates and two ToCV isolates from co-infected tomatoes, along with four ToBRFV isolates from sewage, were obtained. The analysis showed that ToBRFV exhibited higher genetic diversity in environmental samples than in plant samples. Phylodynamic analysis indicated that both viruses had a recent, single introduction in Argentina but predicted different times for ancestral diversification. The evolutionary analysis estimated that ToBRFV began its global diversification in June 2013 in Israel, with rapid diversification and exponential growth until 2020, after which the effective population size declined. Moreover, ToCV’s global expansion was characterized by exponential growth from 1979 to 2010, with Turkey identified as the most probable location with the current data available. This study highlights how sequencing and monitoring plant viruses can enhance our understanding of their global spread and impact on agriculture.

Tomato cultivation is an important agricultural activity in northeast of Argentina, and disease control is indispensable for its production. The purpose of the current study was to identify two fungi isolated from tomato plants cultivated in greenhouses, with symptoms of leaf mould disease and a strain of the genus Cladosporium from a culture collection, and evaluate their in vitro susceptibility to four commercial fungicides. Macro and microscopic examination, molecular characterisation and sequence analysis were applied for identification. Broth dilution and spread plate methods were used to determine the minimal inhibitory concentration (MIC) and minimal fungicide concentration (MFC). The active ingredients of the products were azoxystrobin+difenoconazole, trifloxystrobin+tebuconazole, chlorothalonil and metalaxyl-M+mancozeb. The results were processed using the Kruskal-Wallis method. The isolates were identified as Cladosporium cladosporioidesa-c; consequently, lesions found on tomato plants did not corrspond to Cladosporium fulvum. There was a significant statistical difference between the obtained values. Qualitatively, the three strains had a similar behaviour for chlorothalonil (MIC values: 0.25 - 0.5 μg/ml, MFC values: 4 μg/ml). In all cases, tests with metalaxyl-M+mancozeb yielded higher values than those achieved for chlorothalonil (MIC values: 8 μg/ml, MFC values: 8- 32 μg/ml). trobilurin-formulated fungicides were less effective against C. cladosporioidesa-b (MIC values: 16-256 μg/ml, MFC values: >64 μg/ml). C. cladosporioidesc was the most sensitive isolate. The information about the presence of a non-frequent fungus and its fungicide susceptibility, would be useful for establishing control strategies and enhance production.

Ralstonia solanacearum species complex (RSSC) is a genetically diverse group of plant pathogens, yet genomic data from South America remain limited. Here, we characterize 13 RSSC strains isolated from tomato, pepper, and eggplant in northeastern Argentina. Phylogenetic analysis of the egl marker gene assigned these strains to phylotype IIA and suggested two closely related lineages. Complete genomes (5.63–5.76 Mb) were generated for four representative strains, yielding high-quality (99.94% completeness with f_Burkholderiaceae CheckM markers), closed assemblies with canonical bipartite architecture. Phylogenetic analysis of the egl marker, 49 conserved bacterial genes, and average nucleotide identity (ANI) analyses, consistently assigned one lineage to sequevar IIA-50, forming a coherent and monophyletic group. In contrast, although egl analysis suggested the second lineage was related to one sequevar IIA-38 reference strain, genomic analysis did not support this assignment. Further, the genomic analysis revealed significant genomic distance between the genomes for two sequevar 38 representative strains, supporting a conclusion that sequevar 38 itself was not monophyletic and instead appears paraphyletic. These findings highlight limitations of single-locus classification and support genome-informed refinement of RSSC sub-phylotype taxonomy. Outcome statement: Reports of bacterial wilt disease in Argentina had not yet been published in the international literature although the disease has been long-standing. This study provides complete genome sequences for four Ralstonia solanacearum strains from Northern Argentina and places them within a global phylogenomic framework. The Argentine strains cluster into two closely related phylotype IIA lineages, indicating that bacterial wilt in this regional dataset is associated with genetically similar populations. For clear communication of which strains are present in Northern Argentina, we attempted to classify the lineages to the long-standing sequence variant (sequevar) system for naming R. solanacearum species complex (RSSC) strains. One lineage was confidently assigned to IIA-50 with genomic support that confirmed phylogenetic analysis of the classical genetic marker egl . However, newly available genomes for sequevar reference strains revealed an issue where two distantly related strains are currently recognized as references for sequevars. Overall, these results provide evidence supporting the need for genome-informed refinement of sub-phylotype classification and expand genomic representation of South American RSSC populations. Data summary: Complete genome assemblies and raw reads for INTABV18, INTABV29, INTABV624 and INTABV2657 are deposited to NCBI under the project number PRJNA1407867. The curated dataset of public RSSC genomes is available to users who register a free account on KBase via a KBase narrative ( https://narrative.kbase.us/narrative/189849 ). The narrative described in a living BioRxiv pre-print [1]. Supplemental files such as Figure S1, rectangular versions of all trees (Figure 2 and 3 and S1) and supplementary table S1, S2, S3 and S4 are available on Zenodo at doi.org/10.5281/zenodo.19502890

Ralstonia solanacearum species complex (RSSC) is a genetically diverse group of plant pathogens, yet genomic data from South America remain limited. Here, we characterize 13 RSSC strains isolated from tomato, pepper, and eggplant in northeastern Argentina. Phylogenetic analysis of the egl marker gene assigned these strains to phylotype IIA and suggested two closely related lineages. Complete genomes (5.63–5.76 Mb) were generated for four representative strains, yielding high-quality (99.94% completeness with f_Burkholderiaceae CheckM markers), closed assemblies with canonical bipartite architecture. Phylogenetic analysis of the egl marker, 49 conserved bacterial genes, and average nucleotide identity (ANI) analyses, consistently assigned one lineage to sequevar IIA-50, forming a coherent and monophyletic group. In contrast, although egl analysis suggested the second lineage was related to one sequevar IIA-38 reference strain, genomic analysis did not support this assignment. Further, the genomic analysis revealed significant genomic distance between the genomes for two sequevar 38 representative strains, supporting a conclusion that sequevar 38 itself was not monophyletic and instead appears paraphyletic. These findings highlight limitations of single-locus classification and support genome-informed refinement of RSSC sub-phylotype taxonomy.