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Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus  Exobasidium maculosum , is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of  E .  maculosum  in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of  E .  maculosum  are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry ( Vaccinium virgatum ), highbush blueberry ( V .  corymbosum ), and southern highbush blueberry ( V .  corymbosum  hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry ( V .  angustifolium ) from Maine, USA, and Nova Scotia, Canada. Populations of  E .  maculosum  from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall,  E .  maculosum  showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of  E .  maculosum , but more likely as a result of an increasing host population or an environmental change.

Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum