Elevated Genetic Diversity in the Emerging Blueberry Pathogen <i>Exobasidium maculosum</i>

<div><p>Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus <i>Exobasidium maculosum</i>, 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 <i>E</i>. <i>maculosum</i> in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of <i>E</i>. <i>maculosum</i> 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 (<i>Vaccinium virgatum</i>), highbush blueberry (<i>V</i>. <i>corymbosum</i>), and southern highbush blueberry (<i>V</i>. <i>corymbosum</i> hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (<i>V</i>. <i>angustifolium</i>) from Maine, USA, and Nova Scotia, Canada. Populations of <i>E</i>. <i>maculosum</i> 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, <i>E</i>. <i>maculosum</i> 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 <i>E</i>. <i>maculosum</i>, but more likely as a result of an increasing host population or an environmental change.</p></div

Original <i>Vaccinium</i> host, tissue type, and geographic location for <i>Exobasidium maculosum</i> and <i>E</i>. <i>rostrupii</i> isolates.

<p>^a Isolates from lowbush blueberry marked by an asterisk (*) were previously identifed as <i>Exobasidium</i> sp. A (14). Isolates from Nova Scotia were collected by N. Nickerson and kindly provided by P. Hildebrand, Atlantic Food and Horticulture Research Centre, Kentville, Nova Scotia, Canada. The isolate from Maine was obtained from an infected leaf kindly provided by S. Annis, University of Maine, Orono, ME. Isolates of <i>E</i>. <i>rostrupii</i> from cranberry were obtained from infected leaves kindly provided by J. Polashock, USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Chatsworth, NJ.</p><p>^b Species include: <i>V</i>. <i>virgatum</i> or rabbiteye blueberry (R), <i>V</i>. <i>corymbosum</i> hybrid or southern highbush blueberry (S), <i>V</i>. <i>corymbosum</i> or highbush blueberry (H), <i>V</i>. <i>angustifolium</i> or lowbush blueberry (L), and <i>V</i>. <i>macrocarpon</i> or cranberry (C). Cultivar is listed, if known.</p><p>Original <i>Vaccinium</i> host, tissue type, and geographic location for <i>Exobasidium maculosum</i> and <i>E</i>. <i>rostrupii</i> isolates.</p

Bayesian inferred phylogenies for isolates of <i>Exobasidium maculosum</i> for the loci A. ITS, B. <i>EF-1α</i>, C. <i>CAL</i>.

<p>Phylogenies were rooted with <i>E</i>. <i>rostrupii</i>. Bold nodes indicate bootstrap support values obtained by maximum likelihood and Bayesian posterior probabilities greater than 70 and 0.90, respectively. Isolate names are colored by geographic location: blue = Georgia; green = North Carolina; red = northeastern North America. The first column of boxes to the right of each phylogeny indicates isolates that were collected from leaf (white) or fruit (black) plant tissues. The second column indicates the host from which isolates were collected: violet = rabbiteye blueberry (<i>Vaccinium virgatum</i>); blue = southern highbush blueberry (<i>Vaccinium corymbosum</i> hybrid); red = highbush blueberry (<i>V</i>. <i>corymbosum</i>); yellow = lowbush blueberry (<i>V</i>. <i>angustifolium</i>). Isolates of <i>E</i>. <i>rostrupii</i> were collected from leaf spots on cranberry (<i>V</i>. <i>macrocarpon</i>).</p

Measures of genetic differentiation for populations of <i>Exobasidium maculosum</i> collected from blueberry.

<p>^a Geographic populations consist of isolates from Nova Scotia, Canada and Maine, USA (NE), isolates from the southeastern USA (SE), and isolates from Georgia (GA) and North Carolina (NC). Comparison of populations based on host species within SE include: <i>V</i>. <i>virgatum</i> or rabbiteye blueberry (R), <i>V</i>. <i>corymbosum</i> hybrid or southern highbush blueberry (S), <i>V</i>. <i>corymbosum</i> or highbush blueberry (H). Comparison of populations based on host tissue within SE include fruit spots and leaf spots</p><p>^<b>b</b><i>S</i>_nn and <i>K</i>_ST* calculated in DnaSP (28). Values that significantly differ from neutrality (<i>P</i> ≤ 0.05) based on 1000 permutations of the data are indicated</p><p>Measures of genetic differentiation for populations of <i>Exobasidium maculosum</i> collected from blueberry.</p