Phylogeographic and Phylogenomic Structure of the Quarantine Plant Pathogen Colletotrichum liriopes, Including New Reports in the United States.

Global agricultural trade has accelerated the emergence and re-emergence of new plant pathogens. In the United States, the fungal pathogen Colletotrichum liriopes is still considered a foreign quarantine pathogen that affects ornamental plants (i.e., Liriope spp.). Even though this species has been reported in East Asia on various asparagaceous hosts, its first and only report in the United States was in 2018. However, that study used only ITS nrDNA for identification, and no available culture or voucher specimen was maintained. The main objective of the present study was to determine the geographic and host distribution of specimens identified as C. liriopes. To accomplish this, new and existing isolates, sequences, and genomes obtained from various hosts and geographic locations (i.e., China, Colombia, Mexico, and the United States) were compared with the ex-type of C. liriopes. Multilocus phylogenetic (ITS, Tub2, GAPDH, CHS-1, and HIS3), phylogenomic, and splits tree analyses revealed that all the studied isolates/sequences form a well-supported clade with little intraspecific variation. Morphological characterizations support these findings. The minimum spanning network, low nucleotide diversity, and negative Tajima's D from both multilocus and genomic data suggest that there was a recent movement/invasion of a few East Asian genotypes to other countries where the ornamental plants are produced (e.g., South America) and subsequently to the importing countries, such as the United States. The study reveals that the geographic and host distribution of C. liriopes sensu stricto is expanded to the United States (i.e., at least Maryland, Mississippi, and Tennessee) and on various hosts in addition to Asparagaceae and Orchidaceae. The present study produces fundamental knowledge that can be used in efforts to reduce costs or losses from agricultural trade and to expand our understanding of pathogen movement.

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.

Sarcococca Blight: Use of Whole-Genome Sequencing for Fungal Plant Disease Diagnosis.

Early and accurate diagnosis of new plant pathogens is vital for the rapid implementation of effective mitigation strategies and appropriate regulatory responses. Most commonly, pathogen identification relies on morphology and DNA marker analysis. However, for new diseases, these approaches may not be sufficient for precise diagnosis. In this study, we used whole-genome sequencing (WGS) to identify the causal agent of a new disease affecting Sarcococca hookeriana (sarcococca). Blight symptoms were observed on sarcococca and adjacent Buxus sempervirens (boxwood) plants in Maryland during 2014. Symptoms on sarcococca were novel, and included twig dieback and dark lesions on leaves and stems. A Calonectria sp. was isolated from both hosts and used to fulfill Koch's postulates but morphology and marker sequence data precluded species-level identification. A 51.4-Mb WGS was generated for the two isolates and identified both as Calonectria pseudonaviculata. A single-nucleotide polymorphism at a noncoding site differentiated between the two host isolates. These results indicate that the same C. pseudonaviculata genotype has the ability to induce disease on both plant species. This study marks the first application of WGS for fungal plant pathogen diagnosis and demonstrates the power of this approach to rapidly identify causal agents of new diseases.