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Rapid and accurate molecular diagnostic tools are critical to efforts to minimize the impact and spread of emergent pathogens. The identification of diagnostic markers for novel pathogens presents several challenges, especially in the absence of information about population diversity and where genetic resources are limited. The objective of this study was to use comparative genomics datasets to find unique target regions suitable for the diagnosis of two fungal species causing a newly emergent blight disease of boxwood. Candidate marker regions for loop-mediated isothermal amplification (LAMP) assays were identified from draft genomes of Calonectria henricotiae and C. pseudonaviculata, as well as three related species not associated with this disease. To increase the probability of identifying unique targets, we used three approaches to mine genome datasets, based on (i) unique regions, (ii) polymorphisms, and (iii) presence/absence of regions across datasets. From a pool of candidate markers, we demonstrate LAMP assay specificity by testing related fungal species, common boxwood pathogens, and environmental samples containing 445 diverse fungal taxa. This comparative-genomics-based approach to the development of LAMP diagnostic assays is the first of its kind for fungi and could be easily applied to diagnostic marker development for other newly emergent plant pathogens.

Sudden vegetation dieback (SVD) is the loss of smooth cordgrass (Spartina alterniflora) along intertidal creeks in salt marshes of the Atlantic and Gulf states. The underlying cause of SVD remains unclear, but earlier work suggested a contributing role for Fusarium spp. in Louisiana. This report investigated whether these or other Fusarium species were associated with S. alterniflora dieback in mid- to north-Atlantic states. Isolations from seven SVD sites yielded 192 isolates of Fusarium spp., with more than 75% isolated from aboveground tissue. Most isolates (88%) fell into two undescribed morphospecies (MS) distinguished from each other by macroconidial shape, phialide ontogeny and growth rates. Pathogenicity tests on wound-inoculated S. alterniflora stems and seedling roots revealed that isolates in MS1 were more virulent than those in MS2 but no single isolate caused plant mortality. No matches to known species of Fusarium were revealed by DNA sequence queries of translation elongation factor 1-α (tef1) sequences. A phylogenetic analysis of partial sequences of three genes, β-tubulin (β-tub), calmodulin (cal) and tef1, was conducted on representative isolates from MS1 (n = 20) and MS2 (n = 18); it provided strong evidence that the MS1 isolates form a clade that represents a heretofore undescribed species, which we designate Fusarium palustre sp. nov. Isolates from the more variable MS2 clustered with the F. incarnatum-equiseti species complex as F. cf. incarnatum. Although a strong association exists between both species and declining S. alterniflora in SVD sites, neither appears to play a primary causal role in SVD. However, our findings suggest that F. palustre might play an important secondary role in the ecological disruption of the salt marshes.

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.