Phylodynamic Insights into Global Emergence and Diversification of the Tomato Pathogen Xanthomonas hortorum pv. gardneri.

The emergence of plant pathogens is often associated with waves of unique evolutionary and epidemiological events. Xanthomonas hortorum pv. gardneri is one of the major pathogens causing bacterial spot disease of tomatoes. After its first report in the 1950s, there were no formal reports on this pathogen until the 1990s, despite active global research on the pathogens that cause tomato and pepper bacterial spot disease. Given the recently documented global distribution of X. hortorum pv. gardneri, our objective was to examine genomic diversification associated with its emergence. We sequenced the genomes of X. hortorum pv. gardneri strains collected in eight countries to examine global population structure and pathways of emergence using phylodynamic analysis. We found that strains isolated post-1990 group by region of collection and show minimal impact of recombination on genetic variation. A period of rapid geographic expansion in X. hortorum pv. gardneri is associated with acquisition of a large plasmid conferring copper tolerance by horizontal transfer and coincides with the burgeoning hybrid tomato seed industry through the 1980s. The ancestry of X. hortorum pv. gardneri is consistent with introduction to hybrid tomato seed production and dissemination during the rapid increase in trade of hybrid seeds.

Characterization of Virulence Phenotypes of Heterodera glycines during 2020 in Indiana.

The soybean cyst nematode (SCN, Heterodera glycines) is the most yield-limiting pathogen of soybean in the US. This study was carried out in order to provide updated information on SCN virulence phenotypes in Indiana. A total of 124 soil samples were collected from soybean fields in 2020 and all of them tested positive for SCN. The virulence phenotypes of 42 representative SCN populations were determined with seven soybean indicator lines using the standard HG type test. The most predominant HG types were 2.5.7 and 1.2.5.7, which accounted for 64% and 14% of the SCN populations tested, respectively. None of the SCN populations tested were rated as HG type 0, compared with 28% of the populations in a previous survey in Indiana during 2006-2008. Nearly 88% of the SCN populations evaluated in this study overcame the resistance provided by PI 88788, which is the most common source of resistance in soybean, up from 56% in the 2006-2008 survey. Approximately 14% of SCN populations tested were virulent to PI 548402 (Peking), in contrast to 0% in the 2006-2008 survey. This study reveals a trend of increasing virulence of SCN populations to resistant sources of soybean in Indiana. The results highlighted the importance of rotating soybean varieties with different types of resistance and identifying new sources of resistance for sustainable management of SCN.

Whole Genome Sequencing-Based Tracing of a 2022 Introduction and Outbreak of Xanthomonas hortorum pv. pelargonii.

Globalization has made agricultural commodities more accessible, available, and affordable. However, their global movement increases the potential for invasion by pathogens and necessitates development and implementation of sensitive, rapid, and scalable surveillance methods. Here, we used 35 strains, isolated by multiple diagnostic laboratories, as a case study for using whole genome sequence data in a plant disease diagnostic setting. Twenty-seven of the strains were isolated in 2022 and identified as Xanthomonas hortorum pv. pelargonii. Eighteen of these strains originated from material sold by a plant breeding company that had notified clients following a release of infected geranium cuttings. Analyses of whole genome sequences revealed epidemiological links among the 27 strains from different growers that confirmed a common source of the outbreak and uncovered likely secondary spread events within facilities that housed plants originating from different plant breeding companies. Whole genome sequencing data were also analyzed to reveal how preparatory and analytical methods can impact conclusions on outbreaks of clonal pathogenic strains. The results demonstrate the potential power of using whole genome sequencing among a network of diagnostic labs and highlight how sharing such data can help shorten response times to mitigate outbreaks more expediently and precisely than standard methods.

Everything Is Faster: How Do Land-Grant University-Based Plant Diagnostic Laboratories Keep Up with a Rapidly Changing World?

Plant diagnostic laboratories (PDLs) are at the heart of land-grant universities (LGUs) and their extension mission to connect citizens with research-based information. Although research and technological advances have led to many modern methods and technologies in plant pathology diagnostics, the pace of adopting those methods into services at PDLs has many complexities we aim to explore in this review. We seek to identify current challenges in plant disease diagnostics, as well as diagnosticians' and administrators'perceptions of PDLs' many roles. Surveys of diagnosticians and administrators were conducted to understand the current climate on these topics. We hope this article reaches researchers developing diagnostic methods with modern and new technologies to foster a better understanding of PDL diagnosticians' perspective on method implementation. Ultimately, increasing researchers' awareness of the factors influencing method adoption by PDLs encourages support, collaboration, and partnerships to advance plant diagnostics.

Characterization of Tomato Necrotic Spot Virus, a Subgroup 1 Ilarvirus Causing Necrotic Foliar, Stem, and Fruit Symptoms in Tomatoes in the United States.

The genomic, biological, and serological characterization of tomato necrotic spot virus (ToNSV), a virus first described infecting tomato in California, was completed. The complete genomic sequence identified ToNSV as a new subgroup 1 ilarvirus distinct from the previously described tomato-infecting ilarviruses. We identified ToNSV in Indiana in 2017 and 2018 and in Ohio in 2018. The coat protein coding region of the isolates from California, Indiana, and Ohio have 94 to 98% identity, while the same isolates had 99% amino acid identity. ToNSV is serologically related to TSV, a subgroup 1 ilarvirus, and shows no serological relationship to ilarviruses in the other subgroups. In tomato, ToNSV caused symptoms of necrotic spots and flecks on leaves, necrotic streaking on stems, and necrotic spots and circular patterns on fruit resulting in a yield loss of 1 to 13%. These results indicate that ToNSV is a proposed new subgroup 1 ilarvirus causing a necrotic spotting disease of tomato observed in California, Indiana, and Ohio.